Zoological Journal of the Linnean Society , 2007, 149 , 1?95. With 18 figures ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 1?95 1 Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation. Blackwell Publishing Ltd Oxford, UK ZOJZoological Journal of the Linnean Society 0024-4082? 2007 The Linnean Society of London? 2007 149 1 195 Original Article HIGHER-ORDER PHYLOGENY OF MODERN BIRDS B. C. LIVEZEY and R. L. ZUSI *Corresponding author. E-mail: livezeyb@carnegiemnh.org Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion BRADLEY C. LIVEZEY 1* and RICHARD L. ZUSI 2 1 Section of Birds, Carnegie Museum of Natural History, 4400 Forbes Avenue, Pittsburgh, PA 15213-4080, USA 2 Division of Birds, National Museum of Natural History, Washington, DC 20013-7012, USA Received April 2006; accepted for publication September 2006 In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of mod- ern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neor- nithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palae- ontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and find- ings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, pre- dominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 ran- dom-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six tri- chotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinor- nithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neor- nithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sis- ter-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister- group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill ( Balaeniceps rex ) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconi- iformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the mono- phyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitor- nithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passe- riformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psit- OnlineOpen: This article is available free online at www.blackwell-synergy.com 2 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 1?95 taciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coracii- formes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeonto- logical phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. ? 2007 The Linnean Society of London, Zoo- logical Journal of the Linnean Society , 2007, 149 , 1?95. ADDITIONAL KEYWORDS: Aves ? cladistics ? classification ? convergence ? homology ? morphology ? ontogeny ? palaeontology ? phylogenetics ? Neornithes ? taxonomy. INTRODUCTION ?But as far as the problem of the relationship of the orders of birds is concerned, so many distinguished investigators have labored in this field in vain, that little hope is left for spectacu- lar break-throughs.? (Stresemann, 1959: 277) ?It must be remembered that the basic avian structure was determined at an early stage in the evolutionary history of birds because of the rigorous limitations placed upon a flying vertebrate. Consequently, adaptations in the birds have been along lines that are not always indicated by the details of anat- omy, a fact that makes these vertebrates highly interesting to the student of recent animals but difficult subjects for the palaeontologist.? (Colbert, 1980: 187) M ATURATION OF AVIAN PHYLOGENETICS Confines of tradition : The opening quotation from Col- bert (1980) clearly articulates a fundamental assump- tion of functional constraint under which many avian systematists laboured for more than a century (Wyles et al. , 1983). Apparently retarded rates of morpholog- ical and molecular change (Primmer & Ellegren, 1998; Stanley & Harrison, 1999) strongly influenced evolu- tionary theory as applied to birds, e.g. prompting assessment of phylogenetic principles for morphologi- cally ?uniform? groups (Bock, 1963a). This duality ? higher-order diversity defying phylogenetic inference and study of morphological variation lacking unified phylogenetic focus ? was influential during the last century. Avian systematics has followed a general tri-phasic pattern: (i) a descriptive period ? epitomized by the landmark works by Huxley (1867), F?rbringer (1888) and Gadow (1892, 1893), in which early classifications of the period were based solely on anatomical evidence and distinctly informal in nature (Seebohm, 1888, 1889, 1890a, b, c, 1895; Clark, 1901); (ii) a comparative (multitaxic) period ? typically confined to single skel- etal elements, articulations, limbs or organ systems (e.g. Bock, 1959, 1960a, b; Cracraft, 1968; Ames, 1971); and (iii) a phylogenetic period ? the primary lit- erature considered herein. Important advances in avian systematics have been typified by studies focused on key extant taxa ? e.g. Balaeniceps rex (Cottam, 1957) and Pedionomus torquatus (Olson & Steadman, 1981) ? or promising aspects of anatomy ? e.g. appendicular myology (Garrod, 1873a, 1874) ? as well as a few broad surveys of modern taxa (Cracraft, 1986; Cracraft & Mindell, 1989). Regardless of method, however, scale of avian phylogenetics seldom exceeded single orders prior to 1990, when palaeontological finds revived such broad systematic endeavours. From the earliest years of avian systematics, ornithologists were attracted to taxa posing confusing combinations of characters, and a few systematists showed an uncanny recognition of taxa that were key to problems concerning larger groups (Table 1). Percy Roycroft Lowe (British Museum), despite an idiosyncratic view of ontogeny in evolution (Livezey, 1995a) and pre-Hennigian concepts of phylogenetic reconstruction, undertook early and under-appreciated attempts to resolve the phylogenetic positions of problematic avian groups. Early works by Lowe emphasized the vexing Charadriiformes and allied Gruiformes (Lowe, 1922, 1923, 1924, 1925, 1931a, b), the ratites (Lowe, 1928, 1930, 1942, 1944a), ?primitive? characters of Sphenisciformes (Lowe, 1933), characters of Archaeopteryx possibly germane to an alliance between birds and dinosaurs (Lowe, 1935, 1944b), the perplexingly apomorphic Apodiformes (Lowe, 1939), and preliminary diagnoses for Cuculiformes (Lowe, 1943), Piciformes (Lowe, 1946) and Coraciiformes (Lowe, 1948). Intermittently during the same period, Lowe also considered possible relationships among ratites and some non-avian Theropoda, e.g. Stru- thiomimus and Ornitholestes , although he was hampered by the prevailing confusion between syna- pomorphy and symplesiomorphy and their respective HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 3 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 1?95 T a b le 1 . S el ec te d re fe re n ce s co n ce rn in g n eo gn at h ou s N eo rn it h es q u al if yi n g as p er en n ia l pr ob le m s of h ig h er -o rd er ( su pr a- or di n al ) sy st em at ic s (s ee S ib le y & A h lq u is t, 1 97 2, 1 98 1, 1 99 0) T ax on A lt er n at iv e pr op os al s R ef er en ce s G av ii fo rm es P od ic ip ed if or m es , P ro ce ll ar ii fo rm es S tr es em an n ( 19 34 ); V er h ey en ( 19 59 a, 1 96 1) ; S to re r (1 95 6, 1 97 1a , b ) P od ic ip ed if or m es G av ii fo rm es , P el ec an if or m es , G ru if or m es , H el io rn it h id ae , P h oe n ic op te ri da e S tr es em an n ( 19 34 ); V er h ey en ( 19 59 b, 1 96 1) ; T yl er ( 19 69 ); O ls on ( 19 85 ); V an T u in en et a l . (2 00 1) ; S to re r (2 00 2) ; M ay r (2 00 4a ) P el ec an if or m es P ol yp h yl y (m u lt ip le t op ol og ie s) B ed da rd (1 89 7) ; C h an dl er (1 91 6) ; S im on et ta (1 96 3) ; H ed ge s & S ib le y (1 99 4) ; B ou rd on , B oy a & I ar oc h ?n e (2 00 5) B al ae n ic ip it id ae C ic on ii fo rm es , P el ec an if or m es P ar k er ( 18 60 , 1 86 1) ; R ei n h ar dt ( 18 60 , 1 86 2) ; B ar tl et t (1 86 1) ; G ie be l ( 18 73 ); B ed da rd ( 18 88 ); S h u fe ld t (1 90 1a ); M it ch el l ( 19 13 ); B ?h m (1 93 0) ; C ot ta m (1 95 7) ; F ed u cc ia (1 97 7a ); C ra cr af t (1 98 5) ; M ay r (2 00 3a ); M ay r & C la rk e (2 00 3) S co pi da e C ic on ii fo rm es , P el ec an if or m es B ed da rd ( 18 84 ); S h u fe ld t (1 90 1a ); M ay r (2 00 3a ) F al co n im or ph ae P ol yp h yl y F ? rb ri n ge r (1 88 8) ; G ad ow ( 18 92 ); S ib le y & A h lq u is t (1 99 0) C at h ar ti da e F al co n if or m es , C ic on ii fo rm es L ig on ( 19 67 ); C ra cr af t & R ic h ( 19 72 ); E m sl ie ( 19 88 ); A vi se , N el so n & S ib le y (1 99 4a ); H el bi g & S ei bo ld ( 19 95 ) P h od il id ae T yt on id ae , S tr ig id ae M il n e- E dw ar ds ( 18 78 a) ; B ed da rd ( 18 90 ); S h u fe ld t (1 90 0) ; M il le r (1 96 5) ; H of f (1 96 6) ; M ar sh al l (1 96 6) P h oe n ic op te ri da e A n se ri fo rm es , C ic on ii fo rm es , C h ar ad ri if or m es G ad ow ( 18 77 ); W el do n ( 18 83 ); P ar ke r (1 88 9a ); S h u fe ld t (1 88 9a , 1 90 1b ); C h an dl er ( 19 16 ); F ed u cc ia ( 19 76 , 1 97 7b ); L iv ez ey ( 19 97 a, b , 1 99 8a ) T u rn ic id ae G ru if or m es , G al li fo rm es ; in de te rm in at e, ba sa l N eo rn it h in es P ar ke r (1 86 2) ; O gi lv ie -G ra n t (1 88 9) ; G ad ow ( 18 93 ); L ow e (1 92 3) ; L iv ez ey ( 19 98 b) ; R ot th ow e & S ta rc k (1 99 8) M es it or n it h id ae G ru if or m es , C u cu li fo rm es B ar tl et t (1 87 7) ; M il n e- E dw ar ds ( 18 78 b) ; F or be s (1 88 2) ; G ad ow ( 18 93 ); L ow e (1 92 4) ; L iv ez ey (1 99 8b ); M ay r & E ri cs on ( 20 04 ) P ed io n om id ae G ru if or m es , C h ar ad ri if or m es G ad ow ( 18 91 a) ; B oc k & M cE ve y (1 96 9) ; O ls on & S te ad m an ( 19 81 ); L iv ez ey ( 19 98 b) R h yn oc h et id ae A rd ei fo rm es , G ru if or m es B ar tl et t (1 86 2) ; P ar ke r (1 86 9) ; M u ri e (1 87 1) ; B ed da rd ( 18 91 ); M it ch el l (1 91 5) ; S te in ba ch er (1 96 8) ; L iv ez ey ( 19 94 , 1 99 8b ) O pi st h oc om id ae T in am id ae , R at it ae , G al li fo rm es , C u cu li fo rm es , C ol u m bi da e, P te ro cl id e, R al li da e, O ti di da e, C ol ii da e P er ri n (1 87 5) ; G ar ro d (1 87 9) ; V on N at h u si u s (1 88 1) ; B ed da rd (1 88 9) ; G ad ow (1 89 1b ); P ar k er (1 89 1) ; M it ch el l (1 89 6) ; S h u fe ld t (1 91 8) ; B ?k er ( 19 29 ); B ar n ik ol ( 19 53 ); P ar so n s (1 95 4) ; V er h ey en ( 19 56 a) ; S ib le y & A h lq u is t (1 97 3) ; A vi se et a l . ( 19 94 b) ; H ac ke tt et a l . ( 19 95 ); H ed ge s et a l . ( 19 95 ); H u gh es & B ak er ( 19 99 ); Jo h an ss on et a l . ( 20 01 ); M ay r & C la rk e (2 00 3) ; S or en so n et a l . ( 20 03 ) P te ro cl id ae C ol u m bi fo rm es , G al li fo rm es , C h ar ad ri if or m es P ar ke r (1 86 2) ; E ll io t (1 87 8) ; G ad ow ( 18 82 ); S h u fe ld t (1 90 1c ); C h an dl er ( 19 16 ); S te gm an n (1 95 7, 1 95 9) ; F je ld s? ( 19 76 ) C ap ri m u lg if or m es P ar ap h yl y or p ol yp h yl y, n ot ab ly A eg ot h el id ae , S te at or n it h id ae G ar ro d (1 87 3b ); S h u fe ld t (1 88 5) ; B ed da rd ( 18 86 ); P ar k er ( 18 89 b) ; B ? h le r (1 97 0) ; J oh an ss on et a l . ( 20 01 ); M ay r (2 00 2a ) T ro ch il id ae A po di da e, P as se ri fo rm es L ow e (1 93 9) ; C h an dl er ( 19 16 ); C oh n ( 19 68 ) C ol ii da e C u cu li fo rm es , C or ac ii fo rm es , In di ca to ri da e, C ap ri m u lg if or m es M u ri e (1 87 2a ); G ar ro d (1 87 6) ; V er h ey en ( 19 56 b) ; S ib le y & A h lq u is t (1 97 2) ; B er m an & R ai ko w ( 19 82 ); E sp in os a de l os M on te ro s (2 00 0) T ro go n id ae C ol ii da e, C u cu li fo rm es , C or ac ii fo rm es F or be s (1 88 1) ; E sp in os a de l os M on te ro s (1 99 8, 2 00 0) ; M ay r (2 00 3b ) 4 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 1?95 implications for phylogeny (Lowe, 1928, 1930, 1935, 1942, 1944a, b). Ren? Verheyen (Institut Royale Bel- gique) authored approximately 35 papers during 1950? 60 that centred on problems of avian systematics by means of semi-quantitative methods (e.g. Verheyen, 1956a, b, 1960a, b, 1961). The work by Verheyen, how- ever, was deemed idiosyncratic and largely ignored (Sibley & Ahlquist 1990). Sibley & Ahlquist (1972, 1987, 1990) chronicled avian systematics since the late 18th century. Raikow (1985a) reviewed the philosophical underpinnings of avian systematics in recent decades, and clarified for the time the fundamental differences among various systematic schools. Avian systematics in the late 20th century has been marked by a trough in morphological phylogenetics (Fautin & Watling, 1999; Jenner, 2004a) and a concomitant peak in molecular systematics. The pessimism expressed by Sibley & Ahlquist (1990) regarding the phylogenetic potential of morphological characters, however, contrasts with surveys of the con- tributions of both (Patterson, Williams & Humphries, 1993). Bledsoe & Raikow (1990) concluded that con- siderable congruence existed among reconstructions based on DNA?DNA hybridization, sequence-based analyses, and comparative morphology. In a survey of the history of avian molecular systematics, Meyer & Zardoya (2003) recounted discrepancies between reconstructions of basal lineages based on mtDNA and nuclear genes. As discourse among schools increased, it was evident that the familiar demons of avian sys- tematics haunted both morphological and molecular practices: differential selection and adaptation, con- vergence, extinction of lineages, challenges of homol- ogy and alignment, and heterogeneity of evolutionary rates and branch-lengths. Palaeontological contributions : Fossils essentially are amenable only to morphological study, with the excep- tion of a few, fortunate recoveries of ?ancient DNA? (Cooper et al ., 1992, 2001; Austin, Smith & Thomas, 1997; Cooper, 1997; Sorenson et al. , 1999; Paxinos et al. , 2002), and typically provide only substandard anatomical material or incomplete specimens. Some of the most intense conflicts among avian systematists stemmed either from a commitment to phenetics or the idiosyncracies of palaeornithological perspectives (e.g. Cracraft, 1979, 1980, 1981; Olson, 1982). Influen- tial for avian systematics was the view that avian fos- sils are both fragile and correspondingly rare (Olson, 1985), despite compendia indicative of extensive tax- onomic diversity (Brodkorb, 1963, 1964, 1967, 1971a, b, 1978). Deficiencies in the fossil record (Olson, 1985) and challenges of homology (e.g. Sereno, 2001), however, did not diminish a reliance on new fossils to resolve the broad outlines of avian evolution (Feduccia, 1980, 1995, 1996). Palaeontological contributions have been con- founded by speculative evolutionary scenarios that extend beyond the underlying systematics (Feduccia, 1973, 1977c, 1995, 1996, 2003). The purported issue of ?fossil mosaics? (Eldredge, 1989) ? a predictable conse- quence of heterogeneity in evolutionary rates among characters ? further exacerbated the interpretation of evolutionary change (Livezey, 1997a). Martin (1983: 291) concluded that during the 150 years of avian palaeontology, ?. . . a major burden for palaeornitholo- gists has been a lack of comparative skeletons of recent birds?, and that the ?other major problem is the incompleteness of most avian fossils.? With the latter we agree, but the former is less a problem of availabil- ity than the result of under-utilization, a factor wor- sened by the rush to a molecular era. Ethological and parasitological phylogenetics : Behav- ioural characters are only infrequently used in formal cladistic analyses (e.g. Hughes, 1996; Lee et al. , 1996; Kennedy et al. , 1996, 2000; Slikas, 1998; Birdsley, 2002), or precursors thereof (Van Tets, 1965). Com- plete designs have not been attempted for lack of com- parable data for species of interest (Wimberger & de Queiroz, 1996), and some are limited to assessments a posteriori for phylogenetic signal (Winkler & Sheldon, 1993; Lee, Feinstein & Cracraft, 1997; McCracken & Sheldon, 1997). Phylogeneticists have come to con- sider selected ethological traits ? notably displays of courtship ? worthy of phylogenetic interpretation (Delacour & Mayr, 1945; Johnsgard, 1961; Archibald, 1976; Paterson, Wallis & Gray, 1995). Patterns of interspecific hybridization have perhaps the longest history of study, notably among Anseriformes (Sibley, 1957; Johnsgard, 1960, 1963; Scherer & Hilsberg, 1982). Eventually, interfertility was recognized to be plesiomorphic and comparatively conservative (Prager & Wilson, 1975), and therefore interspecific hybridization to be uniformative with respect to phy- logenetics (Cohen et al. , 1997; Braun & Brumfield 1998; Andersson, 1999). Similarly, phylogenetics of ectoparasites has been explored only infrequently in phylogenetic reconstructions of birds (Paterson, Gray & Wallis, 1993; Paterson & Gray, 1996; Page et al. , 1998; Johnson et al. , 2002; Storer, 2002; Smith, Page & Johnson, 2004; Banks, Palma & Paterson, 2006). Con- sequently, the two primary sources of phylogenetic sig- nal for birds during the 20th century have been morphological variation and molecular (increasingly DNA sequence) data. Molecular phylogenetics : Following an implicit rejec- tion of DNA hybridization on the grounds of its phe- netic nature and woefully incomplete distance matrices, molecular systematics focused on the cla- distics of parsimony or increasingly explored the probabilistics of maximum-likelihood and Bayesian HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 5 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 1?95 methods. Phylogenetic analyses based solely on mito- chondrial genes de jour (e.g. cyt b , 12S) initially were accorded considerable validity (Sraml et al. , 1996; Mindell, Sorenson & Dimcheff, 1998; Johnson & Sorenson, 1998, 1999; McCracken et al. , 1999), but these works effectively were trumped by those based on entire mitochondrial genomes (Paton, Haddrath & Baker, 2002) or including nuclear genes, with few exceptions (Garc?a-Moreno, Sorenson & Mindell, 2003). Similarly, explorations of very limited num- bers of genes (Templeton, 1983; Groth & Barrow- clough, 1999; Paton et al. , 2003; Chubb, 2004a, b; Fain & Houde, 2004) were eclipsed by expanded anal- yses of nuclear data with diversified taxonomic sam- ples (Hughes & Baker, 1999; Donne-Gouss?, Laudet & H?nni, 2002; Sorenson et al. , 2003). This pro- gression of analytical refinements and expanded taxonomic representation, despite the continued challenges discovered in each (e.g. Cotton & Page, 2002), is likely to continue and perhaps accelerate with the implementation of studies based on ?total evidence? (Huelsenbeck, Bull & Cunningham, 1996; Baker, Yu & DeSalle, 1998; Ballard et al. , 1998; Bininda-Emonds, Gittleman & Steel, 2002; Cracraft et al. , 2004). C URRENT STATUS OF AVIAN PHYLOGENETICS ?. . . the currently accepted arrangement of birds in no way reflects the probable evolutionary history of the class. . . . The arrangement used here is predicated mainly on the assump- tions that birds originated on land rather than in the water, and that highly specialized waterbirds are more derived than less specialized ones. . . . a consensus has emerged that birds originated, if not in trees, certainly on land. Therefore, we should look for the most primitive taxa among the land birds.? (Olson, 1985: 83, 84) ?If one had to summarize the current state of knowledge, the most pessimistic view would see the neoavian tree as a ?comb,? with little or no resolution among most traditional families and orders.? (Cracraft et al. , 2004: 475) ?Perhaps the greatest unsolved problem in avian systematics is the evolutionary relationships among modern higher-level taxa.? (James, 2005: 1052) Harrison et al . (2004: 974) concluded: ?It is almost an offense against birds that the deep mammalian tree is virtually resolved . . . whilst there are still major uncertainties about many aspects of the avian evolu- tionary tree.? In support of this sentiment, the authors cited fundamental discordance among phylogenetic inferences for birds based on mitochondrial and nuclear genomes, an assessment at odds with a con- temporary review by Garc?a-Moreno et al . (2003). Dis- cussion of morphological efforts by Harrison et al . (2004) was limited to the uncertainties raised by Crac- raft (1981, 2001) but verified increasingly by analyses (Cracraft, 1982a, 1986, 1988; Cracraft & Mindell, 1989; Cracraft et al. , 2004; Mayr, 2005a). Reconstruc- tions of the higher-order relationships of birds based on morphological characters, in turn, have been dep- auperate in both characters and taxa and seldom genuinely cladistic (e.g. Cracraft, 1986, 1988, 2001; Cracraft & Clarke, 2001; Mayr & Clarke, 2003). Regardless of the taxonomic group considered, how- ever, the sobering truth is that the goal of phylogenet- ics is extremely ambitious and without easy or uniformly reliable means of accomplishment. It is beyond debate that the conceptual framework of morphological cladistics (Hennig, 1966) and ever- increasing computational power has led to significant progress. Nevertheless, it is also clear that many phylogenetic problems have proven resistant to all attempts at solution and seem destined to controversy. Also, phylogenetic endeavours are replete with dis- agreements in method (both for reconstruction and for evaluation of estimates) and types of evidence consid- ered most reliable. Currently, the tendency is to con- sider molecular reconstructions as representing the future of avian phylogenetics, and that it is simply a matter of time, perhaps less than a decade, before a global consensus is achieved within the systematic community (Barrowclough, 1992; Livezey & Zusi, 2001; Stanley & Cracraft, 2002). Deficiencies in taxa or characters typically render comparisons among investigations problematic (Bled- soe & Raikow, 1990), and attempts to reconcile the phylogenetic evidence for Aves substantiate this gen- erality (Cracraft & Mindell, 1989; Mayr, Manegold & Johansson, 2003, 2004a; Dyke & Van Tuinen, 2004; Griffiths et al. , 2004). Indicative of disappointing progress in mid- and lower-order avian phylogenetics is the conclusion that basal (higher-order) nodes may be irresolvable or accurate approximations of genuine, explosive radiations (Poe & Chubb, 2004). While demonstrably true of analyses confined to few charac- ters or limited taxonomically (Kumazawa & Nishida, 1995), a single decade of uninspiring inference is insufficient to judge solution to be beyond hope. The current status of molecular resolution of deep- est neornithine nodes, however, serves to underline the likelihood that many genes provide inadequate phylogenetic signal for the problems at hand, a defi- ciency exacerbated by basal polarities necessarily based on closest extant relatives that are unfortu- nately comparatively distantly related, e.g. Crocodylia and Testudines (Larhammar & Milner, 1989; Iwabe et al. , 2004). The fact that ?nearest? outgroup(s) for molecular analysis need to be be extant has had unfor- tunate implications for rooting, in that for Neornithes these outgroups are comparatively distantly related and may converge on ?white noise? as indicators of 6 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 1?95 avian polarities, especially for rapidly evolving mito- chondrial data. Like morphological estimates, a number of potential pitfalls (rooting aside) afflict molecular reconstruc- tions, e.g. serial homoplasy by misalignment, distor- tions related to silent substitutions, unrealistic treatment of ?gaps?, and unequal evolutionary rates over extended intervals of geological time and among lineages. Furthermore, disagreement persists if not expands regarding methodological preferences ? e.g. classes of data employed, protocols for alignment (i.e. diagnosis of serial homology), choice among recon- structive methods, and assessment of resolution and support (Felsenstein, 2004). Until substantial agree- ment concerning methods is attained and accurate synergism among molecular and morphological meth- ods secured, the field will remain vulnerable to meth- odological bias and a tolerance for poorly supported hypotheses of phylogeny, in which even the best- supported works disagree significantly (see Figs 4?9). G OALS AND OBJECTIVES The primary purpose of this paper is to present a mor- phologically based phylogenetic hypothesis of higher- order relationships of Neornithes. A compendium of characters is provided within the companion work (Livezey & Zusi, 2006), including a bibliographic syn- thesis, annotations of prior uses of synonymous and related characters, and a compact disc of the data matrix for refinement and augmentation. The second- ary objective of this work is to provide a cladistic alter- native to the molecular phenetics of Sibley & Ahlquist (1990), at least for non-passeriform families, and to serve as a framework for lower-level studies of included families. An earlier paper on philosophical and methodogical issues (Livezey & Zusi, 2001), despite an explicit disclaimer to the contrary, fre- quently has been cited as a phylogenetic hypothesis appropriate for comparison with works considered complete by their authors, even regarding positions of individual taxa (e.g. Cracraft et al. , 2003). We began the present study with the opinion that the phyloge- netic signal encoded within avian anatomy is, with adequate study of both definitive and ontogenetic vari- ation of an adequate sample of modern lineages, more than sufficient for the reconstruction of the higher- order phylogeny of Neornithes. We remain at least as optimistic concerning this goal. The present phylogenetic hypothesis is intended to serve both as a baseline estimate and ?scaffold? for finer-scale reconstructions of terminal clades (i.e. fam- ilies), as attempts at broad reconstructions of the phy- logeny of Neornithes to date have been limited, at the very least, in taxonomic representation (e.g. Slack et al. , 2006b) or discredited methods of inference (Sibley & Ahlquist, 1990). We also sought to provide robust nodes supplemental to the few phylogenetic hypothesis currently employed for calibrations of age based on fossils (e.g. Dyke & Van Tuinen, 2004; Pereira & Baker, 2006a) or their surrogates (Van Tuinen, Stidham & Hadly, 2006). Integration of these data with a rich matrix of DNA-sequence data (Crac- raft et al. , 2004) is planned to explore the power of ?total evidence? to recover both higher-level and lower- level avian phylogeny. Perhaps most importantly for the facilitation of future analyses, be these morpholog- ical or molecular, is the identification of sister-groups (optimal outgroups) for purposes of rooting analyses of single orders or families. The comparatively sparse representation of taxa in the present analysis reflected logistical limits, but was considered adequate for achieving the stated objectives. Findings herein principally were compared with modern higher-order reconstructions (e.g. Mindell et al. , 1997; Mayr & Clarke, 2003; Mayr et al. , 2003), the most critical of which are summarized graphically here (Figs 1?9). Works of narrower scope are considered where issues of familial monophyly persist, with emphasis on truly phylogenetic works as opposed to eclectic or phenetic assessments (Raikow, 1985a). METHODS I NCLUDED TAXA Taxonomic sampling and exemplars : Taxonomic diversity generally represents a much greater logisti- cal burden than diversity of characters in phylogenetic analyses, and challenges imposed by taxa can be exacerbated by unfortunate sampling (Maddison & Maddison, 1992; Graybeal, 1998; Swofford, 2002; Felsenstein, 2004). However, it has been demonstrated that density of taxonomic sampling for the ingroup varies directly with expected accuracy, support and resolution of resultant trees (Lecointre et al. , 1993), although the importance of taxonomic density appears to be greatest for sequence data (especially with respect to long-branch attraction). Expectations of res- olution and accuracy that are related to richness of morphological characters, unlike for sequence data (Lecointre et al. , 1994), have not been subjected to numerical assessment, but logically are significantly related. The importance of monophyly of the groups represented by exemplars prompted the citation, where available, of analyses germane to the mono- phyly and content of taxonomic families represented here by exemplars. We sought to maximize richness of characters and represent higher-order taxa within logistic limits that: (i) represented (sub)familial diversity among non- passeriform Neornithes; (ii) provided special insights HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 7 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 1?95 into interfamilial groups (Livezey, 1997a, 1998a); (iii) were suitably represented by essential specimens; and (iv) included taxa of special interest to avian system- atics. Neornithine families were represented by one or more exemplars deemed in most cases to reflect at least a ?basal? member (i.e. candidate sister-taxon of other members) of the taxon in question. This method is not without difficulties, as concerns persist regarding the use of exemplars as terminal surrogates for higher- order taxa (Bininda-Emonds, Bryant & Russell, 1998), notably where polymorphism is involved (Yeates, 1995; Simmons, 2001) or monophyly of terminals repre- sented by single exemplars is in question. Also, limi- tations on specimens of specialized preparations impose critical deficiences on resultant data matrices, an abiding concern of anatomical collections of birds (Livezey & Zusi, 2001; Livezey, 2003a). Relatively strong support for monophyly of most clades alleviated concerns regarding taxonomic sampling, especially given the number of morphological characters employed. However, use of minimal numbers of exem- plars justifies caution in the diagnostics given for diverse orders and families herein (Table 2). Crocodylia and non-avian theropod Dinosauria served as ?ultra-deep? and primary outgroups, respec- tively, to root Neornithes (Maddison, Donoghue & Mad- dison, 1984; Janke & Arnason, 1997), but the inclusion of most published characters in placing these taxa (Benton & Clark, 1988; Evans, 1988; Benton, 1999; Cao et al. , 2000; Brochu, 2001; Brochu & Norell, 2001) chronicled the acquisition of avian characters during the Mesozoic (Carroll, 1997). The recent extension of avian roots, both by newly discovered avialian taxa and confirmation of early roots among non-avian theropods, circumvented difficulties of establishing basal polari- ties for Neornithes based on inadequate diversity of Mesozoic relatives or (for narrower reconstructions) or dubious reliance on the problematic Palaeognathae, notably caused by the complex of apomorphy and plesiomorphy of ratites relative to the Tinaniformes (Bertelli, Giannini & Goloboff, 2002). These outgroups optimized rooting by the hierarchy of information afforded by multiple (nested) outgroups (Barriel & Tassy, 1998; Lyons-Weiler, Hoelzer & Tausch, 1998) and avoided the analytical problems implicit with hypothetical ancestors (Bryant, 1997, 2001). Figure 1. Morphological phylogenetic trees proposed in previous studies, I. A, Cracraft (1988); B, Mayr et al . (2003). Some trees were subjected to topologically neutral modifications of taxa to facilitate comparisons (also Figs 2?9). See correspond- ing papers for analytical methods and topological statistics. 8 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 1?95 F ig u re 2 . M or ph ol og ic al p h yl og en et ic t re es p ro po se d in p re vi ou s st u di es ( se e F ig . 1 f or d et ai ls ), II . A , M ay r & C la rk e (2 00 3) ; B , B ou rd on et a l . ( 20 05 ). HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 9 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 1?95 Four comparatively distant outgroups were sampled for estimating deep polarities ? non- Archosauromorpha (informative states of comparable characters at the approximate origin of the archosau- rian clade), Crocodylomorpha (i.e. non-dinosaurian Archosauria), Ornithischia (i.e. non-saurischian Dino- sauria) and Sauropodomorpha (modalities of non- theropod Saurischia). Among non-avian Theropoda, Herrerasaurus served as the most informative of the generic outgroups (Sereno, 1994; Sereno & Novas, 1994). Groupings among outgroups (i.e. among non- avian taxa) were of only secondary interest, however, whereas establishment of a realiable root for the Neornithes was the principal priority. Indeterminate and redundant contributions of some outgroup taxa with respect to the primary objective of this analysis, as well as excessive proportions of missing data recognized upon com- pletion of the data matrix, prompted limited pruning and merging of taxa (primarily outgroups) for analysis: (a) taxa pruned ? Euparkeria, Syntarsus, Eoraptor, Saurornitholestes, ?Caenognathidae?, Micro- venator, Citipati, Chironestes, Ornitholestes, Segno- saurus, Avimimus, Sinornithosaurus, Microraptor, Erlicosaurus, Shuvuuia, Jehelornis, Gobipteryx, Patagopteryx; Diatrymiformes, Dromornithiformes (Rich, 1979, 1980; Murray & Megirian, 1998; Murray & Vickers-Rich, 2004), Sylviornis (Poplin & Mourer- Chauvir?, 1985; Mourer-Chauvir? & Balouet, 2005); (b) taxa merged: {Allosaurus, Sinraptor}? Allosauroidea; {Tyrannosaurus, Albertosaurus}? Tyrannosauridae; {Sinovenator, Sinornithoides, Troodon}?Troodontidae; {?Enantiornithidae?, Iberome- sornis, Cathayornis, Concornis, Neuquenornis, Eoa- lulavis, Protopteryx}?Enantiornithes; {Mononykus, Patagonykus, Alvarezsaurus}?Alvarezsauroidea. Two subfossil taxa ? Aepyornithiformes and Dinor- nithiformes ? for which character states were only mar- ginally recovered, were excluded for the primary global search, and provisionally placed by means of two dif- ferent protocols. This measure was taken because sim- ple analysis of these imperfectly known, broadly Figure 3. Morphological phylogenetic trees proposed in previous studies (see Fig. 1 for details), III. A, Mayr (2005b); B, Mayr (2005f: fig. 9), excluding fossils Prefica and Paraprefica. 10 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 similar, large ratites led to an apparently artefactual couplet ? ?long-branch? distortions exacerbated by miss- ing data (Wiens, 2005) ? as sister-group of other ratites exclusive of Apterygidae. First, each was analysed in the absence of the other in a global, unconstrained anal- ysis. Second, each was separately placed by means of heuristic searches in which the primary tree was used as a backbone constraint. The Dinornithiformes were scored as two families (Dinornithidae and Emeidae) as approximated by Cracraft (1976a, b) and Worthy and Holdaway (2002) during character analyses, but anal- ysed as a single, merged taxon in light of their virtually identical scores. Accordingly, the ?trimmed-merged? data matrix provided in digital form by Livezey & Zusi (2006) comprised 150 ingroup taxa and 35 outgroups. PHYLOGENETIC ANALYSIS General philosophy: Most standard methodological issues were detailed in the foregoing companion work (Livezey & Zusi, 2006), including the analytical per- spectives that serve to justify the delimitation of char- acters and states, ordering of states, and related options requisite to preparation of characters for anal- ysis. Noteworthy is a principal reliance on the litera- ture for many characters of non-avian Theropoda. In the present installment, the foregoing characters were subjected to phylogenetic analysis sensu morphological cladistics (Kluge & Wolf, 1993) coupled with the crite- rion of parsimony of character evolution as implied by the resultant phylogenetic hypothesis (Eldredge & Cracraft, 1980; Wiley, 1981; Brady, 1982; Farris, 1982; Felsenstein, 1983, 2004; Semple & Steel, 2003). In light of the practical and theoretical implications of adopting the parsimony criterion (Felsenstein, 1983, 2004), alternative methods were not practical for this analysis because of missing data (Felsenstein, 1979; Kluge, 1997a, b, 1999) ? e.g. optimizations of morphological characters on branching models under selected models of stochastic change (Huelsenbeck, Nielsen & Bollback, Figure 4. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), IV. A, Sibley & Ahlquist (1990: figs 354?356), simplified to orders, wherein parenthetical ?para? indicates paraphyly of sampled members, and ?aug? indicates unconventional content; B, Mindell et al. (1997). HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 11 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 2003) or maximum-likelihood analysis (Lewis, 2001). Global parsimony ? i.e. minimal total for character- state changes required by final tree (i.e. ?shortness?) ? served as the criterion of optimality for trees recovered through searches (Sober, 1982, 2005). The data matrix was not revised iteratively conditional on outcomes of analysis, nor was ordering of characters conditional on such runs. Instead, the entire data matrix summarized herein was completed prior to the analytical phase, thereby maintaining a partition between (i) definition of characters and states, coding of taxa, and issues of weighting and ordering, and (ii) phylogenetic analysis. Characters and states: Unfortunate logistic limita- tions, not oversight or philosophical considerations, prevented the inclusion of character descriptions with the present analytical work. Although a reflection of our unexpected success in defining 2954 morphologi- cal characters relevant to the project (Livezey & Zusi, 2006), it precluded the familiar juxtaposition of descriptive material with analytical inferences. We anticipate that this inconvenience will be ameliorated by the coordinated publication of the descriptive atlas of characters and digitally recorded data matrix (Livezey & Zusi, 2006), to be made available virtually at cost. We strongly recommend that those interested in the present work procure a copy of its sister publi- cation, as it is through examination of both that mean- ingful improvements will be made. Where mutually exclusive states of a single charac- ter were diagnosable (Stevens, 2000), a single multi- state character was defined (Mishler, 1994, 2005). Where two or more included states are observed for a single taxon, a coding of polymorphism was used and analysed specifically as given (i.e. not as uncertainty). The expanse of time reflected by the scale of the anal- ysis also is expected to be associated with the number of multistate characters recognized (Lipscomb, 1992; Steel & Penny, 2005), i.e. scale of time and taxonomic divergences may be expected to be related directly to scale in evolution of form (Grant & Kluge, 2004). Multistate characters encode features manifesting Figure 5. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), V. A, Espinosa de los Monteros (2000); B, Johansson et al. (2001). 12 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 comparatively great evolutionary change and may include greater potential phylogenetic signal, and states thereof will be optimized at multiple internodes (Simmons, Reeves & Davis, 2004). Unless otherwise indicated, characters were analysed as unordered. Ordering can impose significant constraints on solu- tion sets (Hauser & Presch, 1991; Forey & Kitching, 2000), and was used only where determined to be defen- sibly realistic, e.g. naturally ordinated (Livezey & Zusi, 2006). For example, multistate characters of forms ?small, medium, large?, ?absent, miniscule, prominent?, courses of passage of types ?depressio, sulcus, arcus, tuba?, and junctura of types ?articulatio, sutura, synos- tosis? were considered naturally ordered, counter-evi- dence lacking. Fundamentally, ordering of states within a character was fundamental to definition and differentiation of characters, basic to the delimitation of states, and represented an extension of parsimony by inclusion of information on linear likelihoods in coding schemes. Such reasoning precluded meaningful use of arbitrary analytical variants such as treating all char- acters or partitions thereof as unordered. Hypotheses of transformation were sufficiently simple to obviate reliance on step-matrices (Ree & Donoghue, 1998), lin- ear ordering being the sole condition imposed. Differ- ent numbers of states among characters can impose different levels of influence simply by different num- bers of state changes among characters (James, 2004), but we considered such differential influence to be real- istic and justified as it encoded diverse richness of evo- lutionary change instead of arbitrarily imposing uniformity on contributions of signal. Therefore, no attempt was made to counter-weight multistate char- acters. Moreover, no method of explicit weighting ? a priori (Neff, 1986; Wheeler, 1986; Sharkey, 1989) or suc- cessive (Farris, 1969) ? was employed in this analysis, although some perceive weighting effects to be implicit by other means (Haszprunar, 1998). In this work, characters qualifying as autapomor- phies at this analytical scale (i.e. apomorphic state limited to single included terminal taxon) were included in all analyses because most served as syna- Figure 6. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), VI. A, Van Tuinen et al. (2000); B, Van Tuinen et al. (2001). HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 13 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 pomorphies of the higher-order groups represented by respective exemplars, and many were included in pre- vious publications as diagnostic of the clades repre- sented by exemplars. In addition, such characters are intended to serve others performing lower-level anal- yses subsequently using some or all of the present matrix. Although autapomorphies did not serve to group taxa at this scale, the limited number detected here were retained because our interests not only included delimitation of clades but also were intended to provide a reasonable representation of evolutionary rates both among internodes and among terminal branches, of interest in many studies of evolutionary rates (e.g. Omland, 1997a, b). Also, autapomorphic dif- ferences (deriving from both unique changes or homoplasy) are critical to long-standing issues of perceived (phenetic) distinction and evolutionary divergence among taxa of debated relationships. Fur- thermore, such characters do not bias support indices such as bootstrapping (Harshman, 1994a), and by def- inition do not influence topologies. Also, a small minor- ity of characters manifesting two or more states in original codings (included in the matrix to permit alternative taxonomic treatments) were rendered invariant by merging and pruning of taxa as detailed herein; this treatment was considered simpler than outright manipulation of the matrix analysed. The pri- mary parameter of logistical concern where parsimony is the criterion of optimization is the number of taxa (Kim, 1998), a dimension that in the present work was favourably countered by number of characters. Included characters manifested a range of homoplasy (Sanderson & Donoghue, 1989). However, the number of morphological characters employed here exceeded the domain for which meaningful com- parison with other works is feasible (Swofford, 1991; Sanderson & Donoghue, 1989, 1996) and evaluation of a suite of related issues ? e.g. rates of evolution, notions of relative ?reliability? of different data types, patterns of homoplasy (Faith, 1989; Sanderson, 1991), Figure 7. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), VII. A, Paton et al. (2002); B, Sorenson et al. (2003). 14 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 and Markovian informativeness (Shpak & Churchill, 2000) ? was not logistically feasible. Search for optimal solution: The character matrix was constructed using MACCLADE (Maddison & Maddi- son, 1992; Prendini, 2003), and analyses were per- formed on a Macintosh G5 2.5-GHz dual-processor computer. Primary phylogenetic analyses were per- formed using PAUP* version 4.0b10 (Swofford, 2002). Given the size of the data set and the corresponding universe of possible trees delimited (Felsenstein, 1978), we undertook a thorough exploration of the tree space to circumscribe the optimal solution set, i.e. the set of maximally parsimonious trees (MPTs), summa- rized graphically by a strict consensus tree of this set. The set of MPT(s) (min [total length] = 19 553) recovered during heuristic searches in PAUP (MUL- PARS, TBR, random-addition of taxa, 10 000 random starting trees, MAXTREES = 20 000) was confirmed by a full ratchet-analysis (Goloboff, 1999; Nixon, 1999; M?ller, 2004, 2005), including five random-addition cycles of 200 ratchet iterations each; the ratchet anal- yses, employed to escape local suboptima, recovered 97 trees across 1000 topological islands. Choice of opti- mizations (DELTRAN vs. ACCTRAN) was ineffectual, and neither DOLLO nor IRREVERSIBLE options were used. Of particular relevance to this compara- tively large analysis were recent discussions of: (i) effi- cient means for finding solutions for large data sets (Maddison, 1991; Page, 1993; Rice, Donoghue & Olm- stead, 1997; Quicke, Taylor & Provis, 2001; Salter, 2001), (ii) effects of missing data (Wilkinson, 1995, 2003; Wiens, 2003) and (iii) analytical relevance of branch lengths (Maddison, 1993; Lyons-Weiler & Hoe- lzer, 1997; Farris, K?llersj? & De Laet, 2001; Norell & Wheeler, 2003; Wilkinson, LaPointe & Gower, 2003). Summary statistics used here were: total length, L; consistency index, CI (Klassen, Mooi & Kicke, 1991; Kim 1996; K?llersj?, Albert & Farris, 1999); retention index, RI (Farris, 1989); rescaled consistency index, RC; and skewness index (g1) based on 105 topologies randomly generated from the same data matrix (Huelsenbeck, 1991; K?llersj? et al., 1992). Despite its popularity, the CI is negatively correlated with num- Figure 8. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), VIII. A, Chubb (2004a); B, Harrison et al. (2004). HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 15 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 ber of both taxa and characters analysed (Archie, 1989; Sanderson & Donoghue, 1989), making mean- ingful comparisons of indices across scales of analysis and classes of characters is difficult. Characters man- ifesting homoplasy can impose structural resolution and thereby result in smaller solution sets of MPTs (K?llersj?, Albert & Farris, 1999). The set of equally parsimonious topologies (i.e. solutions differing only in optimization of characters on branches of trees of iden- tical topology or solutions differing in branching struc- ture but of equal length) were summarized using a strict consensus tree. Summary statistics for strict consensus trees were component information, Nelson? Platnick term and total information, and Mickevich consensus information. Support for individual clades was measured by two statistics (Mort et al., 2000; Wilkinson et al., 2003): (i) percentages of 10 000 bootstrapped replicates in which the node was conserved (Felsenstein, 1985; Sanderson, 1995), indices considered informative even if assumptions concerning precision and absence of bias are unrealistic (Felsenstein & Kishino, 1993; Hillis & Bull, 1993); and (ii) Bremer (support) indices, the estimated minimal number of additional steps required wherein the given node, by inverse con- straint, is not conserved (Bremer, 1994, 1997). The lat- ter were estimated using PRAP (M?ller, 2004, 2005), metrics similar to the PC-compatible algorithms of Goloboff (1999) and Nixon (1999). Ratchet methods were used in order to find the minimum Bremer index by avoidance of entrapment in local optima (Maddi- son, 1991). For the Bremer (support) indices, 20 ratchet replicates per node were used (M?ller 2004, 2005). The popular alternative protocol, TREEROT, was not employed because its primary asset ? ?parti- tioned? support indices ? were not a priority here and (most importantly) the algorithm lacks the ratchet (Sorenson, 1999). Comparisons with other trees: Tests of alternative hypotheses proposed by other authors were equivalent to local penalties, i.e. minimal differences in total length imposed by the alternative hypothesis, while other aspects of the MPT (exclusive of pruning of taxa essential for comparability) were conserved (Kluge, 1997a, b). These estimates were made by simple trans- fer of branch(es) within the consensus cladogram using MACCLADE (Maddison & Maddison, 1992), Figure 9. Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), IX. A, Pereira & Baker (2006a); B, Slack et al. (2006a). 16 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 T a b le 2 . M ed ia n b ra n ch l en gt h s (L ) su bt en di n g cl ad e id en ti fi ed b y ta xo n a m on g M P T s (v al u es i n b ra ck et s pe rt ai n t o po ly to m ie s) , re sp ec ti ve B re m er ( su pp or t) in di ce s (B ) f or c la de s (i .e . n on -t er m in al t ax a in a n al ys is ), a n d ap om or ph ie s bo th u n am bi gu ou s (i .e . i n va ri an t fo r se t of M P T s) a n d di ag n os ti c (C I = 1 .0 0) o r su pp or ti ve (0 .5 0 ? C I < 1 .0 0) f or c or re sp on di n g ta xa ( A pp en di x 1) . C h ar ac te rs ( n u m be re d) a n d st at es ( le tt er ed i n i ta li cs ) id en ti fy t er m in al c on di ti on o f tr an sf or m at io n at tr ib u te d to i n te rn od e in q u es ti on ; ch ar ac te rs , s ta te s an d pr ov en an ce o f fe at u re s w er e de sc ri be d by L iv ez ey & Z u si ( 20 06 ) T ax on L B D ia gn os ti c ap om or ph ie s S u pp or ti ve a po m or ph ie s A ve s [8 2] 12 1b , 2 14 b, 1 51 8b , 1 91 2b , 1 98 7d , 2 21 8c 33 8b , 7 08 b, 7 89 a, 1 32 9b , 1 31 2c , 1 51 0a , 2 43 8b , 2 44 6b O rn it h u ra e 12 4 2 ? 14 70 b E oa ve s 13 9 13 41 8c , 5 15 b, 1 28 0b , 1 29 7b , 1 47 4b , 2 10 8b , 2 21 2c 13 33 d , 1 45 2b , 1 70 1c , 2 22 7c , 2 44 0c , 2 44 6d N eo rn it h es 98 11 22 c 22 1b , 1 58 6a , 1 68 7a , 1 68 8a , 1 69 0a , 1 81 9d , 2 13 4b , 2 38 3a P al ae og n at h ae 10 6 13 54 0b , 6 31 b, 6 56 b, 6 59 b, 1 75 0b , 2 02 9b , 2 43 6c , 2 94 5b 13 30 b, 1 52 3a , 2 02 8b , 2 13 3c C ry pt u ri * 10 2 ? 92 4b 13 61 b, 1 45 3b , 1 63 5b , 1 64 5b , 1 84 4b , 2 35 1b , 2 49 7a R at it ae ? 24 1 50 12 9a , 25 0b , 47 4a , 52 3b , 54 7b , 55 5b , 76 5b , 76 7a , 90 1b , 92 3b , 92 6b , 95 8b , 10 46 b, 1 05 1b , 12 63 b, 13 41 b, 1 53 7b , 1 55 4b , 1 56 4c , 1 86 1a , 2 02 2b , 2 04 5b , 21 65 b, 2 18 4b , 2 51 2b , 2 72 1b , 2 75 7c , 2 79 4b , 2 79 8b , 28 67 b 47 6b , 5 06 b, 6 00 a, 9 27 b, 1 00 8e , 1 01 9b , 1 04 1a , 1 05 3b , 1 09 8f , 1 12 2b , 12 58 a, 1 33 3e , 1 33 6c , 1 33 7c , 1 34 6c , 1 34 6b , 1 35 3a , 1 36 4c , 1 37 1c , 1 45 0a , 14 97 b, 1 50 9b , 1 54 8b , 1 69 4b , 1 70 7a , 1 70 9a , 1 74 4a , 1 74 7c , 1 75 6d , 17 66 b, 1 77 3b , 1 92 4b , 1 99 8a , 2 01 5d , 2 16 7a , 2 47 9b , 2 52 2b , 2 54 7b , 25 68 b, 2 71 7b , 2 76 9b , 2 80 8b , 2 81 1a , 2 82 1a , 2 86 8a C as u ar ii m or ph ae 88 31 35 2b , 1 12 0b , 1 12 1b , 1 16 7b , 1 17 0b , 1 39 0b , 2 30 6b 41 3c , 9 30 b, 9 52 b, 9 62 b, 1 15 6b , 1 78 9b , 1 84 4b , 1 35 5b , 2 66 7b , 2 94 9b S tr u th io n im or ph ae 10 0 44 10 7b , 10 65 b, 1 15 4b , 11 69 b, 1 78 4b , 18 96 b, 2 00 2b , 23 02 b, 2 32 6b , 2 39 8c , 2 79 5b , 2 82 4b 13 71 c, 1 55 1b , 1 56 8b , 1 75 6c N eo gn at h ae 14 2 52 21 3b , 5 23 c, 5 79 b, 6 01 b, 1 09 6b , 1 10 6b , 1 48 7c , 1 80 9b , 19 53 b, 2 06 8b , 2 10 8c , 2 20 9b , 2 21 6b , 2 21 7b 2e , 4 c, 1 09 b, 1 12 c, 4 68 b, 5 83 c, 6 00 d , 7 31 d , 1 49 7d , 1 63 3c , 1 78 9b , 2 29 4b G al lo an se ri m or ph ae 82 18 11 7b , 51 3b , 54 6b , 60 1c , 69 8b , 72 3b , 20 73 b, 2 85 5b , 29 15 b ? G al li fo rm es 13 7 86 54 2b , 62 5b , 10 77 b, 1 10 9b , 12 47 b, 1 25 7b , 13 62 b, 16 57 b, 1 90 6b , 2 69 3b , 2 85 9b , 2 90 7b 10 9d , 3 78 b, 5 24 b, 6 00 c, 7 50 b, 1 17 5c , 1 19 6b , 1 33 0b , 1 79 2c , 2 14 6a A n se ri fo rm es 97 41 95 b, 2 78 b, 2 05 2b , 2 07 3c , 2 14 8b , 2 45 4b , 2 72 4b , 2 74 7b , 29 13 b 42 2b , 1 33 3b , 2 49 7a N eo av es 81 18 12 80 c, 2 50 2b , 2 58 6b , 2 89 3b , 2 89 5b , 2 89 6b , 2 90 0d 48 0c , 5 17 c, 6 00 e, 1 72 1b N at at or es 51 1 ? ? P yg op od o- tu bi n ar es 10 4 43 19 5c , 1 43 2b , 2 07 6b , 2 41 3a ? G av io m or ph ae 95 52 53 4c , 5 38 b, 7 48 b, 2 11 7b , 2 14 7b , 2 24 9b , 2 25 6b 92 7b , 9 46 c, 1 51 4b , 1 76 6b , 1 92 4b , 2 07 7b , 2 08 9d , 2 28 7b , 2 36 2b , 2 40 2a G av ii fo rm es 12 5 ? 45 7b , 14 07 b, 1 53 2b , 18 93 b, 2 00 2c , 23 20 b, 2 33 1b , 24 11 b, 2 64 4b , 2 69 4b , 2 88 2b , 2 88 6b 11 93 b, 1 82 0b , 2 13 3b , 2 32 2b , 2 34 9c HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 17 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 P od ic ip ed if or m es 12 1 ? 82 3b , 2 30 4b , 2 43 5c , 2 64 2b , 2 65 8b , 2 77 1b , 2 78 4b 16 4b , 1 00 8d , 1 65 7b , 2 05 4d , 2 05 6b , 2 42 9b P ro ce ll ar ii m or ph ae 66 12 19 6b , 7 22 b, 1 34 7b , 2 40 4b , 2 63 0b , 2 74 4b , 2 93 3b 22 25 c, 2 35 6b , 2 72 9d S ph en is ci fo rm es 22 5 ? 44 8b , 5 34 b, 9 10 b, 9 33 b, 1 42 2b , 1 42 4b , 1 49 5b , 1 51 7b , 15 30 b, 1 54 1b , 1 54 2b , 1 54 4b , 1 55 6b , 1 57 1b , 1 73 6b , 17 49 c, 1 75 1b , 2 29 3c , 2 36 6b , 2 52 8b , 2 54 3b , 2 54 6b , 27 20 b, 2 79 0b , 2 79 1b , 2 87 0b 38 5e , 9 94 b, 1 30 2b , 1 35 3c , 1 36 4d , 1 44 3b , 1 45 1c , 1 51 6c , 1 58 0c , 1 58 1b , 16 94 b, 1 70 7c , 1 73 3a , 1 75 5c , 1 75 6c , 1 82 0b , 2 00 4b , 2 13 3b , 2 44 6c , 25 22 b, 2 56 3b , 2 58 4b , 2 58 8b , 2 61 0c , 2 81 0c , 2 81 2d , 2 86 8a P ro ce ll ar ii fo rm es 33 64 13 05 b, 1 30 6b , 2 84 7b 28 19 a S te ga n o- gr al la to re s 61 8 ? 11 38 b P el ec an im or ph ae 10 2 24 72 0b , 1 24 1b , 2 10 7b , 2 75 1b 24 a, 3 72 b, 1 14 4b , 1 54 0d , 1 99 9b , 2 08 9b , 2 72 9b B al ae n ic ip it if or m es 15 8 ? 25 7b , 2 88 b, 2 93 b, 4 33 b 15 3b , 2 86 b, 3 04 b, 5 66 b, 7 40 b, 7 62 b, 7 69 c, 7 80 c, 1 30 9b , 1 51 4b , 2 34 6b P el ec an if or m es 11 1 16 33 5b , 8 89 b, 1 83 2b , 2 57 3b 35 b, 4 8b , 1 47 b, 9 46 d , 2 18 1b , 2 35 1b , 2 38 8b , 2 40 6b , 2 54 8b C ic on ii m or ph ae 55 9 15 43 b 11 38 c, 2 17 9b , 2 83 0b C ic on ii fo rm es 58 9 ? 24 20 b A rd ei fo rm es 10 6 66 11 6b , 1 75 b, 7 54 b, 2 09 7b , 2 39 1b , 2 39 6b , 2 45 8b , 28 00 b, 2 83 4b , 2 83 6b , 2 85 1b 35 b, 1 47 b, 5 29 b, 5 35 b, 8 31 b, 1 23 8c , 2 02 8b , 2 33 0b , 2 38 8b T er re st ro rn it h es ? 42 1 ? ? C h ar ad ri im or ph ae 45 10 ? 25 75 b G ru if or m es 40 7 21 11 b 21 46 a, 2 19 7b C h ar ad ri if or m es 30 25 ? 24 62 b D en dr or n it h es ? 54 4 ? ? F al co n im or ph ae 62 6 29 16 b 24 31 b F al co n if or m es 83 19 12 0d , 1 85 7b , 1 93 8b , 2 34 3b , 2 42 8b 11 53 c, 2 13 3b , 2 85 4b , 2 89 9b S tr ig if or m es 17 2 12 2 13 b, 1 54 b, 1 74 b, 1 93 b, 5 48 b, 1 54 9b , 1 71 4b , 2 07 2b , 22 00 a, 2 28 6b , 2 30 0b 12 8c , 24 9b , 15 40 c, 1 56 9c , 17 79 b, 1 82 2b , 24 07 b, 2 41 2b , 25 83 c, 2 60 2a , 26 94 b, 2 71 0d , 2 74 3b A n om al og on at es ? 56 6 ? ? C u cu li m or ph ae 18 5 33 15 72 b 10 07 b, 1 33 6b , 1 61 4b , 1 65 1d , 1 65 8c , 1 86 6b , 2 63 4c , 2 84 9a O pi st h oc om if or m es 13 1 ? 95 9b , 1 06 4b , 2 85 7b 38 5e , 5 66 b, 8 50 e, 1 06 3b , 1 14 0b , 1 32 9d , 1 65 1e , 1 65 8d , 2 09 1b , 2 51 0b , 25 75 b, 2 71 0d , 2 84 5b C u cu li 85 42 93 7b , 2 03 4b , 2 04 6b , 2 06 1b , 2 20 0c , 2 33 4e 11 22 b, 2 49 8b P si tt ac im or ph ae 52 1 ? ? P si tt ac if or m es 17 7 13 0 11 8b , 2 46 b, 3 54 b, 4 10 b, 4 29 b, 5 93 b, 6 05 c, 6 50 b, 6 79 b, 70 3b , 7 61 b, 1 06 0b , 1 21 0b , 2 33 4d , 2 40 5d , 2 49 0b , 27 03 b, 2 71 2b , 2 83 2b , 2 87 6c , 2 87 8b , 2 88 4b 77 2b , 2 02 8b , 2 12 7b , 2 13 3d , 2 20 3b , 2 49 1b , 2 49 8b , 2 67 3b , 2 71 0c , 2 84 9e , 28 54 c, 2 93 5b , 2 94 1b C ol u m bi fo rm es 10 6 62 17 23 b, 2 11 9b , 2 55 7b , 2 84 6b 35 1b , 1 17 5b , 1 30 7b , 1 35 6b , 1 36 9b , 1 41 7c , 2 03 6b , 2 57 5b , 2 71 0d , 2 72 2b T ax on L B D ia gn os ti c ap om or ph ie s S u pp or ti ve a po m or ph ie s 18 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 In ce ss or es ** 10 1 2 ? ? C yp se lo m or ph ae 70 11 27 86 b 13 65 b, 2 90 3b A po di fo rm es 97 49 11 25 b, 1 37 5b , 1 41 6b , 1 45 5b , 1 46 5b , 1 46 6b , 2 44 9c , 26 61 b 38 b, 1 34 6b , 2 46 6a , 2 54 9c , 2 67 4b C ap ri m u lg if or m es 77 9 28 0b , 1 27 1b , 1 97 9b , 2 19 8c , 2 92 1b 12 8c , 2 30 b, 2 49 c, 4 50 b, 1 99 9b , 2 58 3c , 2 90 3d , 2 93 3b T ro go n es ?? 38 2 ? ? T ro go n om or ph ae 43 2 19 19 b ? T ro go n if or m es 83 58 45 0b , 9 35 b, 1 72 0b , 2 33 3b 24 4b , 5 31 b, 2 10 0b , 2 59 3c , 2 61 3b C ol ii fo rm es 10 8 ? 51 2b , 1 03 2b , 2 33 8b , 2 36 7b 39 8b , 2 03 6b , 2 12 7b , 2 67 3b , 2 70 2b P as se ri m or ph ae ?? [6 2] 13 18 07 b, 2 59 0b 71 8b , 1 45 3b C or ac ii fo rm es 51 6 23 60 b 27 23 b P ic if or m es 58 9 23 34 g, 2 33 5b 13 00 b, 1 70 9c , 1 98 1b , 2 49 8d P as se ri fo rm es 96 55 15 9b , 1 22 8b , 1 46 3b , 1 89 5c , 2 66 9b , 2 68 7b , 2 87 4b , 28 77 b, 2 89 0b , 2 89 1b 11 27 b, 1 54 0e , 1 55 9b , 2 78 9c T ax on L B D ia gn os ti c ap om or ph ie s S u pp or ti ve a po m or ph ie s *R ed u n da n t w it h t ax on o f n ex t- lo w er r an k ? D ro m ae om or ph ae ? b y h ie ra rc h ic al c la ss ifi ca ti on , an d eq u iv al en t to a po m or ph ie s of t er m in al t ax on T in am if or m es . O th er e xa m pl e ar e (i ) S u bc oh or t G al lo an se re s co m pr is in g so le ly t h e S u pe ro rd er G al lo an se ri m or ph ae ; an d (i i) S u pe ro rd er C as u ar ii m or ph ae c om pr is in g so le ly t h e O rd er C as u ar ii fo rm es . ?P er ta in s to e st im at e ex cl u si ve o f tw o ex ti n ct m em be rs ( D in or n it h if or m es , A ep yo rn it h if or m es ); s ee M et h od s. ?R ed u n da n t w it h t ax on o f n ex t- lo w er r an k ? T el m at or ae ? a n d th er ef or e la tt er w as n ot t ab u la te d. ?R ed u n da n t w it h t ax on o f n ex t- h ig h er r an k ? R ap to re s ? an d th er ef or e la tt er w as n ot t ab u la te d. ? R ed u n da n t w it h t ax on o f n ex t- lo w er r an k ? C oc cy ga e ? an d th er ef or e la tt er w as n ot t ab u la te d. M u so ph ag id ae . ** R ed u n da n t w it h t ax on o f n ex t- lo w er r an k ? C yp se lo m or ph ae ? a n d th er ef or e la tt er w as n ot t ab u la te d. ?? R ed u n da n t w it h t ax on o f n ex t- lo w er r an k ? T ro go n om or ph ae ? a n d th er ef or e la tt er w as n ot t ab u la te d. ?? R ed u n da n t w it h t ax on o f n ex t- h ig h er r an k ? P ic o- cl am at or es ? a n d th er ef or e la tt er w as n ot t ab u la te d. T a b le 2 . C on ti n u ed HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 19 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 which holds other topological groupings constant. This procedure differs from searches constrained only to the grouping of interest, typically performed using ancillary searches under inverse constraints, as in protocols for estimation of Bremer (support) indices. CRITICAL CONCEPTS AND TERMINOLOGY ?It is possible [50% likelihood] that ? 1) a distant relationship exists between Apteryx and a tinamou-galliform assemblage; . . . (5) the diurnal birds of prey may be allied to the owls through the Falconidae . . . It is improbable [formerly widely believed, since discredited] that ? 1) a close relationship exists between Rhea and the tinamous; . . . (3) Pandion deserves familial status in the Falconiformes . . .? (Sibley & Ahlquist, 1972: 241), emphasis added. ?. . . the mousebirds, or colies, [i] have no close living relatives, . . . [ii] they are the only survivors of an ancient divergence . . . Their [iii] closest living relatives are probably . . .? (Sibley & Ahlquist, 1990: 363) Before considering specific findings in the present study, a clarification of critical terms is essential. The first of the foregoing quotes comprises four statements of perceived probability that either make no objective sense or are self-contradictory by conventional stan- dards. Also, the second quote contains three conclu- sions (i?iii) for a single group based on a single data set that are: either mutually contradictory (i and iii), or of undetermined meaning (ii vs. either i or iii). In cladistic terms, ?most closely? implies ?closely? in that hierarchy defines relative relationships. Sister-groups are by definition the ?most closely related? of any taxa compared. For example, in cladistic terms, an assump- tion of monophyly of life on earth implies that every taxon has a close relative and/or closest relative, regardless of extinctions. In other words, degree of relatedness is relative: all lineages have a closest rel- ative and therefore a close relative. Sister-groups need not meet some standard of similarity or absolute antiquity of divergence to qualify. However, under an expectation of at least a limited correlation between evolutionary change in morphology with time ? nei- ther ?clock-like? nor wildly heterogeneous and com- pletely disassociated ? sister-taxa can be expected to share degrees of similarity broadly related to time since divergence, such that recency of divergence between sister-taxa tends to be associated with simi- larity, and antiquity of such divergence to be associ- ated with dissimilarity. RESULTS MINIMAL-LENGTH TREES OR MPTS The search for MPTs recovered 97 trees of minimal length (19 553 steps) under standard ordering of mul- tistate characters and rooting by outgroup taxa as given (see Methods). This solution set (2.04 ? 1011 rearrangements assessed) had the following summary statistics: CI = 0.2432; RC = 0.1664; RI = 0.6842; and skewness, g1|105 = ?0.4258. A strict consensus tree of the MPTs (Figs 10?18) was completely resolved for the Neornithes with the exception of six polytomies (mostly trichotomies, some nested, discussed below), uncertainties sufficiently limited so as to obviate a majority-rule consensus tree for the primary solutions set, or to delimit ambiguity where one or more ?rogue taxa? may be influential (Sumrall, Brochu & Merck, 2001). The strict consen- sus tree for the 97 MPTs shared the following sum- mary statistics: (i) component information, 173; (ii) Nelson?Platnick term information, 4367; (iii) Nelson? Platnick total information, 4540; and (iv) Mickevich consensus information, 0.168. OUTGROUP TAXA: MESOZOIC ROOTS OF AVES Non-Neornithine Aves: In light of the growing con- sensus regarding fossil lineages of the Mesozoic and widely employed characters thereof, broad agree- ment between our findings and those of others treat- ing pre-neornithine birds was not unexpected. Relationships among outgroup taxa in this analysis generally were consistent with recent analyses (Mar- tin, 1983; Witmer, 1991; Holtz, 1998; Padian & Chi- appe, 1998; Clarke & Chiappe, 2001; Chiappe, 2001, 2002; Clarke & Norell, 2002, 2004; Clark, Norell & Makovicky, 2002; Chiappe & Dyke, 2002; Maryanska, Osm?lska & Wolsan, 2002; Pisani et al., 2002; Snively, Russell & Powell, 2004; Mayr, Pohl & Peters, 2005; Zhou & Zhang, 2005). Critical for empirical rooting of ingroup taxa, as opposed to hypothetical ancestors or other synthetic means of proposing polarities, this congruence lends credence to assessments of polarities of characters at the most basal of neornithine nodes (e.g. the diver- gence of neognathous from palaeognathous taxa). Crocodylians fell as predicted among the basal Archosauria (Larhammar & Milner, 1989; Hedges, 1994). Principal exceptions from a growing consensus of palaeontologists were reversed positions or irreso- lution within two pairs (Fig. 12): (i) Troodontoidea (Troodon and Saurornithoides) and Dromaeosauroi- dea; and (ii) Rahonavis and Apsaravis, the latter cou- plet being equally parsimonious whether paraphyletic to other taxa or as sister taxa. Details of positions among outgroups are of secondary interest here, but it is noteworthy that the few instances of incongruence with other studies were associated with exceptionally poorly supported nodes or polytomies in the present work (Fig. 12). It is likely that the generally lower sup- 20 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 port indices among pre-Neornithes reflect missing key taxa and poor preservation of those coded. NEORNITHES ?. . . it is probable that the majority of living genera [of birds] were in existence by the end of the Tertiary. . . . Most, perhaps all, of the [modern] orders of birds had become established by the end of the Eocene.? (Brodkorb, 1971a: 42) ?The phylogenetic position of Palaeogene birds thus indicates that diversification of the crown-groups of modern avian ?fam- ilies? did not take place before the Oligocene, irrespective of their relative position within Neornithes (crown-group birds).? Mayr (2005a: 515) Strong support for monophyly of the Neornithes (Table 2; Figs 10, 11) was conferred. Notable, however, in the present reconstruction was its poor congruence with the ?tapestry? depicted by Sibley & Ahlquist (1990), in which only three higher-order taxa ? their Ratitae, Galloanserae and Procellarioidea, and mono- phyly of one contentious order (Caprimulgiformes) ? Figure 10. Ordinal-level strict consensus tree for orders of Neornithes based on 2954 morphological characters, indicating delimitations of segments detailed in Figures 12?18. HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 21 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Figure 11. Simplified summary tree for uppermost, supraordinal ranks of avian classification. Dashed internodes corre- spond to marginally supported clades. For complete classification, see Appendix 1. 22 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 were in significant agreement with corresponding clades in the present analysis. Points of disagreement, however, were abundant and included much of the topological (diagrammatic) structure in the two works, and notably included the following groupings depicted by Sibley & Ahlquist (1990: fig. 4A): (i) monophyly of {Ratitae, Galloanserae}; (ii) provisional, exceptionally basal placement of Turnix; (iii) very basal positions and interposition of Piciformes, Coraciiformes, Coliiformes, Trogoniformes and Passeriformes; (iv) multiple discrepancies associated with hypotheses of polyphyly of Pelecaniformes and Ciconiiformes, and (v) inclusion of some Gaviiformes, Podicipediformes, Sphenisciformes and Falconiformes among these groups. Topological dichotomies that hierarchically group modern orders of Neornithes were sought Figure 12. Detailed segments of strict consensus tree of all MPTs recovered in present study. Part A. Outgroup (non-neornithine) taxa. Nodes are labelled by percentages of bootstrapped replicates in which node was retained (numer- ator), and below by Bremer support indices (denominator). HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 23 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 (Fig. 10), and these formed the ordinal basis for a higher-order classification (Appendix 1). In the following, descriptions of findings, statistics of support, etc., were presented in figures, and refer- ence to these was employed in place of repetition of metrics in the text. Consequently, readers are directed to the appropriate figures and tables where narratives refer to robustness, support and relative parsimony of alternative hypotheses. MODERN PALAEOGNATHOUS BIRDS This analysis revealed the relationships among the palaeognathous birds to be exceptionally resolved, well supported, virtually unambiguous, empirically rich, markedly traditional, and supported by an unprecedented sample of outgroups. The ratites or flightless modern palaeognathous birds have been the subject of more anatomical and molecular study than any other avian group, an important motivation for which concerned diagnoses of plesiomorphic and apo- morphic morphological characters in a group widely recognized to represent an early branch among Neor- nithes but for which useful outgroups were lacking (Balouet, 1984; Zusi, 1993). Basal polarities of charac- ters of plesiomorphic condition among modern and closely related fossil palaeognathous taxa (Houde & Olson, 1981; Houde, 1988; Leonard et al., 2005) awaited resolution by means of the most primitive Aves, many recovered only recently (Appendix 1). Taxonomically orientated anatomical studies, em- phasizing ratites or more inclusive in scope, ensued during the 19th and 20th centuries (F?rbringer, 1888; Feduccia, 1980; Houde & Haubold, 1987), and inves- tigations of phylogenetic emphasis were among the earliest for Neornithes (Verheyen, 1960a; Sibley & Ahlquist, 1972; Cracraft, 1974a; Wattel, Stapel & de Jong, 1988). In some cases, inference of the primary grade of divergences of palaeognathous, galloanserine and other neognathous taxa aided in the recovery of historical patterns and broad outlines of phylogeny of palaeognathous taxa, patterns that were to prove beyond the limits of mtDNA for resolution (H?rlid, Janke & Arnason, 1997, 1998). Most prior studies regardless of method ? notably excepting early works conceptually confined by the dated biogeographical paradigm of static continents (Briggs, 2003) or phenetic perspectives on affinities (McDowell, 1948; de Beer, 1956; Storer, 1960a, 1971a, b; Sibley & Frelin 1972) ? have hypothesized that the palaeognathous birds are the sister-group of other Neornithes, the Tinamiformes are the sister-order of the ratites among palaeognathous taxa (Caspers, Wat- tel & de Jong, 1994; de Kloet & de Kloet, 2003), and accordingly the ratites are monophyletic (Bock, 1963b; Prager et al., 1976; Stapel et al., 1984; Bock & B?hler, 1988; H?rlid et al., 1997; Lee et al., 1997; Van Tuinen, Sibley & Hedges, 1998; Dyke, 2001a; Dyke & Van Tuinen, 2004; Slack et al., 2006a, b). These findings counter early disputes based in part on biogeography, isolated interpretations of fossils (Houde & Olson, 1981), speculations regarding heterochrony (Feduccia, 1985) and (subsequently admitted) analytical anoma- lies (H?rlid & Arnason, 1998). Notable in the last of the foregoing categories was the initial inference of a sister-relationship between a neognathous group com- prising the Galliformes and Anseriformes and the palaeognathous birds by Sibley & Ahlquist (1990), a topology rendering at the outset the polyphyly of neog- nathous taxa; subsequently these authors depicted the neognathous birds as monophyletic. Monophyly of the Tinamiformes was supported by the molecular analyses by Paton et al. (2002) and Har- rison et al. (2004), but minimal taxonomic sampling diminished the generality of these inferences. Sister- group relationships of palaeognathous orders ? Struthioniformes and Rheiformes, and Dromaiiformes and Casuariiformes ? were supported strongly here (Fig. 13) and elsewhere (Lee, Feinstein & Cracraft, 1997; Leonard, Dyke & Van Tuinen, 2005). A minority of earlier findings (Figs 7A, 8B) provided weak evi- dence of paraphyly of the Struthioniformes and Rheiformes with respect to a sister-grouping of Dromaiiformes and Casuariiformes and also provided weak support for the Apterygiformes as as sister- group to the latter (Van Tuinen, Sibley & Hedges, 2000; Cooper et al., 1992, 2001; Paton et al., 2002; Harrison et al., 2004). Despite support indices sugges- tive of robustness in several of the molecular works, questions regarding Bayesian bootstrap values (Simmons, Pickett & Miya, 2004) justify caution in such assessments. The Apterygiformes, herein placed as sister-group to all other ratites (Fig. 13), have been inferred to occupy a marked diversity of positions in prior studies (Crac- raft, 1974a, 2001; Lee et al., 1997; Cooper et al., 2001; Haddrath & Baker, 2001; Paton et al., 2002; Harrison et al., 2004). Also, the position of the Apterygiformes relative to the extinct Dinornithiformes varied (Vickers-Rich et al., 1995). The Apterygiformes are the most speciose and genetically subdivided of extant orders of ratites (Baker et al., 1995; Burbridge et al., 2003), but are significantly less diverse than the for- merly sympatric Dinornithiformes. The position of the Dinornithiformes also remains a point of controversy, in part because of missing data for this extinct, diverse group; monophyly and rela- tionships among members have been confirmed (Baker et al., 2005). Cracraft (1974a, 2001) considered the Dinornithiformes to be the sister-group of the Apterygiformes, contrary to Cooper et al. (1992, 2001), Van Tuinen et al. (1998, 2000), Haddrath & Baker 24 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 (2001) and the present provisional inferences. In most respects, the topologies for ratites inferred by Lee et al. (1997) and Dyke & Van Tuinen (2004: fig. 4) most closely approximated that inferred here (Fig. 13). Missing data for two orders of ratites ? Dinornithi- formes and Aepyornithiformes ? proved analytically problematic if included unconditionally with extant ratites. Unrestricted analysis of these extinct, moder- ately related, highly divergent, sparsely coded lin- eages resulted in a suspicious placement of these two orders as sister taxa. The large numbers of missing data in the two extinct lineages, many lacking in both taxa, prompted two alternative analyses to be performed. Global searches of Dinornithiformes (excluding the poorly known Aepyornithiformes) and placements within the MPT as backbone-constraint placed the moas to be the sister-group of other ratites exclusive of Apterygiformes (Fig. 13), contrary to a sis- ter-relationship between these New Zealand endemics as advocated by Cracraft (1974a, 2001). By backbone- constraints or exclusion of the Dinornithiformes, the Aepyornithiformes were placed as the sister group of the clade comprising Struthionidae and Rheidae (Fig. 13). Figure 13. Detailed segment of strict consensus tree of all MPTs recovered in present study. Part B. Neornithes: Palaeog- nathae and Galloanserae. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type). HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 25 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 GALLIFORMES AND ANSERIFORMES: LAND AND WATER FOWL Interordinal relationships: The sister-group relation- ship between the Galliformes and Anseriformes, reaf- firmed here (Fig. 13), was inferred previously by Cracraft (1981, 1988), Cracraft & Mindell (1989), and substantiated thoroughly using morphological (Dzerzhinsky, 1995; Caspers et al., 1997; Livezey, 1997a, 1998a; Cracraft & Clarke, 2001; Dyke, 2003; Mayr & Clarke, 2003) and molecular data (Bleiweiss et al., 1994, 1995; Groth & Barrowclough, 1999; Van Tuinen et al., 2000, 2001; Cracraft, 2001; Prychitko & Moore, 2003; Chubb, 2004a; Harrison et al., 2004; Simon et al., 2004; Smith, Li & Zhijian, 2005). How- ever, marginally supported counter-proposals persist (Ericson, 1996, 1997; Ericson, Parsons & Johansson, 1998; Bourdon, 2005). Anseriformes: Within the waterfowl (Anseriformes), sequential sister-group relationships of the Anhimi- dae, Anseranatidae and Anatidae, respectively, was previously demonstrated by Livezey (1997a) and con- firmed here (Fig. 13). Monophyly of the morphologi- cally diverse and speciose Anatidae, including the true geese (Anserinae) and typical ducks (Anatinae), is essentially beyond dispute (Livezey, 1986). There exist departures from this arrangement by a minority of workers (Olson & Feduccia, 1980a; Sraml et al., 1996), but this topology has been substantiated using diverse evidence (Livezey, 1986, 1997a; Quinn, 1992; Donne- Gouss? et al., 2002). The historical hypothesis placing the Phoenicopteridae within the Anseriformes (Table 1) was among the early casualties of formal phylogenetics (Livezey, 1997a, 1998a). Galliformes: The pioneering myological works by Hudson, Lanzillotti & Edwards (1959) and Hudson & Lanzillotti (1964) provided early hints concerning relationships of Galliformes, but unfortunately these surveys were not cladistic and followed Peters (1934) in considering unique Opisthocomus as an aberrant galliform. Studies of galliform fossils continue to be phenetic in approach (Mourer-Chauvir?, 2000; G?hlich & Mourer-Chauvir?, 2005). Fortunately, this pattern is likely to change with the increasingly com- mon phylogenetic analyses of galliforms (Dyke, Gulas & Crowe, 2003) and an improved fossil record (Mayr & Weidig, 2004; Mayr, 2005a). In the present work, relationships of two families within the Galliformes ? Megapodiidae (Birks & Edwards, 2002) and Cracidae (Pereira & Baker, 2004; Grau et al., 2005) as mutually monophyletic, sequential sister-groups to all remaining galliforms ? agree with placements by other investigators (Prager & Wilson, 1976; Cracraft et al., 2004). Some workers (Hudson et al., 1966), however, suggested a sister-group relation- ship between the two families (superfamily Cracoidea), as opposed to placement as successive sister-groups (paraphyletic) to other galliforms (Fig. 13). The robust placement of Meleagrididae as sister- group to the Phasianidae sensu lato in the present work (Fig. 13) opposes inclusion of the family among the enormous complement of other galliforms (reviewed by Sibley & Ahlquist, 1990). The present finding also differs with the indeterminate placement of this distinctive group from most galliforms by Dyke et al. (2003). Dyke et al. (2003: fig. 3) depicted the Megapodiidae and Cracidae as basal, successive sis- ter-groups to the diverse and speciose ?Phasianoidea?; the latter group included Numida and Acryllium (Numidinae) as members of a polytomous assemblage immediately basal to Meleagris, Agriocharus, Tetra- onidae, and a clade comprising 39 taxa of other galli- forms inviting taxonomic subdivision. Most of the large-bodied genera of phasianoids (e.g. Gallus, Pha- sianus) and the ?Old World quail and partridges? were among a large, basal polytomy of the ?phasianoids? exclusive of the guineafowl (Numidinae). Some of the nodes within this large group, including those resolv- ing Meleagridae and Tetraonidae relative to megapo- diid and cracid galliforms, were not sustained by Dyke et al. (2003: fig. 3) in a strict consensus of 1700 MPTs based on 102 characters. Also, the tree inferred here (Fig. 13) departed from those recovered using molecu- lar data (Dimcheff, 2002; Dimcheff, Drovetski & Min- dell, 2002). The vast majority of galliform taxa are members of a morphologically conservative group (Holman, 1961), many formerly included among the Perdicidae or Odontophoridae (Sibley & Ahlquist, 1990). These taxa also posed problems of resolution in the present work (Fig. 13), and nodes among these taxa were suffi- ciently weak as to permit alternative local topologies (i.e. a terminal polytomy). Armstrong, Braun & Kim- ball (2001) found that mitochondrial and nuclear DNA similarly resolved groupings within a sparse but broad sample of Galliformes. Basal nodes of the latter taxa are broadly consistent with some higher-order topolo- gies (Prager & Wilson, 1976; Helm-Bychowski & Wilson, 1986; Crowe et al., 1992; Kimball et al., 1999; Guti?rrez, Barrowclough & Groth, 2000; Lucchini et al., 2001; Dimcheff et al., 2002; Pereira, Baker & Wajntal, 2002). The single exception among this group (based on included genera) is the strongly supported sister-group relationship between Gallus (Phasian- idae) and Numida (Numidinae). The Numidinae were inferred to be the sister-group of the Phasianidae by Kimball et al. (1999) and Pereira & Baker (2006a). MARINE ASSEMBLAGE A diversity of mutually distinctive groups of aquatic birds have been the focus of much early speculation 26 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 regarding the potentially misleading effects of similar- ities of locomotion leading to morphological conver- gence. Most evocative of these speculations concerned the Gaviiformes and Podicipediformes (e.g. Stolpe, 1935; Storer, 1956, 1960b), foot-propelled diving spe- cialists that prompted arguments based on phenetics, assumptions of ancestral status for fossils, simplistic proposals of evolutionary trends and (most fundamen- tally) a failure to meet conventional standards of phylogenetic inference. These shortcomings notwith- standing, such proposals from this era gave rise to a general and uncritical acceptance of rampant conver- gence uniquely afflicting morphological characters, claims that persist to the present day. Various alliances among the Gaviiformes, Podicip- ediformes and Procellariiformes were suggested by Mayr & Amadon (1951), and proved consistent with myological data analysed by McKitrick (1991a, b) and molecular patterns recovered by Watanabe et al. (2006). A relationship between the Gaviidae and Charadriiformes was considered plausible by Storer (1956). Without explanation, however, Storer (1971b) listed the loons and grebes together immediately fol- lowing the Charadriiformes, in apparent contradiction to his previous opinion. Foreshadowing a natural radi- ation of marine birds, Ho et al. (1976) inferred a com- paratively close relationship of the Sphenisciformes with other primarily marine orders, and fossil evi- dence for loons ? of only marginal quality, optimistic appraisals by Olson (1992a) and Mayr (2004a) not- withstanding ? suggests an early origin at least for the Gaviiformes. A phylogenetic alliance among the Sphe- nisciformes, Procellariiformes, Gaviiformes and Podic- ipediformes was substantiated as well by Cracraft (1982a), and this was indicated by Nunn & Stanley (1998) and Slack et al. (2006a) on molecular grounds. The comparatively robust skeletal elements of pen- guins predispose them to fossil preservation, and recently recovered remains hold promise for strati- graphic chronology (Slack et al., 2006b). The clade of basal marine taxa inferred herein evolved myriad modes of foraging (Storer, 1971a): (i) Gaviiformes and Podicipediformes being extremely specialized foot- propelled diving birds; (ii) Sphenisciformes and Pele- canoididae (Procellariiformes) being wing-propelled diving birds, submarine ?flight? of the former rendering members aerially flightless (Livezey, 1989a); and (iii) Procellariiformes, comprising hover-foraging Oceaniti- dae and other families combining wind-powered glid- ing and plunge-diving (Del Hoyo, Elliott & Sardgatal, 1992). Some fossil groups remain of uncertain ordinal affinity ? e.g. the wing-propelled Plotopteridae (Olson & Hasegawa, 1979, 1996; Olson, 1980; Goedert, 1988; Goedert & Cornish, 2002; Mayr, 2004b) ? and did not merit analysis herein, where states for cranial char- acters are critical but specimens are woefully incom- plete. Early descriptions suggested the inclusion of the Plotopteridae among Pelecaniformes is competitive with an alternative relationship to Sphenisciformes for which pectoral similarities were emphasized (Mayr, 2004b). Dissent regarding the ordinal relationships of the Plotopteridae is consistent, to a point, with the interordinal relationships of the Pelecaniformes and Sphenisciformes inferred herein (Fig. 14). Monophyly of the Sphenisciformes seldom has been doubted, and resolution of relationships among mod- ern and fossil species was achieved (Ksepka, Bertelli & Giannini, 2006), but the position of this distinctive marine group remains a long-standing controversy. This duality of distinct synapomorphy and symplesio- morphy underlies a number of classificatory problems of Aves, in which marked distinction of groups tends to confound comparisons with other groups. Of the alter- natives proposed, an affinity with the Procellarii- formes has received broadest support, both in the present analysis (Fig. 14) and elsewhere (Cracraft, 1981, 1986, 1988). Despite agreement with the inferences by Cracraft (1982a), it is predictable that strong confirmation of a sister-group relationship between the Gaviiformes and Podicipediformes (Fig. 14) herein will engender concerns of artefactual pairing by convergence (Storer, 1956, 1971a, 2000, 2002). Storer (2002: 16) felt that the non-phylogenetic work by Stolpe (1935) ?. . . demonstrated that the similarities among the loons, grebes, . . . resulted from convergent evolution . . .? The inclusion of the Mesozoic Hesperor- nithiformes with modern Gaviiformes and Podicipedi- formes by Cracraft (1982a), a finding not supported here (Figs 10, 14), was the inference subjected to greatest criticism. Obvious similarities of form and life history have prompted exceptional attention to differ- ences between the two orders (e.g. Sibley & Ahlquist, 1972: table 1), tallies without benefit of polarities or phylogenetics. In many cases, these rationalizations are undermined with respect to functional compari- sons, e.g. the Gaviidae employ feet for primary propul- sion but also use their wings (Olson, 1985), and members of the two orders also differ in the move- ments typical of the pelvic limb (Storer, 1956). Pairing of the Gaviiformes with the Podicipediformes as sister- groups has been championed by Cracraft (1982a, 1988), a proposal not without opposition (e.g. Storer, 1956, 1960b, 1971a; Sibley & Ahlquist, 1972, 1990). Additional support for this ordinal pairing has been reported (Cracraft & Mindell, 1989; Bourdon, Boya & Iaroch?ne, 2005), but most other analyses excluded one or both of these key orders, rendering comparisons among such works regarding these orders impossible. Without a consensus regarding a relationship between the Podicipedidae and Gaviidae, the former have been the subject of several extraordinary propos- HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 27 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 als, based on relatively weak evidence or mere specu- lation. Olson (1985: 168), under the subheading ?Family Incertae Sedis Podicipedidae?, stated: ?In looking beyond their obvious specializations for diving, I can- not see that the grebes (Podicipedidae) would be out of place in the Gruiformes.? A more precise proposal for the latter is a possible affinity on myological grounds with the gruiforms Rhynochetos and Eurypyga (Zusi & Storer, 1969). An apparent variant of this speculation was a possible relationship with the Heliornithidae and the closely related Rallidae (Beddard, 1893; Olson, 1985; Houde, 1994). Also, a tenuous alliance between the Podicipedidae and Cuculidae was depicted by Van Tuinen et al. (2000), but subsequent works have failed to support this grouping. Another position recently inferred for the Podicipediformes relates to the Phoe- nicopteridae (Van Tuinen et al., 2001; Mayr, 2004c), a proposal considered further below. In most respects, inferences herein regarding the Procellariiformes were among the least contentious for the marine assemblage, whether in comparison with traditional (Kuroda, 1954) or modern reconstruc- tions (Nunn & Stanley, 1998; Kennedy & Page, 2002; Watanabe et al., 2006). A moderate departure from traditional arrangements is the finding herein of the Diomedeidae (albatrosses) as comparatively derived, with other Procellariiformes paraphyletic to the typi- cal Procellariidae (Austin, 1996; G?mez-D?az et al., 2006) and Diomedeidae (Nunn et al., 1996). PELECANS AND ALLIES: TOTIPALMATE BIRDS The totipalmate or pelecaniform birds, as traditionally defined, remain a higher-order group of extraordinary controversy, but in reality the suite of unifying char- acters, stressed by Beddard (1898), has been expanded for decades beyond the totipalmy cited as sole uniting anatomical character for the order by Sibley & Ahl- quist (1972). Polyphyly of the order was inferred sub- sequently by Sibley & Ahlquist (1990) and Hedges & Sibley (1994). The status of the Pelecaniformes has been debated since the core assemblage was included in widely recognized classifications (Mayr & Amadon, 1951; Wetmore, 1930, 1960), and points of controversy include those of monophyly, content and interordinal position, as empirically derived from metric (Ver- heyen, 1960b), neontological (Cracraft, 1985), palae- ontological (Bourdon, 2005; Bourdon et al., 2005) and molecular perspectives (Siegel-Causey, 1997; Farris et al., 1999). The exceptional heterogeneity of traditionally included families ? e.g. frigatebirds, gannets and pel- icans ? render questions of membership especially problematic. Perhaps most intriguing of the debated memberships is that of the shoebill or Balaeniceps (Reinhardt, 1860, 1862; Cottam, 1957; Feduccia, 1977a; Mayr, 2003a). Purportedly intermediate fea- tures of ?stork-like? and ?pelican-like? forms (Van Tuinen et al., 2001; Bourdon et al., 2005) have extended to proposals of pelecaniform affinity of the hammerkop (Scopidae). In agreement with the present analysis, the consensus of available phy- logenetic works places the distinct Phaethontidae as sister-group to other pelecaniforms exclusive of Balaeniceps (Mayr & Clarke, 2003), with an alterna- tive position hypothesized for the Phaethontidae as an exceptional plesiomorph allied to some pelecaniforms and the Procellariiformes (Bourdon et al., 2005). The present study also resolved Balaeniceps as sister- group to the clade comprising Phaethontidae and other (traditional) Pelecaniformes. Scopus was not inferred here to be closely related to the Pelecani- formes (Fig. 14), contra Mayr (2003a). Relationships among traditional Pelecaniformes (excluding Balaeniceps), inferred cladistically by Crac- raft (1985: figs 6, 7), agreed with the inferences pre- sented herein (Figs 10, 14), whereas comparisons between the studies with respect to the orders Sphe- nisciformes, Gaviiformes, Podicipediformes and Pro- cellariiformes were not possible. Sibley & Ahlquist (1990) proposed a ?four-fold? polyphyly of Pelecani- formes among the most notable departures of their analysis from contemporary arrangements, whereas several other traditional elements were conserved in their scheme. Hedges & Sibley (1994), based on an analysis impoverished in both data and taxa, also sug- gested polyphyly of taxa traditionally considered pele- caniform in a work remonstrated by Farris et al. (1999). Syntheses by Van Tets (1965) and Siegel- Causey (1997: fig. 6.3) reaffirmed ordinal monophyly (exclusive of Phaethontidae) using morpho-ethological data, whereas molecular reconstructions violated ordi- nal monophyly by topologically variable inclusions of the Diomedeidae, Procellariidae and Cathartidae (Sie- gel-Causey, 1997: fig. 6.2). One minor departure from tradition by Sibley & Ahlquist (1990) was a terminal triad in which the Phalacrocoracidae were placed as sister-group to the Anhingidae and Sulidae. Kennedy & Spencer (2004) weakly confirmed mono- phyly of the traditionally constituted order, in part by use of appropriate outgroups but despite heteroge- neous taxonomic sampling of ingroup families. Three weakly resolved departures by Kennedy & Spencer (2004) from the hypothesis inferred herein (Fig. 14) were: (i) reversal of the positions of the Phaethontidae relative to the Fregatidae + Pelecanidae; (ii) a sister- relationship between the Pelecanidae and Phae- thontidae; and (iii) paraphyly of Phalacrocoracidae and Anhingidae to the Sulidae. The Phalacrocoracidae and Anhingidae ? families long considered closely related and strikingly similar in external and skeletal aspects (Siegel-Causey, 1988) 28 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 ? have been subjected to unexpected hypotheses of relationship. A series of related papers (Kennedy, Spencer & Gray, 1996; Kennedy, Gray & Spencer, 2000; Kennedy & Spencer, 2000, 2004; Kennedy et al., 2005), based on limited taxonomic representation of pelecan- iform families and unconventional analytical methods, mustered mtDNA sequences and behavioural data that favoured paraphyly of these two families to the Sulidae, also inferred phenetically by Sibley & Ahl- quist (1990). Based on the present analysis (Table 3), however, a sister-group relationship between Phalac- rocoracidae and Anhingidae is strongly favoured. STORKS, HERONS AND ALLIES ?Wading birds?, as delimited here, comprise the typi- cally long-legged, long-necked storks and herons, and exclude the morphologically reminiscent cranes and allies (Gruiformes) and the potentially allied shore- birds (Charadriiformes). Highest-order nodes resolved in the present study defined a primary division of (i) ?herons? from (ii) ?storks? and allies as sister-groups (Fig. 14). Among the ?storks?, Scopus is the sister- group to other members, the latter comprising clades partitioning the (i) ibises and spoonbills, and (ii) fla- mingos and typical storks. Within the ?herons?, the only notable finding is the placement of Cochlearius as sister-group to other herons (Fig. 14), an inference consistent with traditional classifications (e.g. Wet- more, 1960) and earlier findings (Cracraft, 1967a; Sheldon, Jones & McCracken, 2000). Shufeldt (1901b) suggested affinities between the Phoenicopteridae (flamingos) and both the Anseri- formes (waterfowl) and the Ciconiiformes (storks and traditional allies). Olson (1978) questioned the mono- phyly of the traditional Ciconiiformes on phenetic grounds, suggested charadriiform affinities of Phoeni- copteridae and Threskiornithidae, and expressed uncertainty regarding the ordinal placement of the herons (Ardeidae). Van Tuinen et al. (2001), based on conventional molecular estimates and the phenetics of DNA?DNA hybridization, found no support for mono- phyly of the Ciconiiformes in an analysis including representatives from several other traditional groups. Molecular reconstructions by Slikas (1997), however, confirmed monophyly of the morphologically diverse, ?true? storks (Scopus and Balaeniceps not sampled), groupings that also were afforded significant etholog- ical support (Slikas, 1998). It has been hypothesized in recent years that the Phoenicopteridae may be the sister-group of the grebes (Podicipediformes), a proposal supported by tenuous molecular (Van Tuinen et al., 2001) and mor- phological evidence (Mayr & Clarke, 2003; Mayr, 2004c; but see Storer, 2006). Given the variable view- points expressed regarding the Phoenicopteridae as well (Gadow, 1877; Shufeldt, 1889a; Feduccia, 1976, 1977a), this couplet offered the hope of dispensing with two challenging taxonomic placements by means of a single union, a circumstance not uncommonly an artefact of long-branch attraction (Philippe et al., 2005). Both of these autapomorphic taxa have been subjected to classificatory confusion for more than a century (e.g. Weldon, 1883; Shufeldt, 1901b; Jenkin, 1957), with affinities of the flamingos considered plau- sible between either the Ciconiiformes or the Anseri- formes. Despite robust support for the more traditional position in the present analysis (Tables 2, 3; Figs 10, 14) and the minimal evidence presented by others for the proposal of the Podicipediformes, the latter hypothesis merits examination on the grounds of its superficial implausibility and the marked rear- rangements of higher-order avian relationships it would imply. Supplementary morphological support for a sister-group relationship between grebes and fla- mingos marshalled by Mayr & Clarke (2003), however, required the exclusion (in a second analysis) of the loons ? heretofore the global sister-group of the grebes ? to sustain the grouping in question. Both exclusion of the Gaviiformes and narrow sampling of characters and taxa with which the Phoenicopteriformes were evaluated by Mayr (2004c) weakened the resultant inferences regarding the relationships of flamingos. Chubb (2004a: 148) recovered 50% and 78% boot- strap support for this taxonomic couplet in analyses of different partitions of the ZENK gene, and joined Van Tuinen et al. (2001) in the speculation that: ?. . . because both grebes and flamingos are highly derived morphologically and adapted to unique aquatic niches, their potential evolutionary alliance has previously gone unnoticed.? Unfortunately, this rationalization is vulnerable to criticism because: (i) modifications for foot-propelled diving of grebes are comparable with those of several other groups of Neor- nithes ? e.g. some Anatidae (Oxyurini, Mergini), Gavi- idae, Phalacrocoracidae and Anhingidae; and (ii) the ?unnoticed alliance? between grebes and flamingos rec- ognized by Chubb (2004a) instead was countered by a number of apomorphies in each genus that are shared with other taxa ? e.g. Podiceps with Gavia, Phoenicop- terus with (other) Ciconiiformes. The present data set (Livezey & Zusi, 2006) supports the rejection of this novel proposal involving the grebes and flamingos (Table 3; Fig. 14), and suggests that the taxonomic pro- posal for the couplet by Sangster (2005) is premature. CRANES, RAILS, SHOREBIRDS AND ALLIES The remaining long-legged, statuesque denizens of early successional, often wet habitats, together with the true shorebirds, compose the sister-group of remaining neornithine taxa (Fig. 15). These families, HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 29 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 1?95 Table 3 . Alternative topological inferences and minimal differences in tree length (additional steps) relative to placements in MPTs (Figs 11?17), conditional on other topological alterations being prohibited (optimizations of characters thereon permitted). Higher-order taxa correspond to classification proposed in Appendix 1 Taxon Alternative hypothesis* ? length References Palaeognathae ? Galloanseromorphae 54 Sibley & Ahlquist (1990) Ratitae (global)? ? topology 31 Cracraft (1974a) Ratitae (local)? ? topology 63 Cracraft (1974a) ? topology? 17 Cooper et al . (2001) ? topology? 13 Haddrath & Baker (2001) Galloanserimorphae Polyphyly? [19] Bourdon et al . (2005) Galliformes Polyphyly 90 Dyke et al . (2003) Megapodiidae ? Cracidae 10 Dyke et al . (2003) Meleagrididae ? Phasianidae 20 Dyke et al . (2003) Anseriformes ? familial topology 54 Olson & Feduccia (1980a); Livezey (1997a) Anhimae ? ? ? Galliformes 41 Olson & Feduccia (1980a); Livezey (1997a) Gaviomorphae ? Charadriomorphae 72 Storer (1956); Olson (1985) Podicipediformes ? Phoenicopteridae 146 Mayr & Clarke (2003); Mayr (2004a) ? Charadriomorphae 54 Storer (1956) ? Eurypygidae 182 Zusi & Storer (1969) ? Ralliformes 159 Olson (1985); Houde (1994) Pelecaniformes ? topology 344 Kennedy & Spencer (2004: fig. 1B) Sulae ? topology 125 Kennedy et al . (2005: fig. 8) Balaenicepitidae ? ? Pelecaniformes 30 Cracraft (1985); Mayr (2003a) Scopidae ? ? ? Pelecaniformes 23 Mayr (2003a) Threskiornithidae ? ? ? Charadriiformes 174 Olson (1978) Ardeidae ? (Turnices ? Eurypygae) 75 Olson (1978) Phoenicopteridae ? Anseriformes 107 Feduccia (1976, 1977b); Hagey et al . (1990) ? Cladorhynchini 154 Olson & Feduccia (1980b) Gruiformes (traditional) Monophyly? 11 Livezey (1998b) Charadriiformes ? topology 60 Strauch (1978) fide Chu (1995: fig. 1) ? topology 106 Sibley & Ahlquist (1990) fide Paton et al . (2003) ? topology 82 Chu (1995: fig. 8), excluding Ibidorhyncha Mesitornithidae ? Cuculiformes 107 Mayr & Ericson (2004) Strigiformes ? Caprimulgiformes 43 Hoff (1966) Cathartidae ? ? ? Ciconiiformes 112 Ligon (1967); Rea (1983); Avise et al . (1994a) Opisthocomidae ? ? ? Galliformes 120 Hudson et al . (1959); Hudson & Lanzillotti (1964) ? Cuculiformes** 22 Avise et al . (1994b); Hughes & Baker (1999) Caprimulgiformes Polyphyly 31 Mayr (2002a, b) ? Cypselomorphae 42 Mayr (2002a, 2003c, 2004d, 2005f, g) Aegothelidae ? Apodiformes 31 Mayr (2002a, 2003c, 2004d, 2005f, g) Steatornithidae ? Trogoniformes 102 Mayr (2003b) Hemiprocnidae ? Apodidae, monophyly 5 Sibley & Ahlquist (1990: fig. 361) Apodidae ? Passeri (Hirundinidae) 193 Shufeldt (1889b); Van Tuinen (2002) Galbulae ? ? ? Coraciiformes 20 Olson (1983a) Coraciiformes ? topology, ? Trogoniformes 199 Lowe (1946); Maurer & Raikow (1981) Coracii ? topology 64 Cracraft (1971b) Menura ? ? ? Passeri 11 Irestedt et al . (2001); Barker et al . (2002) *Set-symbolism coopted for concise statement of phylogenetic hypotheses, as follows: ? , sister-group (disjoint) union; ? , included as subclade; ? , included as a member taxon; ? , or; ? , change in; ? , not (negation of predicate argument). ?Local optima for Aepyornithiformes and Dinornithiformes (as bi-ordinal sister-group to ratites exclusive of Apterygi- formes) and global optima (former as sister-group to Struthionidae and Rheidae, latter as sister-group to ratites exclusive of Apterygiformes). ?Comparisons excluded effects due to differences in outgroup taxa, as well as tentatively placed Aepyornithiformes. ?Doubtful comparability given differences in taxonomic samples between studies. ?Corresponds to that proposed by Livezey (1998b), exclusive of Pedionomidae and fossil gruiforms ( Cracraft 1969, 1971a, 1973a). **Alternative hypothesis compared sister-grouping with Cuculiformes exclusive of Musophagidae. 30 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 typically included within the traditional Charadrii- formes and Gruiformes, have a long, perhaps unequalled history of debate in the ornithological lit- erature (reviewed by Sibley & Ahlquist, 1972, 1990; Livezey, 1998b). Primary points of controversy concern the monophyly of the Gruiformes, and relationships between the taxa traditionally referred to the Grui- formes and the Charadriiformes; the latter order is known for especially great diversity in structure of the skull (Kozlova, 1961). Gruiformes and allies: In an analysis of phylogeny and flightlessness of the Rallidae (Livezey, 1998b, 2003b), the traditionally delimited Gruiformes appeared to be monophyletic when analysed with only limited outgroups. However, in the more extensive sampling of higher-order groups of the present analy- sis (Fig. 15), this assemblage was resolved to be paraphyletic to the Charadriiformes. Most families included among the Gruiformes have been the subject of comparatively intense debate with respect to taxo- nomic position, e.g. Sibley, Ahlquist & DeBenedictus (1993) prepared an addendum for the Rallidae and allied families, and Houde (1994) revealed the difficul- ties of resolving the phylogenetic position of the Heliornithidae within the order. Nonetheless, the order contributed to early perceptions of southern- hemispheric origins of many non-passeriform birds (Cracraft, 1982b). In the present work, most families formerly included among the Gruiformes were inferred to be monophyletic (Fig. 15), forming a single clade within Figure 14. Detailed segment of strict consensus tree of all MPTs recovered in present study. Part C. Neornithes: nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type). HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 31 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 which a primary bifurcation established the first of two subclades comprising the Otididae (Pitra et al., 2002) and Cariamidae (Livezey, 1998b). The second of the primary gruiform clades, and sister-group of the foregoing clade, comprised the sister-groups of (i) Eurypygae (i.e. Eurypygidae, Rhynochetidae and Aptornithidae as sequential sister-groups) and (ii) the nominate suborder Grues (i.e. Psophiidae, Aramidae and Gruidae as sequential sister-groups). New infor- mation on the Eocene fossil Eogrus (Cracraft, 1969; Clarke et al., 2005a) is consistent with monophyly of the Gruidae inferred by other means (Krawjewski & King, 1996). With the exception of an alternative posi- tion hypothesized for the subfossil Aptornithidae (Livezey, 1994; Houde et al., 1997), arrangements of these ordinally defining families have engendered Figure 15. Detailed segment of strict consensus tree of all MPTs recovered in present study. Part D. Neornithes: Gruiformes and Charadriiformes. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type). 32 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 only limited dissent (Mitchell, 1915; Livezey, 1994, 1998b). Several families formerly included within the Grui- formes by Livezey (1998b), as detailed above, were inferred herein to be members of the sister-group of the Gruiformes, and specifically were resolved as two sequential sister-groups of the Charadriiformes (Fig. 15). Several of these have attracted an inordinate interest pertaining to phylogenetic position, diversity of form, intraordinal membership (e.g. Turnicidae) and manifestation of morphological intermediacy of others ? e.g. Pedionomidae and Otididae (Gadow, 1891a; Bock & McEvey, 1969; Olson & Steadman, 1981). The present analysis provisionally placed the Turnicidae and Mesitornithidae as sister-taxa and the first of the two sequential sister-taxa (taxa paraphyl- etic) to the Charadriiformes (Fig. 15). Rotthowe & Starck (1998) agreed with both the present analysis and that by Livezey (1998b) regarding an affinity between the Turnicidae and Gruiformes, but Mayr & Ericson (2004) proposed a close relationship between the Mesitornithidae and Cuculiformes. The remaining sequential sister-group (lineage in this grade) com- prised the Rallidae and its sister-group Heliornithidae (Fig. 15), a close relationship inferred both by Houde (1994) and Livezey (1998b), among others. Charadriiformes: The preceeding clades subtended a clade herein interpreted as comprising the Charadri- iformes. The true shorebirds, as resolved here (Fig. 15), comprise families of comparatively obvious ordinal affinity and great apomorphy, and generally accepted as monophyletic (Strauch, 1978; Bj?rklund, 1994; Chu, 1994, 1995; Moum et al., 1994; Moum, Arnason & Arnason, 2002; Friesen, Baker & Piatt, 1996; Thomas, Wills & Sz?kely, 2004a; Bridge, Jones & Baker, 2005). Relationships among several major groups of charadriiform birds have been inferred (e.g. Thomas, Wills & Sz?kely, 2004b); however, the system- atics of the group remains markedly controversial (Strauch, 1985; Christian, Christidis & Schodde, 1992; Paton et al., 2002; Ericson et al., 2003a; Van Tuinen, Waterhouse & Dyke, 2004; Paton & Baker, 2006; Pereira & Baker, 2006b). The present analysis established the monophyly of the Charadriiformes, of which the Pedionomidae con- stituted the sister-group to other members (Fig. 15). The latter finding represents a slight departure from the marginal inclusion of Pedionomus among Grui- formes and affinities of the genus with the charadrii- form Jacanidae (Whittingham, Sheldon & Emlen, 2000) and Rostratulidae inferred by Livezey (1998b), and is consistent with the inferences by Olson and Steadman (1981) and Ericson (1997). Within the Charadriiformes, Pedionomus is the sister-group to: (i) the bifamilial couplet comprising the Jacanidae and Rostratulidae, (ii) the monotypic Dromadidae and (iii) a clade comprising Thinocoridae and the sister- families Scolopacidae (e.g. Heteroscelus) and Phalaro- podidae (Fig. 15); and (iv) a terminal clade comprising two major subclades and multiple, only partially dichotomously resolved families (Fig. 15). These broad groupings bear notable similarities with the suborders defined by Lowe (1931a). The remaining clade of the Charadriiformes com- prises two major subclades, both of which are weak- ened by three marginally robust, defining nodes (Fig. 15). The first comprises in turn three lineages or subclades: (i) the Charadriidae; (ii) the sister-groups Cursorinae and Glareolinae (collectively constituting the Galreolidae); and (iii) a clade comprising the Burhinidae and its sister-group comprising two bifur- cate clades, the Haematopodidae (united exclusively with monotypic Ibidorhynchus), and the Recurvi- rostridae (united exclusively with monotypic Cla- dorhynchus). The other major, pectinate subclade within the Charadiformes comprises, respectively, the sequential sister-groups Chionididae, Alcidae, Sterco- rariidae, Rynchopidae and Laridae (Fig. 15). BIRDS OF PREY ? DIURNAL AND NOCTURNAL Raptors or birds of prey ? comprising the diurnal Fal- coniformes and (principally) nocturnal Strigiformes ? share a primary reliance on carnivory, by scavenging or capture of prey and associated functional common- alities. The sister-relationship of these raptorial orders inferred herein (Figs 10, 16) and by Mayr et al. (2003) has been the subject of suspicion based on phe- netic tallies of differences (Gadow, 1893; Beddard, 1898) and speculations concerning convergences and raptorial specializations (Sibley & Ahlquist, 1972; Cracraft, 1981). However, these orders differ in many respects and manifest substantial diversity within orders, conditions as suggestive of comparatively ancient divergence of sister-groups sharing general raptorial lifestyles and independent (order- and family-specific) morphological refinements. This clade is first in a sequence of four ? the birds of prey, Opisthocomus, Cuculiformes, Psittaciformes and Columbiformes ? that are sequential sister-groups of remaining Neornithes. Although all of these orders were robust with respect to individual monophyly, the four highest-order branches supporting these orders were not (Figs 10, 15?17), rendering the branching sequence provisional. In addition to suspicions of convergence, several concerns may be seen as opposing the phylogeny inferred herein: (i) an alternative interordinal hypoth- esis that presumes the Strigiformes to be most closely related to the non-raptorial but similarly nocturnal Caprimulgiformes; (ii) an hypothesis that holds the HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 33 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 New World vultures (Cathartidae) to be more closely related to the Ciconiidae than to typical birds of prey; and (iii) several counterproposals concerning certain families and genera of Falconiformes, notably posi- tions of the terrestrially specialized secretary-bird (Sagittarius serpentarius), the piscivorous ospreys (Pandion haliaetus), and the distinctive Falconidae relative to other diurnal raptors. Falconiformes: In the present analysis, however, Cathartidae was resolved as the sister-group of other Falconiformes ? an inference considered ?probable? by Figure 16. Detailed segment of strict consensus tree of all MPTs recovered in present study. Part E. Neornithes: Falconiformes, Strigiformes, Cuculiformes and Psittaciformes. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type). 34 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Sibley & Ahlquist (1972) ? and the Sagittariidae was sister-group of the order exclusive of the Cathartidae. The Falconiformes, exclusive of the foregoing two fam- ilies, comprised a pair of sister-clades: (i) the Accipi- tridae, including Old World vultures (e.g. Gyps), and (ii) a clade comprising the Pandionidae and its sister- group the Falconidae, the latter including the cara- caras (Fig. 16). Jollie (1976, 1977a, b, c) comparatively surveyed morphological characters of the Falconiformes in a monograph largely limited to anatomical phenetics and influenced by suspicions of functional conver- Figure 17. Detailed segment of strict consensus tree of all MPTs recovered in present study. Part F. Neornithes: Colum- biformes, Caprimulgiformes, Apodiformes, Coliiformes, Trogoniformes and Coraciiformes. Nodes are labelled above by per- centages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type). HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 35 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 gence. Exclusive of primarily syringeal evidence (Grif- fiths, 1994), the only phylogenetic study of diurnal raptors based on morphological characters remains that by Holdaway (1994). Unfortunately, most studies treat most families within the Falconiformes (as con- strued herein) in only limited capacitiy or secondary focus, e.g. as outgroups for the Falconidae (Griffiths, 1994, 1999; Haring et al., 2001; Griffiths et al., 2004), or in treatments of other phylogenetic issues within the Accipitridae (Seibold & Helbig, 1996; Helbig et al., 2005; Lerner & Mindell, 2005). Cytotaxonomy appears to possess signal, especially in the comparatively intensively studied Falconiformes, but even phenetic groupings of cytotaxonomy have defied interpretation (Ansari & Kaul, 1986). The recent sequence-based phylogeny proposed for the diurnal birds of prey (Lerner & Mindell, 2005) emphasized species-level relationships within the Accipitridae, and Fain & Houde (2004) failed to resolve relationships among the diurnal raptors. Lerner & Mindell (2005) differed from the present analysis in the placement of Pandion as more closely related to the Accipitridae than to the Falconidae or Phalcobaeninae. A sister-group relation- ship between Cathartidae and other Falconiformes, as inferred herein (Fig. 16), was recovered by Mayr & Clarke (2003), although the latter differed regarding the Strigiformes, Accipitridae and Falconidae. Ligon (1967) tallied characters suggestive of a phe- netic ?affinity? between the Cathartidae and Ciconii- formes. Evidently derived from studies by Gadow (1893), Beddard (1898) and Jollie (1953, 1976, 1977a, b, c), works that included Pelecaniformes and Procel- lariiformes as alternative candidates, the work by Ligon (1967) was a comparison of favoured features solely between the Cathartidae and selected represen- tatives of Ardeidae, Ciconiidae and Accipitridae. Ligon (1967) did not consider polarities or include a formal analysis based on a broad array of characters, and most of the phenetic differences are not convincingly distinct; many features were cast in terms of anti- quated typology (Cracraft et al., 2003; Zusi & Livezey, 2006), such as the ?palatal types? of Huxley (1867). Nevertheless, this hypothesis found a receptive audi- ence (Cracraft, 1972a; Cracraft & Rich, 1972; K?nig, 1982; Rea, 1983; Emslie, 1988; Seibold & Helbig, 1995; Slikas, 1997; Lerner & Mindell, 2005), and it arguably is more popular than it is empirically robust. Seibold & Helbig (1995) concluded that limited mtDNA sequence data supported a close relationship between the Cathartidae and storks. Subsequent analyses of the data used by Seibold & Helbig (1995) ? revised and augmented by Hackett et al. (1995) and Avise & Nelson (1995) ? largely were not comparable because of methodological differences. Avise, Nelson & Sibley (1994a) and Wink (1995) compiled weak molec- ular evidence to test the hypothesis, the results of which were equivocally consistent with the hypothesis of Ligon (1967). Analyses including these taxa during the following decade (Figs 1?10) failed to support the exclusion of the Cathartidae from Falconiformes sensu stricto, or associate the family with the Ciconiiformes. Strigiformes: The other substantive debate regarding birds of prey concerns the relative support for a sister- group relationship between: (i) diurnal and nocturnal raptors, or (ii) the similarly noctural Strigiformes and Caprimulgiformes (Hoff, 1966; Sibley & Ahlquist, 1972; Randi et al., 1991; Wink & Heidrich, 1999). The current analysis strongly confirmed a sister-group relationship between the Strigiformes and the Falco- niformes (Fig. 16), a union also supported by Cracraft (1988), Mayr & Clarke (2003) and Mayr et al. (2003). Recent molecular studies have placed the Strigiformes tenuously with a striking diversity of taxa, including the Psittacidae, Picidae and Rhamphastidae (Espi- nosa de los Monteros, 2000; Van Tuinen et al., 2000). Fossils that exhibit generalized raptorial characters or those of both Strigiformes and Falconiformes also have been described (Mayr, 2000a, b, 2005b; Mayr & Daniels, 2001). With respect to familial relationships within the Strigiformes, the present analysis reaffirmed a basal bifurcation between barn-owls (Tytonidae) and typical owls (Strigidae), with the former including Phodilus (Fig. 16). Phodilus (bay owl) has been considered of variable intermediacy to both strigiform families (Table 1), but most recent molecular data bearing on Phodilus (G. Barrowclough, pers. comm.) are consis- tent with the present findings (Fig. 16). HOATZIN, CUCKOOS, PIGEONS, PARROTS AND ALLIES This group of medium-sized landbirds approximates part of the ?Anomalogonatae? of Garrod (1874) and Beddard (1898), largely synonymous with the earlier branches within the ?higher landbird assemblage? of Olson (1985). Clades informally included in this grade of modern landbirds are characterized by mutually exclusive apomorphies rendering many of the groups among the most readily recognized of birds. Members of this subterminal grade of avian orders have been the subject of numerous studies, but nonetheless a clear consensus regarding their interordinal affinities has failed to emerge (Bleiweiss, Kirsch & Lapointe, 1994; Bleiweiss, Kirsch & Shafi, 1995; Johansson et al., 2001). As noted previously, these taxa ? Opis- thocomus, Cuculiformes, Psittaciformes and Columbi- formes ? traditionally were accorded ordinal rank, and were resolved here as a grade in which defining nodes achieved only marginal support. Accordingly, this series of clades conservatively can be considered to compose a tri-ordinal grade or corresponding polytomy 36 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 that bridges the Cuculiformes with the Caprimulgi- formes and Apodiformes. The latter ambiguity prima- rily relates to the failure to resolve the order of branching of the Psittaciformes relative to the Colum- biformes (Fig. 17). Nevertheless, the orders branching from this grade were each strongly supported. The Opisthocomidae ? solely comprising the unusual hoatzin (Opisthocomus hoazin) ? has been allied with Tinamidae, Galliformes, Cuculiformes, Columbidae, Pteroclidae, Rallidae, Otididae and Coliidae, among other higher-order groups (Table 1). Recent attempts to resolve the uncertainty of position of this monotypic lineage by molecular means have proven largely unsuccessful, principally by mutual contradiction or ambiquity of findings (Avise, Nelson & Sibley, 1994b; Hedges et al., 1995; Marceliano, 1996; Sorenson et al., 2003), and also because of con- taminated sequence data (Avise & Nelson, 1995; Hackett et al., 1995). A growing number of works are at least consistent with an affinity between Opisthoc- omus and the Cuculidae (Sibley & Ahlquist, 1972, 1990; Hughes & Baker, 1999), despite disputes regarding method and differences in taxonomic sam- pling. In the present analysis, Opisthocomus was placed as the sister-group of the Cuculiformes, the latter weakly including the Musophagidae (Veron, 1999) as sister-group to the Cuculidae (Table 2; Fig. 16). Uncertainties of phylogenetic position and super- ficial plesiomorphy of Opisthocomus led some (e.g. Feduccia, 1980, 1996; Olson, 1985) to suggest that the taxon derives from the ?roots? of Neornithes. This pro- posal is consistent with a perception that the species descended from uniquely primitive ancestry, a view exemplified by its description as a ?reptilian? bird by Parker (1891), its use as the only neornithine explicitly figured with Archaeopteryx or non-avian Theropoda (Brodkorb, 1971a; Feduccia, Lingham-Soliar & Hinchliffe, 2005: fig. 26), and the much-publicised retention and use of weakly functional ungues alulares in the genus prior to fledging (Shufeldt, 1918). In actu- ality, such ?wing claws? are retained by members of many modern avian orders in variably vestigial states (Livezey & Zusi, 2006). Accordingly, morphological and molecular evidence for the purported plesiomorphy of Opisthocomus is ambiguous at best: most studies place the genus as closely related to the Cuculiformes (Hughes & Baker, 1999; present study), whereas a few analyses suggest a more distant relationship (Mayr et al., 2003; Mayr, 2005b). Various other studies, most with only marginal tax- onomic sampling, have inferred a sister-group rela- tionship between Opisthocomus and the Cariamidae (Mayr & Clarke, 2003; Mayr, 2005c) or inclusion within an eclectic assemblage defying plausible expla- nation in light of other findings (Fain & Houde, 2004). The unique alimentary features of Opisthocomus, notably refinements for herbivorous or ruminant digestion (Dominguez-Bello, Ruiz & Michelangeli, 1993; Kornegay, Schilling & Wilson, 1994), are of little phylogenetic significance as they are autapomorphic among Neornithes. However, the lysozymes associated with fermentation by Kornegay et al. (1994, 2003) sug- gest Opisthocomus to be more similar to Columba than Gallus. Phylogenetic studies of the Cuculidae per se are sur- prisingly few, but include taxonomically inclusive attempts at morphological and ethological insights (Seibel, 1988; Hughes, 1996, 2000; Posso & Donatelli, 2001) as well as a molecular exploration (Sorenson & Payne, 2003). Berger (1960) compiled characters dis- tinguishing the Cuclidae from the Musophagidae, many of which show homoplasy at wider scales of com- parison. The molecular study by Johnson et al. (2000), the primary focus of which were the Malagasy couas, resulted in a topology within the family broadly sim- ilar to that inferred herein, differences in sampling notwithstanding (Fig. 16). Pigeons and sandgrouse: The Columbidae tradition- ally are recognized as monophyletic, whereas the interordinal position of the Columbiformes remains a primary point of dispute. The incompletely resolved position inferred here (Fig. 17): (i) compares reason- ably well with the semi-speculative tree by Cracraft (1988); (ii) accords acceptably with the poorly resolved reconstructions by Mayr & Clarke (2003), Mayr et al. (2003) and Mayr (2005c); and (iii) is only weakly con- gruent with the placements by Van Tuinen et al. (2000) and Fain & Houde (2004). The fossil record of the Columbidae from the Palaeogene is poor, and described as non-existent by Mayr (2005a). Sampling of the Columbidae was comparatively intense in the present study so as to affirm the monophyly of such a diverse family and to expand the thoroughness of placements of the extinct ?raphids? Raphus and Pezop- haps (Livezey, 1993). The present analysis indicated monophyly of flight- less Raphus cucullatus and Pezophaps solitaria, one of the principal hypotheses proposed for the ?raphids? (Livezey, 1993). Goura and Didunculus, historically speculated to be sister-genera, were placed as para- phyletic to the raphids (Fig. 17). These inferences gen- eral agree with those by Shapiro et al. (2002: fig. 1) and Johnson & Clayton (2000a, b), and revealed generic partitions within the Columbidae in consider- able agreement with the present work. The Ptero- clidae (sand-grouse) have been the topic of study for more than a century (Gadow, 1882; Shufeldt, 1901c; Stegmann, 1957, 1959; Fjelds?, 1976). The pteroclids were placed herein as the sister-group of the Colum- bidae ? a view favoured by the majority over an HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 37 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 hypothesized alliance with the Charadriiformes (Sib- ley & Ahlquist, 1972, 1990). Parrots and allies: The primary mystery of this unique order is its interordinal position, a debate clearly manifested by the myriad groupings inferred for it in phylogenetic works during the last two decades. Monophyly of the Psittaciformes, not amena- ble to testing with the few exemplars included here, has been assumed (Smith, 1975) or affirmed by diverse morphological (Sibley & Ahlquist, 1972, 1990) and molecular means (Ovenden et al., 1987; Christidis et al., 1991; Leeton et al., 1994; Miyaki et al., 1998; Eberhard, Wright & Bermingham, 2001; Eberhard & Bermingham, 2001, 2004; Groombridge et al., 2004; Russello & Amato, 2004; de Kloet & de Kloet, 2005; Ribas et al., 2005; Tavares et al., 2006). Higher-order relationships are less clear, and the order has been allied with: (i) groups comprising sufficient diversities of neognathous taxa as to establish little progress (Sibley & Ahlquist, 1990; Fain & Houde, 2004); (ii) Trogonidae and/or Coliidae (Espinosa de los Monteros, 2000; Mayr, 2000b, 2005d, e; Mayr & Clarke, 2003); (iii) Picidae (Van Tuinen et al., 2000); (iv) Coliidae and some Pici (Mayr et al., 2003); and (v) Strigidae (Harrison et al., 2004). Although the present analysis provides no single, well-supported and precise position for the order, the evidence compiled herein is conso- nant with a (perhaps deep) relationship between the Columbiformes and Psittaciformes. This interordinal union was inferred by Burton (1974) in a study of Didunculus, and also confirmed by Sibley & Ahlquist (1972: 241) and Cracraft (1981). GOATSUCKERS, SWIFTS AND HUMMINGBIRDS, MOUSEBIRDS AND TROGONS Overview: This heterogeneous group of moderate to small landbirds of controversial relationships ? approximately synonymous with the ?Coccygomor- phae? (Huxley, 1867), the Anomalogonatae (Garrod, 1874; Beddard, 1898), or part of the ??higher? landbird assemblage? (Olson, 1985) ? includes some of the most specialized and distinctive of modern birds. Unlike the foregoing groups, most higher-order nodes within this assemblage ? i.e. those structuring relationships among orders ? are robustly resolved (Fig. 17). Essen- tial findings herein were monophyly of the traditional Caprimulgiformes (including Aegothelidae), and monophyly of its sister-group Apodiformes. The Apod- iformes comprised the crested-swifts (Hemiprocnidae) as sister-group to a clade comprising the mutually monophyletic typical swifts (Apodidae) and humming- birds (Trochilidae). Caprimulgiformes: A minority of works failed to recover monophyly of the Caprimulgiformes, either by unresolved polytomy (Johansson et al., 2001), variably constituted paraphyly to Trogonidae or Apodiformes (Mayr & Clarke, 2003; Mayr et al., 2003; Mayr, 2005f; Barrowclough, Groth & Mertz, 2006), or uniquely pro- posed alternative alliances with the Accipitridae and Sulidae (Van Tuinen et al., 2000), Sagittariidae (Min- dell et al., 1997), or Mesitornithidae (Fain & Houde, 2004). The present phylogeny affirms monophyly of the traditional Caprimulgiformes, although recent analyses suggest that the present study may not have been adequate to capture all ?family-level? variation in the order by omission of Batrachostomus and Eurosto- podus (Sibley et al., 1988; Mariaux & Braun, 1996). The moderately distant relationship between the noc- turnal Caprimulgiformes and Strigiformes ? consid- ered closely related by some (Sibley et al., 1988) ? was favoured herein, a finding consistent with the hypoth- esis that at least the ocular refinements for nocturnal- ity in these two orders are not homologous (Fidler, Kuhn & Gwinner, 2004). In this context it is notewor- thy that another aspect of colour vision shows low con- sistency with avian phylogeny (?deen & H?stad, 2003). Support for groups within the Caprimulgi- formes in the present work was marginal at best, and for practical purposes might be considered to be a polytomy of the included families. Palaeontological proposals suggest that fossil members of the Caprimulgiformes (and certain other groups) cur- rently endemic to the southern hemisphere previously extended to the Palearctic (Olson, 1987; Mayr, 1999a, b, 2002a, b, 2005b, f ). Fidler et al. (2004) also presented equivocal evi- dence that the owlet-frogmouths (Aegothelidae) are not members of the Caprimulgiformes, as tradition- ally classified, a proposal augmented by some morpho- logical evidence (Mayr 2002a, b) and DNA sequences (Barrowclough et al., 2006). The latter studies led to marginally supported transfers of the Aegothelidae ? herein inferred to be the sister-family of other Caprimulgiformes ? to an alternative position as sister-group of the Apodiformes, a reasonably eco- nomical concession from global parsimony using the present data set (Table 3). Although the position of the Aegothelidae remains uncertain, mtDNA sequence data are consistent with the monophyly of this family (Dumbacher, Thane & Fleischer, 2003). A complete picture of caprimulgiform phylogeny must await com- prehensive integration of putative fossil members (Olson, 1987; Mayr, 1999a, 2002a, b, 2005b, f). The oilbird (Steatornis caripensis) ? a nocturnal, cav- ernicolous frugivore ? is one of the most challenging of avian genera with respect to phylogenetic position, irrespective of method. Recent analyses have differed regarding even the ordinal placement of this taxon, tra- ditionally assigned to a monotypic family (Garrod, 1873b; Mariaux & Braun, 1996; Livezey & Zusi, 2001; 38 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Mayr, 2003b; Barrowclough et al., 2006). The present work tentatively resolved Steatornis to be a highly apo- morphic member of the Caprimulgiformes (Fig. 17). Apodiformes: This order is monophyletic and, as tra- ditionally construed, comprises the highly derived crested-swifts, swifts, swiftlets and hummingbirds. The interfamilial relationships inferred here (Fig. 17) ? Hemiprocnidae (crested-swifts) as sister-group to a clade comprising the mutually monophyletic Apo- didae (swifts) and Trochilidae (hummingbirds) ? have received growing support from other works (e.g. Chubb, 2004b) in tabling the largely antiquated con- tention that the hummingbirds were closely related to the Passeriformes and related variants of this hypoth- esis (Table 1). Departures from the present hypothe- sis included that of monophyly of the Hemiprocnidae and Apodidae (Chubb, 2004b). The molecular phenet- ics of Sibley & Ahlquist (1990), including where re- analysed (Harshman, 1994b) or augmented (Bleiweiss et al., 1994, 1995), also differed by resolving the Tro- chilidae as phenetic ?sister-group? to all other Apodi- formes, prompting the former to be ordinally distinguished as Trochiliformes. The speciose hum- mingbirds (Trochilidae) achieved phylogenetic diver- sity in concert with the related apodids (Mayr, 2003c, 2004d, 2005g), a radiation second only to passeri- forms in scale (Bleiweiss, Kirsch & Matheus, 1997; Bleiweiss, 1998a, b, c; Garc?a-Moreno et al., 2006), and evolved a diversity of concomitant apomorphies, some of which overcame unique locomotory challenges (e.g. Altshuler, Dudley & Ellington, 2004). Phyloge- netic study of the swifts (Apodidae) by palaeontologi- cal (Mayr, 2001a, 2003c, 2005g) and molecular means (Dumbacher et al., 2003; Chubb, 2004b; Thomassen et al., 2005), resolved a fundamental dichotomy between taxa possessing capacities for echolocation (Thomassen et al., 2003). Coliiformes and Trogoniformes: Modest support was afforded herein to a sister-group relationship between the Trogoniformes and Coliiformes (Fig. 17). Both orders have proven challenging to place among other avian orders (Garrod, 1876; Forbes, 1881), but mono- phyly of these orders has not be questioned (Espinosa de los Monteros, 1998, 2000). The present analysis confirms earlier anatomical (Verheyen, 1956b) and molecular analyses (Espinosa de los Monteros, 1998, 2000), in which this couplet also was inferred in turn to be closely related to Coraciiformes (Berman & Raikow, 1982). Johansson & Ericson (2004) conceded that appropriate outgroups for rooting analyses of these orders was problematic, a problem that led Moyle (2005) to employ a suite of outgroups. Among the more notable expansions of palaeodistributional limits have pertained to the Trogoniformes (Mayr, 1998a, 2001b) and Coliiformes (Mayr, 2000b, 2001a), although diagnostic evidence was poor by general neontological standards. This couplet raises the possibility of artefactual grouping by way of long-branch attraction (Lyons- Weiler & Hoelzer, 1997; Wilson, 1999; Bergsten, 2005). Examination of ranges of terminal branch lengths compiled in the MPTs ? Colius (84?133) and Trogonidae (10?17), with the branch subtending clade having a range of lengths 36?97 ? suggests that the Trogonidae are not obviously vulnerable to an artefac- tual grouping. This judgement is supported further by the inclusion of a number of multistate, supportive characters (W?gele, 1996). CORACIIFORM, PICIFORM, AND PASSERIFORM BIRDS Overview: Long recognized as a speciose, diverse and widespread group, historical disagreements pertain- ing to these orders have turned on familial member- ships (e.g. Trogonidae) and delimitation of orders within the assemblage (Lowe, 1948; Wetmore, 1960; Sibley & Ahlquist, 1972: 241). Predictably, some sub- groups manifested intermediate suites of characters and have proven least tractable (Burton 1984: fig. 32); the latter have been addressed most pointedly, per- haps, in palaeontological diagnoses (Ballmann, 1979; Mayr 1998b, c; Mayr & Daniels, 2001). Also, where data are less numerous, a common alternative to monophyly of the Coraciiformes or Piciformes is resolution of the two as sequential sister-groups (paraphyletic) to the Passeriformes. Although mono- phyly of the tri-ordinal assemblage was substantiated here (Figs 17, 18), the analysis revealed several alter- native arrangements among the three orders, repre- sented by the polytomy in the strict consensus tree of MPTs (Figs 17, 18). Coraciiformes: Monophyly of the families traditionally included within the Coraciiformes has been a point of disagreement for almost a century (Murie, 1872b, c, 1873; Lowe, 1948; Sibley & Ahlquist, 1972, 1990), and persists as a palaeontological challenge (Mayr, 2000d, 2005h, i; Mayr & Mourer-Chauvir?, 2003; Mayr et al., 2003). This state of affairs has been prolonged by poor representation of the order in many recent family- level, multi-ordinal analyses (e.g. Espinosa de los Monteros, 2000; Van Tuinen et al., 2000), with notable exceptions including the analyses by Johansson et al. (2001) and Kirchman et al. (2001). Taxonomically nar- row analyses include morphological works by Cracraft (1971b), Burton (1974) and Maurer & Raikow (1981), and the molecular phenetics of Sibley & Ahlquist (1990) and Bleiweiss et al. (1994). The Coraciiformes were found herein to be a mono- phyletic member of a trichotomy that included the Piciformes and Passeriformes (Figs 10, 11, 17, 18), but the magnitude of support for monophyly of the HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 39 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Coraciiformes was only moderate, and generally was exceeded by that for included nodes. The ordinal work by Maurer & Raikow (1981) proved most relevant in this context, but conclusions of the two analyses dif- fered considerably. Evidently, restriction of the out- groups and characters included in the analysis by Maurer & Raikow (1981) resulted in contradictory findings symptomatic of diminished signal, e.g. inver- sions of taxa within the ingroup and inclusion of Trogonidae within the ingroup. Figure 18. Detailed segment of strict consensus tree of all MPTs recovered in present study. Part G. Neornithes: Piciformes, and Passeriformes. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type). 40 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 The very distinctive hornbills (Bucerotidae), together with a sister-group comprising the Upupidae and Phoeniculidae, were situated as the sister-group of other coraciiforms (Fig. 18). This group was consid- ered a separate order allied to other Coraciiformes by Burton (1984) and Kemp (1995). Manegold (2005), however, inferred the Coraciiformes to be polyphyletic and comprising: (i) the ?Bucerotes? (Upupidae, Phoen- iculidae and Bucerotidae) as sister-group to the mutu- ally monophyletic Piciformes (including Galbulae) and Passeriformes; (ii) the ?Alcediniformes? (all other mem- bers of the traditional order not included elsewhere); and (iii) Leptosomus, excluded from the Coraciiformes and of indeterminate ordinal relationship. The remaining members fell into two sister-groups: one of these comprised the Motmotidae and its sister- group comprising the Todidae and Alcedinidae, the Todidae of uncontested monophyly (Overton & Rhoads, 2004), and the Alcedinidae monophyletic but perhaps comprising two or more distinct subgroups (Fry, 1980; Marks & Willard, 2005). The remaining member of this pair of sister-groups comprised the sequential sister-groups of Meropidae, Coraciidae, Brachypteraciidae and Leptosomatidae (Fig. 17). The Motmotidae were inferred herein to be the sister- group of a clade comprising the Todidae and Alce- dinidae (Moyle, 2006). However, some ?intermediacy? of morphological and molecular characters of the tody- motmot (Hylomanes) and the Todidae suggests possi- ble paraphyly of the Motmotidae (as traditionally con- stituted) or the Todidae (Overton & Rhoads, 2004). The Meropidae (bee-eaters), of established monophyly (Fry, 1984; Burt, 2004), were inferred here to be the sister-group to remaining Coraciiformes (Fig. 17), the latter known in the vernacular as ?rollers?. As detailed above, morphological assessments of the memberships and positions of these families differ significantly (Manegold, 2005). Piciformes: The Galbulidae and Bucconidae were inferred herein to be sister-groups, and together as forming the sister-group of other Piciformes. The remaining Piciformes in this analysis comprised two sister-groups (Fig. 18), each of which comprised two, provisionally monophyletic families: (i) Capitonidae (Moyle, 2004) and Rhamphastidae (Eberhard & Ber- mingham, 2001; Wechstein, 2005); and (ii) Indicatori- dae and Picidae (Prychitko & Moore, 1997; DeFilippis & Moore, 2000; Weibel & Moore, 2002a, b). Support for neither of the latter clades was strong, approximating only 50% bootstrap support (Fig. 18). This arrange- ment is consistent with much of the classification pro- posed by Burton (1984). One point of current debate is the possible paraphyly of the Capitonidae, in which member taxa represent successive sister-groups to the (monophyletic) Ramphastidae (e.g. Prum, 1988; Sibley et al., 1988; Lanyon & Hall, 1994; Barker & Lanyon, 2000). Unfortunately, despite comparative richness of the record, fossil members of these groups have pro- vided few insights into the phylogeny of modern pici- forms (Mayr, 2001c, d, 2004e, 2005h, i). Monophyly of the Piciformes, most often challenged regarding membership of the Galbulae, has been con- troversial ? e.g. Olson (1983a), Raikow & Cracraft (1983), Lanyon & Zink (1987), Johansson & Ericson (2003) ? despite comparatively detailed anatomical study (Burton, 1974) and related phylogenetic analy- ses (Simpson & Cracraft, 1981; Swierczewski & Raikow, 1981; Avise & Aquadro, 1987; Manegold, 2005). Most attempts to reconstruct the phylogenetics of the order have been variably inclusive with respect to included families and limited to molecular evidence (Webb & Moore, 2005; Wechstein, 2005; Benz, Robbins & Peterson, 2006), and resultant findings posed no serious contradictions to the inferences made here. Passeriformes: The Passeriformes are a dominant evo- lutionary component of the global avifauna, and the phylogeny of the order has figured prominently in ter- minological disputes regarding faunal ?radiations? (Barker et al., 2004), ?key innovations? of evolutionary change (Raikow & Bledsoe, 2000; Olson, 2001) and ?evolutionary success? (Raikow, 1988). Current consen- sus by avian systematists holds the Passeriformes to be one of the most recently differentiated and apomor- phic of lineages of modern birds, with a growing body of evidence for Gondwanan genesis (Ericson et al., 2002a). However, analyses limited to the mitochon- drial genome (Moore & deFilippis, 1997), the early mainstay of sequence analyses (Kessler & Avise, 1985; Ast et al., 1997; Braun & Kimball, 2002), resulted in several studies in the placement of Passe- riformes as the sister-group of most or all other Neoaves (Mindell et al., 1997, 1999), a topological shift of exceptional magnitude and enormous evolu- tionary implications. This finding, mirrored by the phenetics depicted by Sibley & Ahlquist (1990) and very recent analyses based principally on mitogenom- ics (Pereira & Baker, 2006b; Slack et al., 2006b), since has been attributed (Cracraft et al., 2003, 2004) in subsequent works to (unavoidable) reliance on most closely related but nevertheless distant outgroups ? e.g. Crocodylia, Testudines ? which probably serve as unreliable sources of information on avian polarities. This circumstance, compounded by weak taxonomic sampling or shortcomings of mitochondrial data for reconstruction of deep nodes (e.g. Mindell et al., 1996; Tsaousis et al., 2005), necessitate caution in corre- sponding inferences. Fortunately, with respect to genomes analysed, principal differences reduce to rotations of three or four variably nested nodes (Johnson, 2001: fig. 3). HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 41 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 As for monophyly and composition of the Passeri- formes (Beecher, 1953; Mayr, 1958; Olson, 1971; Feduccia, 1973, 1977c; Brom, 1990), the present anal- ysis was necessarily limited to selected genera and families of this enormous group, as were the few pre- vious morphologically based phylogenies of the group (Raikow, 1982, 1994a, b). A number of passeriform subgroups, mostly at comparatively low taxonomic levels, appear to have undergone cladogenesis suffi- ciently recently to reflect vicariance related to recent glaciations and current continental patterns (Edwards & Wilson, 1990), but controversy regarding this tempo persists (Klicka & Zink, 1997; Johnson & Cicero, 2004; Zink & Klicka, 2006). The meagre palaeontological evidence available indicates an origin of the Passeri- formes to be no later than the early Eocene (Boles, 1995, 1997; Barker et al., 2004; Mayr & Manegold, 2004). The present analysis substantiated the interordinal position and monophyly of representatives of major subgroups of the Passeriformes (Fig. 18). Within the narrow taxonomic sample analysed herein (cf. Sibley, 1974; Cracraft, 1992a; Helm-Bychowski & Cracraft, 1993; Nunn & Cracraft, 1996; Barker et al., 2002; Irest- edt et al., 2002), Menura was resolved as the sister- group of other members of the order, i.e. a member of the non-passerines (Fig. 18). Menura typically is situ- ated crownward of basal Acanthisitta (but see Gadow, 1893; Ames, 1971) and included among the basal oscine passerines (Sibley & Ahlquist, 1970; Sibley, 1974; but see Ericson et al., 2002a, b, 2003b, 2006). This mini- mally exemplified and questionably resolved subgroup was inferred to be the sister-group of remaining pas- seriforms, first followed by a poorly represented grade of suboscine passerines (Tyrannides) ? Tyrannidae and Pittidae (Prum, 1993). The Tyrannides in turn sub- tends the oscine passerines (Passerides), within which two major subgroups (Ericson et al., 2006) were sparsely represented but arranged in accord with cur- rent consensus (Fig. 18). Barker et al. (2002) inferred the Ptilonorhynchidae (Stonor, 1938; Cracraft, 1992a; Nunn & Cracraft, 1996; Cracraft & Feinstein, 2000; Johansson et al., 2001) to be the sister-group of the remaining passeriform taxa. Among other Passerides, the single exemplar of the Corvida (Aphelocoma) was the sister-group of the three representatives of the Pas- serida ? Bombycilla, Parus and Passer (Ericson et al., 2000; Ericson & Johansson, 2003). With the exception of the position of Menura in the present analysis, the broad subdivisions inferred here agree with the major- ity of other recent works (Edwards, Arctander & Wil- son, 1991; Irestedt et al., 2001; Ericson et al., 2003b; Cracraft et al., 2004; Spicer & Dunipace, 2004) and are consistent with palaeogeographical evidence for an Australasian origin for the oscines (Boles, 1995, 1997; Barker et al., 2004). BRANCH LENGTHS AND EVOLUTIONARY CHANGE Morphological characters employed in cladistic analy- ses tend to be held to unrealistic standards, and to serve as sources of insights (not expected of molecular characters) beyond mere inference of phylogenetic relationships. For example, in some circles there is an expectation that, in addition to resolving phylogenetic relationships of multiple taxa, apomorphies support- ive of nodes should make obvious functional sense (e.g. debates regarding aquatic lineages and possible con- vergences) and permit interpretation resembling lists of (semi)diagnostic characters for nested series of taxa. In some cases, particularly where taxonomic scale is low and a functional focus pertains, such pat- terns and trends are discernible. However, with increasing taxonomic scale, these are in the minority, and like DNA sequence data, such diagnostic trans- parency and functional interpretation is seldom attainable. Many subtle features possessed of phylo- genetic signal may be structural artefacts of function- ally neutral details of anatomy, historical accidents that prove variably reliable through the process of evo- lutionary modification with descent. Nevertheless, quantification of evolutionary change is critical to estimates of rates and correlation of change among characters and related evolutionary topics (e.g. Omland, 1997a, b; Nunn & Stanley, 1998), and exploration of this aspect of reconstruc- tions is intended to pre-empt misplaced expectations or distorted perspectives. The tempo and mode of morphological evolution and cladogenesis have held the interests of systematists for decades (Simpson, 1944; Cracraft, 1984), pre-dating the advent of molecular methods or assumptions made for them (e.g. uniform or ?clock-like? evolutionary rates). Anti- quity of lineages provides opportunity, other parame- ters being equal, for increased expectation of evolutionary changes (probabilistic, not determinis- tic expectation), and where such lineages comprise only modest numbers of members ? i.e. limited evolu- tionary opportunities for departures from uniformity or reversals within a given lineage ? such change also tends to lead to comparatively direct diagnostic- ity of terminal lineages. Intuitive relevance of ori- gins, ages, longevities of lineages and expectations of evolutionary divergence notwithstanding, these top- ics have been underserved by newly acquired empiri- cal evidence. Van Tuinen et al. (2006: table 2) listed 14 avian families construed to show molecular varia- tion significantly lower than that expected on the basis of current taxonomic status. Given present findings, however, this issue appears illusory, with virtually all taxa in question having early origins, including the Anhimidae (Anseriformes), Podicipe- didae and Spheniscidae, three being members of the 42 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Pelecaniformes, and the remaining examples mem- bers of either the Ciconiiformes, the Gruiformes or the Charadriiformes. Unlike molecular evolution, no strict assumptions or dependence on constant or uniform rates of change have been made for morphological characters. In the present analysis, branch lengths varied substantially depending on specific optimizations, and therefore comparisons of lengths, like the internodes in trees, were not restricted to unambiguous changes. Instead, central tendencies of branch lengths of MPTs were quantified by median lengths, and variation among optimizations by standard deviations and ranges of lengths recovered. For Neornithes, numbers of changes optimized as autapomorphies averaged 41 (SD = 33, range 4?186). By contrast, for single lin- eages, maximal lengths of terminal branches were: 186 for Spheniscus, 132 for Phoenicopterus and 131 for Mesitornis. Minimal lengths of terminal branches were: 4 for Francolinus and Alectoris. At higher phy- logenetic scales (interordinal and interfamimlial), branch lengths had the following summary statistics: mean = 36, SD = 33, range 5?133. In general, then, terminal branch lengths were approximately 10% greater than those of the branches subtending them (i.e. deeper internodes). A pattern of short internodes has been inferred previously (Cracraft et al., 2004), but the attribution of cause to realities of evolutionary intervals vs. diminished power of resolution remains contentious. A survey of the minimal branch lengths included in the MPT revealed that branches among higher-order nodes were extraordinarily similar to associated ter- minal branches (latter being those subtending individ- ual taxa) in means and variances of branch lengths. However, comparative numbers of the more critical diagnostic and supportive characters within the Neornithes revealed that character-based definitions of highest-order clades (corresponding to the most ancient of synapomorphies) were disappointingly low, whereas those for superorders and orders (Appendix 2) were comparatively robust and included suites of diagnostic character-states (Table 2). However, the correspondence among ?raw? branch lengths, statistics of nodal support and numbers of ?diagnostic? apomor- phies generally was poor (Table 2), in agreement with the findings of Farris et al. (2001) and Wilkinson (2003). DISCUSSION BROAD COMPARISONS WITH PRIOR STUDIES ?Survival of the fittest will decide which of the many competing theories [of avian phylogeny] will prevail. Only one can sur- vive. Each revisor attempts to shorten the struggle by acting as a selective factor.? (Stresemann, 1959: 269) ?Where the root of the Neoaves goes, however, is highly uncer- tain and seems likely to remain a very difficult problem.? (Stanley & Cracraft, 2002: 39) Perspectives and findings: In the published record of phylogenetics, it has become virtually customary sim- ply to generate phylogenetic hypotheses of varying consonance with little or no consideration of factors underlying divergent inferences (Figs 1?9). This tra- dition has led to a false sense of congruence among studies, especially among molecular systematists. We consider that it is incumbent upon authors to consider the points of disagreement as well as the most plau- sible underlying philosophical and empirical reasons for the differences. A reasonable degree of detail in such deliberations inevitably will include points of contention and opinion, and we hope that these will challenge the current ambience of consensus and invite constructive debate of these important issues. At the same time, however, it is logistically unfeasible that large-scale studies (e.g. the present work) be held to standards of character descriptions and illustra- tions in analytical works that are logistically realistic in more common, small-scale works. For example, in the present study, a conservative estimate of charac- ter-states eligible for illustration would approach 7000. Nonetheless, access to underlying data for all studies should be made practically available by alter- native means, and include formal descriptions of characters as analysed, and essential figures and references to critical descriptive works (e.g. Livezey & Zusi, 2006). Deep tradition and the ?tapestry?: Broad affinities of long standing between avian orders ? traditionally only implied to variable degrees by adjacency in linear classifications (Clark, 1901; Wetmore, 1930, 1960; Mayr & Amadon, 1951) ? that were not supported by the present analysis were: (i) Galliformes as closely allied with Falconiformes; (ii) Gaviiformes, Podicipedi- formes and Sphenisciformes placed as the most basal of ?Carinatae?; and (iii) a truly basal position of Opis- thocomus among Neornithes. Although confidence in the ?tapestry? (e.g. Monroe, 1989) diminished markedly within a few years of publication, the proposals by Sib- ley & Ahlquist (1990) were ?rewoven? by Harshman (1994b), ?dusted off ? by Mooers & Cotgreave (1994), and continue to be cited for justification and design of sequence-based analyses (e.g. Fain & Houde, 2004). Limited reverence for the tome by Sibley and Ahlquist (1990) lingers, most conspicuously in the non- systematic literature (e.g. Del Hoyo, Elliott & Sardgatal, 2001), principally because of its taxonomic scale and molecular basis (e.g. Chubb, 2004b; Fain & Houde, 2004). Given the controversy and contradictory nature of the era, it is appropriate to compare our findings with HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 43 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 the groups delimited by Sibley & Ahlquist (1990), bearing in mind that the present phylogenetic analy- sis is of limited comparability with the phenetics of DNA?DNA hybridization. First, despite the unprece- dented number of taxa analysed, the earlier work was invalidated shortly after its appearance because of problems stemming from phenetic methodology, sparsity of the distance matrix, absence of a root and irreducibility of data-type, some deficiencies having been identified prior to its release (Cracraft, 1987, 1992b; Houde, 1987; Sarich, Schmid & Marks, 1989; Barrowclough, 1992; Lanyon, 1992; Mindell, 1992). Simplification of the reconstruction by Sibley & Ahl- quist (1990: figs 354?356) to ordinal terminal taxa (Fig. 4) reveals the diagram to be continuously pecti- nate throughout most of the neognathous birds, and largely reflects ?chaining? of least dissimilar elements, an artefact common to some agglomerative algo- rithms. Cracraft et al. (2004) considered current knowledge of avian phylogeny to be of comparable irresolution. A most peculiar aspect of the ?tapestry? is the rever- sal of mid-basal and apical higher-taxa ? e.g. Pici- formes and Passeriformes as sister-groups to the ?Ciconiiformes? (sensu Sibley & Ahlquist, 1990) and allies ? a finding countered by the vast majority of other analyses (Cracraft & Mindell, 1989; Johansson et al., 2001; Braun & Kimball, 2002; Edwards et al., 2002; Paton et al., 2002; Mayr & Clarke, 2003; Mayr et al., 2003; Prychitko & Moore, 2003; Dyke & Van Tuinen, 2004; Harrison et al., 2004; Poe & Chubb, 2004). This phenetic artefact undoubtedly contributed to the poor congruence of the present phylogenetic hypothesis with that by Sibley & Ahlquist (1990), in which only four higher-order groups ? their Ratitae, Galloanserae and Procellarioidea, and monophyly of one currently contentious order (Caprimulgiformes) ? showed broad agreement in both works. The present analysis strongly countered the polyphyly inferred by Sibley and Ahlquist (1990) for the Pelecaniformes and Columbiformes, and differed as well regarding para- phyly of the Coraciiformes and Cuculiformes, the alternative positions of Galliformes + Anseriformes, and the provisional placement of the Turniciformes (Fig. 4). Sibley & Ahlquist (1972: 240?241) listed 34 sum- mary inferences entitled ?Probabilities and Possibili- ties?, presented under four levels of perceived likelihood. Of the conclusions listed, agreement (with minor qualifications) with the present analysis was achieved for: all eight (100%) of the ?highly probable? conclusions; seven of ten (70%) deemed ?probable?; four of ten (40%) considered ?possible?; and only two of six statements (33%) classified as ?improbable?, essen- tially logical negations of views included among the ?highly probable?. Contemporary studies: Comparisons among most phy- logenetic hypotheses are compromised by differential taxonomic sampling and nodes afforded only tenuous support. The present phylogenetic hypothesis, depicted to ordinal scale (Figs 10, 11), approximated the tree depicted by Cracraft (1988) most closely of prior works, issues of comparability notwithstanding. The present analysis, almost 20 years subsequent to that by Cracraft (1988), represents a return to the broad outlines of the latter, seminal work. Given the different scales of the two analyses in terms of taxa and characters, however, it is unreasonable to assume similarities to be the result of reliance on ?the same characters?. An increasing proportion of all studies confirm posi- tions and monophyly of Palaeognathae, Galloanseri- morphae and major subclades thereof. However, most molecular studies (e.g. Van Tuinen et al., 2000, 2001; Paton et al., 2002; Van Tuinen, 2002; Chubb, 2004a), as well as analyses based on combined data (Dyke & Van Tuinen, 2004), differed significantly with parts of the present hypothesis, especially those pertaining to the Pelecaniformes, Ciconiiformes, Podicipedidae, Opisthocomiformes, Cathartidae, Caprimulgiformes and Coraciiformes (Figs 12?18). There was consider- able disagreement among recent molecular studies alone (e.g. Espinosa de los Monteros, 2000; Johansson et al., 2001; Poe & Chubb, 2004), regardless of data analysed (Philippe et al., 1996; Graur & Li, 2000), which reveals contrasts only between morphological and molecular inferences to be oversimplifications of modern study (e.g. Braun & Brumfield, 1998; Van Tuinen, 2002). Comparisons with the limited number of other anal- yses (Figs 1?3) were virtually uniformative because palaeontological works have tended to emphasize nar- row taxonomic groups considered likely to accommo- date newly described or controversial taxa, and also to limit characters to those scoreable for the taxon or fos- sil of interest (e.g. Clarke et al., 2005b), with some exceptions (e.g. Mayr & Clarke, 2003). Several provi- sional and ongoing reconstructions by Cracraft et al. (2004) were not considered here. A survey of compa- rable cladistic studies of morphological or molecular bases (cf. Cracraft, 2001; Mayr & Clarke, 2003; Crac- raft et al., 2004; Fain & Houde, 2004; Clarke et al., 2005b) revealed that the present analysis achieved considerable agreement with most of the latter studies concerning the widely supported (com)positions of the Palaeognathae and Galloanserimorphae, and an allied clade dominated by marine and wading birds (Figs 10?18). Adjudication of success: It is to be hoped that diverse approaches will converge empirically toward common analytical standards (Lake, 1997) and a solution for 44 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 which acceptance is widespread and merited. How- ever, there are no standards of accuracy against which phylogenetic analyses of natural lineages can be cali- brated (i.e. known histories), and therefore the assess- ment of progress is elusive. Hypothetico-deductive empiricism may reveal critical characteristics of sci- entific hypotheses, but cannot provide ?proof ? of a hypothesis (Helfenbein & DeSalle, 2005). Given that proof of hypotheses or certain recogni- tion of the single, true phylogeny is unattainable, the strongest support for a specific reconstruction (beyond intrinsic robustness) lies in common elements shared by other analyses ? empirical (not popular) consensus. Such studies are most potent where performed inde- pendently using new data. Likelihood of correctness of molecular and morphological reconstructions cannot be judged a priori, especially across all classes of investigation. Such assessments are conditional on individual cases, and decisions based on consistency with prior analyses, degree of resolution (assuming bifurcations are the primary cladogenetic mode), size and diversity of data on which the hypothesis was based, and analytical properties of included charac- ters. The relevance of statistics internal to single trees ? e.g. robustness of nodes and consistency indices ? to the likelihood of global accuracy is undecided (Benton, 2001). Consequently, an important element of phylogenetic study is comparison of findings with the estimates of other investigators, especially comparisons of those aspects of trees that withstand variations in method or data base. However, against which topology or topologies does one compare specific findings? This quandary especially afflicts those disposed to a dichot- omous view of morphological and molecular estimates of history. Provision of a sample of trees (Figs 1?9) was intended, in part, to emphasize the dilemma that faces investigators wishing to evaluate hypotheses compar- atively. It appears that until some kind of genuine con- sensus is achieved, systematists are compelled to pit their findings against a plethora of other, marginally comparable works. MOLECULAR SYSTEMATICS: COMPETITOR OR COLLABORATOR? At present, molecular systematics is characterized both by the coexistence of general (if not unbridled) optimism (Van Tuinen, 2002) and by profound doubts regarding resolution of substantial segments of neor- nithine phylogeny (Poe & Chubb, 2004). Yet the cur- rent dominance of avian systematics by molecular methods is sufficiently profound as to lead some to consider palaeontology to be the sole justification for a continued role for morphology in systematics or to question its value altogether (e.g. Stevens, 2000; Scot- land, Olmstead & Bennett, 2003; Jenner, 2004a, b). Nevertheless, historical signal from genes and their morphological products offer a potentially fruitful syn- ergy (Jenner 2004a: 340), one that exceeds the use of morphology for placements of fossils. An unfortunate pattern has emerged in molecular circles, however, in which perennial problems of avian systematics (Table 1) are attributed to the relative impotence or unreliability of morphological clues to phylogeny (e.g. Monroe, 1989; Sibley & Ahlquist, 1990; Givnish & Sytsma, 1997a, b; Sorenson et al., 1999; Paton et al., 2003; Paton & Baker, 2006), or as justifi- cation for merely mapping morphological characters a posteriori onto molecular trees (e.g. Gittleman et al., 1996; Slikas, 1997; McCracken et al., 1999; Van Tuinen, 2002; Huelsenbeck et al., 2003). Therefore, it would be negligent to forego this opportunity to counter this perception explicitly (e.g. Shafer, Clark & Kraus, 1991; Hillis & Wiens, 2000; Marques & Gnas- pini, 2001). We do not intend an assault on molecular methodology, but seek to refute persistent prejudices that afflict morphological phylogenetics (cf. Smith, 1998; Baker & Gatesy, 2002), to underline the distinct- ness between ease of application and reliability in phylogenetic methods, and to encourage objectivity in assessment of findings. Perhaps the deficiency attributed most widely to morphological phylogenetics stems from suspicions of morphological convergence, concerns seldom empiri- cally substantiated and to which molecular methods are widely assumed to be immune (Lockhart et al., 1994; Goldring & Dean, 1998; Lee, 1997, 1999; Sorenson et al., 1999; Yang & Bielawski, 2000). To date, assumptions of morphological convergence prin- cipally are made where convenient and are seldom reversed, with few exceptions (e.g. McCracken et al., 1999; McCracken & Sorenson, 2005). However, verifi- cation of convergence in molecular data (Holmquist, Pearl & Jukes, 1983; Kornegay et al., 1994; Philippe et al., 1996) is increasingly frequent. For morphology, we hope that intuitive claims of convergence will be supplanted by phylogenetically framed analyses of refined morphological and functional data (Raikow, 1985b), especially those pertinent to the: pectoral limb (Middleton & Gatesy, 2000; Burness, Chardine & Darveau, 2005); pelvic limb (Gatesy, 1991; Gatesy & Biewiener, 1991; McKitrick, 1993; Patak & Baldwin, 1998; Carrano & Biewener, 1999; Abourachid, 2000, 2001; Abourachid & Renous, 2000; Hutchinson, 2001a, b, 2002; Zeffer & Norberg, 2003; Zeffer et al., 2003; Fujita, 2004); skull and associated musculature (M?ller, 1961a, b, 1963; Weber, 1990, 1993; Zusi & Livezey, 2000; Bout, 1997; Meekangvan et al., 2006); and general body form (Nudds & Rayner, 2006; Bybee, Lee & Lamm, 2006). HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 45 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Studies based both on molecular and morphological phylogenetics (Figs 1?9) manifest substantial dis- agreement both within and between schools (Patterson et al., 1993), and remain comparable in resolution and support, with disputes often conjectural in nature. Both classes of data present substantial challenges of homology (further below), and those that face molec- ular systematists (Wheeler et al., 1995; Philippe et al., 1996; Phillips et al., 2000; Jenner, 2004a, b; Wiens, 2004) are remarkably similar to those afflicting mor- phological phylogeneticists. Problems of homology in molecular applications, principally related to ?gaps?, indels, and their implications for serial homology and sequence alignment (Redelings & Suchard, 2005), include: bias in substitution and codons (Collins, Wim- berger & Naylor, 1994; Kreitman & Antezana, 2000); concerted evolution (Drouin & Moniz de S?, 1995; Eberhard et al., 2001); pseudogenes (Nielsen & Arctander, 2001); silent substitutions and undetected heterogeneity in rates of substitution (Wakeley, 1994; Simon et al., 1996); selectively constrained evolution- ary rates of repetitive DNA families (Chen et al., 1991); homoplasy indirectly related to the four-state sam- pling universe of nucleotides (W?gele, 1995, 1996); and independence of molecular ?characters? (Zardoya et al., 1998; Graur & Li, 2000; Felsenstein, 2004). Similarly, subjectivities of sampling and analysis beset both morphologists and molecular systematists, including: sampling of genes (Zardoya & Meyer, 1996; Moore & deFilippis, 1997; Pollock et al., 2002) and taxa (Bergsten, 2005); comparative weighting (Garc?a- Moreno, 2004); branch support (Felsenstein & Kish- ino, 1993; Suzuki, Glazko & Nei, 2002; Alfaro, Zoller & Lutzoni, 2003); and model selection (Mort et al., 2000; Buckley, Simon & Chambers, 2001; Huelsenbeck et al., 2002; Simmons et al., 2004; Lee & Hugall, 2005; Pickett & Randle, 2005; Pickett et al., 2005; Steel & Pickett, 2006). In addition, the critical distinction between ?gene trees? and ?species trees?, which can dif- fer significantly (Page & Charleston, 1997; Berglund- Sonnhammer et al., 2006), may be overlooked or ignored (Pamilo & Nei, 1988; Doyle, 1992, 1996; Moore, 1995; Maddison, 1997; Page & Charleston, 1997; Thornton, 2002; Geeta, 2003). Despite these considerable challenges, molecular systematics clearly holds great potential for resolution of many problems of avian systematics, particularly in the Passeriformes. An informal survey of the passeri- form literature since 1990 revealed studies of diverse taxonomic scales: 11 subordinal, five superfamilial, 34 (sub)familial, 55 generic and 24 (super)specific. This considerable success notwithstanding, largely unex- plored is the potential of enterprises jointly including molecular characters of sequence and higher-order genomic structure (Kadi et al., 1993; Delport, Fergu- son & Bloomer, 2002; Prychitko & Moore, 2003; Slack et al., 2003; de Kloet & de Kloet, 2003, 2005; Edwards, Jennings & Shedlock, 2005), the latter ignored at con- siderable peril (Winnepennincks & Backeljau, 1996). Together with morphological data of fossil and modern taxa, such molecular diversity appears to be essential for progress at many scales of avian phylogeny (Gray- beal, 1994; Edwards et al., 2002; Harrison et al., 2004; Simon et al., 2004). Appeal of the novel and unexpected: Apparent depar- tures from taxonomic groups supported throughout much of the cladistic or molecular eras have been fre- quent during recent years (Cracraft et al., 2003, 2004). Fain & Houde (2004: 2570) proposed the entertain- ment of a number of counter-intuitive and weakly sup- ported groupings in their analysis, in the spirit of freeing systematists from being ?. . . guided by precon- ceptions of relationships.? The latter appeal for objec- tivity is unquestionably laudable, but the fact that the proposed groups were merely novel does not constitute affirmation of any kind. Similarly, Pons, Hassanin & Crochet (2005: 686) stated that their study: ?. . . identifies for the first time some sister relation- ships that had never been suggested before.? [emphasis added]. Although many traditionally recognized higher-order groups deserve formal analysis, novelty of resultant proposals is irrelevant to these endeav- ours. Realization of this potential primarily turns on two issues of modern systematics ? rigorous and nomenclaturally transparent analyses that bridge subdisciplines (beyond the recent penchant to use fos- sils in molecular phylogenies for estimates of evolu- tionary rates), and empirically justified views and integration of morphological evidence in an era of increasing reliance on molecular inference. MORPHOLOGICAL HOMOLOGY ? ONTOGENY, FUNCTION AND PHYLOGENY Insights from avian phylogeny: Hope for success lies in a pluralistic approach to evidence (Cracraft et al., 2004). This goal, in turn, is conditional on the surren- der of prejudice and a common concept of homology. Ornithological systematics is replete with assump- tions, assertions and inferences concerning homology and its role in the recognition of characters and evo- lutionary patterns (Freudenstein, 2005). In practice, variously defined ?sameness? is the basis for pre- analytical (a priori) assessments of homology in phy- logenetics (Wake, 1999), but resultant phylogenies provide the historical framework within which homol- ogy is confirmed a posteriori (Haszprunar, 1998). How- ever, non-historical criteria have been attached to the concept of homology virtually since its theoretical origins, of which ontogeny and function were perhaps the most common. Accordingly, alternative percep- 46 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 tions have influenced avian phylogenetics virtually throughout its history, particularly regarding homol- ogy and paedomorphic characters, homoplasy and convergence, the concept of Grundplans (e.g. Weber, 1990), and implications of ontogeny and genetics for homology of characters. Phylogenetics and homology: Homology is synapomor- phy at some phylogenetic level (Nelson, 1994), and is defined a priori as ?similarity due to common descent? (West-Eberhard, 2003: 485). Hall (2003) equated homology with identity (despite change) made evident by phylogeny: homology, reversals, rudimentia, vesti- gia, atavisms and parallelisms. Considerations of parallelism and convergence for Aves involve aspects of cranial structures (Starck, 1969) among outgroups (Carroll, 1988, 1997; Unwin, 1993; Brochu, 2001). Examples of atavism are few, but include the recur- rence of a plesiomorphic pelvic muscle among Paradiesidae (Raikow, Borecky & Berman, 1980). Strong examples of morphological parallelism in birds involve the evolutionary loss of flight by flightless Ral- lidae (Livezey, 2003b). Similarity and homology: Homology is conditional on essential, potentially mutable ?sameness? of a charac- ter manifesting continuity of descent within a phylo- genetic hypothesis, whereas common function and ontogeny are not conditions thereof (Hall, 1994, 2003; Wake, 1999). M?ller & Newman (1999) advocated sec- ondary qualities of generation, integration and auton- omy of a structure for the status of homology to be conferred, nuances herein considered components of the essential ?sameness?, if considered at all. Variants of characters recognized in a phylogenetic context (putative homologues) and manifesting modification with descent ? affected by any of a number of mecha- nisms of evolutionary change (selection, drift, muta- tion, ontogenetic deviation) ? are treated as ?states? of a given character here. Ontogeny and homology: The ontogenetic mechanisms that produce homologous states of a character are of considerable evolutionary interest and may prove crit- ical in particular cases of diagnosis (Wagner, 1989), but do not qualify as criteria of homology of terminal features per se (Cracraft, 1967b; Hall, 2003). Genetics of ontogeny, however, can provide unique insights into the bases of likely homologues, e.g. odontogenesis and the edentuly of modern birds (Chen et al., 2000; Mitsiadis, Caton & Cobourne, 2006). A synthetic view of homology holds that respective developmental stages of members of lineages, inter- preted hierarchically within a phylogenetic frame- work, are each potential homologues capable of partitioned evolutionary patterns (Abouheif, 1997). Thus, homologues are defined within each develop- mental stage of each character (Hall, 2003), e.g., genes, developmental processes and stages thereof. However, judgements of homology based on ontoge- netic processes are mistaken extensions of identity of descent across quasi-autonomous developmental mod- ules (Rieppel, 1992, 1994; Wagner, 1994; Santini & Stellwag, 2002; Arthur, 2004). Traditional assertions that homologues must share genetic foundations rep- resent similar overextensions of historical identity (Hall, 2003). Variants, including asymmetry, of a ter- minal character evolved during phylogenetic descent by means of developmental change are homologues of the given character, and variation in the ontogenetic mechanisms behind evolution of the character are not necessarily evidence of non-homology of the resultant states (Hall, 1994; Cooke, 2004). For practical consid- erations, predefinitive homologues are problematic for fossil birds as useful fossil embryos are rare (Elza- nowski, 1981; Norell et al., 1994). Developmental sequences include potentially dis- tinct components such as developmental cascades, changes in timing (heterochrony) and position (hetero- topy), and frame shifts (Hall, 1984; McKinney et al., 1990; Schulmeister & Wheeler, 2004). Where ontoge- netic mechanisms per se are potential characters, the concept of modularity of development (Minelli, 1998; Raff & Raff, 2000) implies a delimitation of ontoge- netic processes as characters in themselves. Of recent concern is the digital frame-shift within the digiti manus avium (Wagner & Gauthier, 1999), which counters the former embryological hypothesis of Hinchliffe (1985) that is still advocated by Burke & Feduccia (1997) and Feduccia (1999). Subsequent study has implicated Hox genes in such shifts (Chiu et al., 2000; Vargas & Fallon, 2005a, b), although the proposal is not without controversy (Galis, Kundr?t & Metz, 2005). The modularity of development permits the view of the hypothesis of Wagner & Gauthier (1999) as but one characterization of several plausible candidates based on embryological principles (Galis, van Alphen & Metz, 2002; Hamrick, 2002; Welten et al., 2005). Several other instances are variably conspicuous cases of heterochrony (McKinney et al., 1990; Klingen- berg, 1998; Livezey, 2003b) ? e.g. shifts in general developmental trajectories of Megapodidae (Starck & Sutter, 2000) and that of the avian furcula (Hall, 2001). Perceptions regarding the diagnostic relevance of anatomical position with respect to homology vary (Zelditch & Fink, 1996), e.g. the partly positional argu- ment of the ?rostro-parasphenoid? process as distinct from the traditionally defined processus basipterygoi- deus (Weber, 1993), typological paradigms (Richard- son, Minelli & Coates, 1999), and the role of function (Elzanowski, 1977). Patterns imposed by altered prox- imodistal developmental axes of appendages (Richard- HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 47 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 son, Jeffrey & Tabin, 2004) or action of regulatory (e.g. Hox) genes (Galis, 1999; Telford, 2000) increasingly are recognized in changes among transitional and ter- minal (definitive) developmental homologues. To date, most references to heterochrony have emphasized paedomorphic characters, i.e. variants of homologues typical of juveniles of plesiomorphic relatives (Livezey, 1995a, 2003b; Fink, 1988), and include more than sim- ple alteration of growth rates (Starck & Sutter, 2000). Instead of undermining homology, such instances of heterochrony provide potentially novel synapomor- phies among paedomorphs (Cracraft, 1981; Raff et al., 1990). The law of Von Baer (Gould, 1977) ? the biogenetic law ? postulated that the order of developmental stages in an individual reflects the phylogenetic series of increasingly apomorphic states found in that lin- eage. In some cases, this series approximates the evo- lutionary changes leading to the terminal state (Gould, 1977), and may provide possible insights into polarities and transformation series (Kraus, 1978; Alberch, 1985; Shubin, 1994; Jeffrey et al., 2002; Grant & Kluge, 2004; Schulmeister & Wheeler, 2004) ? i.e. states consistent with the ?ontogenetic criterion? (Alberch, 1985; Meier, 1997; Mabee, 2000). Avian can- didates for this criterion include the angulus coracos- capularis and mutliple unions of elements or anlagen of the definitive avian shoulder girdle (Livezey & Zusi, 2006). Function, homology and convergence: Cladistic (parsi- mony) analysis often is charged with a disregard for functional implications and convergence of character states, causing systematists to mistake similar but independently derived features among distantly related taxa as homologous. Convergence without demonstrated phylogenetic influence, as well as naive historical examples ? e.g. purported affinities of swifts and swallows, tabled decades ago (e.g. Shufeldt 1889b; Lowe, 1939; contra Van Tuinen, 2002) ? do not merit consideration here. Bock (1967, 1979) and Homberger (1980) considered function to be a critical criterion of homology, the independent study of which being required prior to inclusion of the structure in question in a phylogenetic analysis. Notable examples of this paradigm concern specializations of the feeding appa- ratus of Coraciiformes (Rawal & Bhatt, 1974) and Picidae (Bock, 1999), or cranial refinements among Charadriidae (Kozlova, 1961). Hypotheses of homol- ogy between features require a phylogenetic frame- work, and mere similarity of function in two potential homologues fails to demonstrate or exclude homology or convergence. Convergence frequently is invoked in the context of adaptation (Coddington, 1994) and, at least in orni- thological tradition, by superficial comparisons of the structures among distantly related lineages that share function, e.g. pelvic limbs of pursuit divers (cormorants, mergansers, loons), forelimbs of wing- propelled divers (alcids, diving petrels, penguins), or bills of piscivores (herons, anhingas, kingfishers). It is notable, however, that phylogenetic relationships among these examples were not obfuscated herein by these analogous similiarities in light of the totality of characters analysed, and that the purported instances of convergence were limited to a minority of phyloge- netically analysed characters. Given that character-states are homologous vari- ants of a particular character defined a priori by critical similarity and a posteriori by continuity of descent, considerations of function, although of evolu- tionary interest, are not directly germaine to homol- ogy or its diagnosis (Lauder, 1994). Function, and its possible relationship to form, constitute but one poten- tial precondition of convergence ? one component of homoplasy (Hall, 2003). Examples of homologues cited independently of ontogeny in birds include: the pro- cessus basipterygoideus (Elzanowski, 1977) and mod- ifications for dorsoventral movements of the carpus (Vazquez, 1992). Given that homology, and therefore homoplasy, are diagnosed reliably only within a phy- logenetic context, non-hierarchical assessments of homoplasy (Faith, 1989; Zeffer et al., 2003) offer few if any insights. Simpson (1944) discussed the differentiation of con- vergence from parallelism in closely related taxa under the term ?parallel evolution?, and Bock (1963a) described it in the context of ?evolutionary homody- namy?. Attribution of taxonomic groupings to conver- gence is conditional on: (i) the case for homology and plausible selection effecting changes (Fusco, 2001); (ii) reliability of phylogenetic analyses indicating disjunc- tion of the disputed groups (Sommer, 1999); and (iii) the independence of phylogenetic reconstructions from sources of potential bias (Lee & Doughty, 1997). Two avian examples follow that might be taken by some to exemplify cases of ?convergence? of morphological char- acters leading to erroneous phylogenetic groups, exer- cises critical to assessing perceptions relative to empirical evidence (Wiens et al., 2003). Ratites. We found strong support for monophyly of ratites, a finding in agreement with current consensus. The prior hypothesis of polyphyly was confounded by a perspective of static continents, convergence (Cracraft, 1974a) and a phenetic emphasis on differences (McDowell, 1948; Starck, 1955; Lang, 1956; Romer, 1968; Storer, 1971a). Synapomorphies of ratites not reasonably related to flightlessness or giantism fail as cladistic support for polyphyly. Finally, advocates of convergence fail to propose an empirically supported, plausible alternative hypothesis of relationship(s) con- sistent with the morphological (and molecular) data. 48 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 In our analysis, no support was found to ally any ratites to other non-ratite taxa; by contrast, 75 char- acters were ?diagnostic? or ?highly supportive? of mono- phyly of ratites (Table 2). Of these, 30 referred to the pectoral girdle or wing. If these 30 characters are accepted to be homologous as coded, they would lend support to the monophyly of ratites and (by parsi- mony) their shared flightlessness. On the other hand, if analysis had indicated that these same characters were optimized parsimoniously as non-homologous (but not coded a priori as such, absent evidence), the inference would be consistent with the possibility that flightlessness evolved in parallel more than once within a palaeognathous clade. Neither the present phylogeny nor alternative scenarios provide conclu- sive evidence for hypotheses concerning relative sequence(s) in the evolution of flightlessness in ratites; evolutionary trends of this kind are best explored through optimizations of character-suites a posteriori on the phylogenetic hypothesis (Fig. 13). Candidates for parallelism of potential phylogenetic influence include the synostosis scapulocoracoideum of ratites and its marked similarity with those of non- avian Theropoda (Feduccia, 1986), and convergent enlargement of the angulus coracoscapularis of flight- less Neornithes (Livezey & Humphrey, 1986; Livezey, 1988, 1989a, b, c, 1990, 1992a, b, 1993, 1995a), espe- cially in the ratites and Rallidae (Livezey, 2003b). Diagnosis of the scapulocoracoideum as atavism would hinge on the phylogenetic history of the feature. A similar challenge attends classification of other pec- toral changes among ratites as plesiomorphy, synapo- morphy, parallelism or convergence. Grebes and loons. We inferred the loons and grebes to be sister taxa, with no comparable support for positioning either taxon more strongly elsewhere (Table 3). Of the 17 characters diagnostic or highly supportive of this relationship (Table 2), 11 are from the pelvic girdle and limb (Livezey & Zusi, 2006). Those who considered these taxa to be only distantly related typically espoused a certainty that the simi- larities of the hindlimb and pelvis were misleading convergences associated with foot-propelled diving (Storer, 1956: 426; Storer, 1971a: 5). Suspected conver- gence is not supported by the differences in the hind- limbs of loons and grebes in that such are at least as parsimoniously interpreted to be: (i) symplesiomor- phies differentially lost or modified in the lineages fol- lowing divergence; or (ii) autapomorphies acquired independently following divergence of the orders. Nei- ther has been shown to be parsimoniously synapomor- phic with one or more other avian orders (Fig. 14). It is noteworthy that proponents of an alliance between the grebes and flamingos are tolerant of multiple dissim- ilarities between the groups (Chubb, 2004a). What- ever the scenario, the support index for this couplet of orders (Table 2; Fig. 14) significantly counters a con- vergent history for these characters, and an alliance with either the Charadriomorphae or the Phoenicop- teridae entailed substantial sacrifices in parsimony (Table 3). PALAEORNITHOLOGY: CONTRASTING PERSPECTIVES, COMMON GOALS Contrasts of ends and means: Until recently the fossil record for birds was marginalized with respect to for- mal phylogenetics, with most fossil taxa being frag- mentary representatives or close relatives of modern groups. A spate of newly discovered fossils from the late Mesozoic has clarified greatly the theropod roots of birds. Despite consensus concerning the phyloge- netic implications of new Mesozoic fossils and a num- ber of shared goals, neontological and palaeontological schools often work at cross purposes. A former obstruc- tion to unified analysis was a tradition of speculative evolutionary scenarios with strong palaeontological underpinnings, notably concerning evolutionary tran- sitions and diversification (Olson, 1985; Feduccia, 1995, 2003; Chatterjee, 1997; Kardong & Zweers, 1997; Zweers & Vanden Berge, 1997a, b; Zweers et al., 1997; Bleiweiss, 1998c; Feduccia et al., 2005) and avi- faunal ?assemblages? (Brodkorb, 1971a, 1976; Olson, 1985), that served as surrogates for ecological data not available for fossil lineages and past eras. A signifi- cant convergence in cladistic methods notwithstand- ing, it remains an unfortunate impediment that goals, expectations, nomenclature and assumptions of avian palaeontologists and neontologists (Cracraft, 1972b, 1974b, 1978, 1979, 1980) exist in largely parallel cir- cles and have failed to realize a commonality of professional purpose. The most serious analytical challenges posed by avian fossils derive from missing data (Kearney, 2002; Kearney & Clark, 2003), which may affect the characters admitted for analysis. Nomenclatural divergence, analytical corollaries: Issues of strict taxonomy aside, philosophical differ- ences between the subdisciplines also involve long- standing perceptions of the diagnosibility of direct ancestry (e.g. Brodkorb, 1976; Olson, 1976). Palaeon- tological viewpoints regarding ancestral status of fos- sils also hold implications for nomenclature of fossil lineages (e.g. ?stem-groups?) in phylogenetics (Benton, 2000), analytical validity of ?ghost lineages? (Norell, 1992), and the evolutionary significance of fossil ?mosaics? (Norell & Clarke, 2001; Dyke & Van Tuinen, 2004). A neontological perspective, however, considers fossils to differ from modern representatives solely by extinct status and quality of preservation, with many modern lineages representing more informative plesi- omorphs of extant clades than any fossil member ? e.g. HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 49 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 anseriforms Anhimidae, Anseranas vs. fossil Presbyor- nis (Livezey, 1997a). Where adequately preserved for phylogenetic placement, fossils also may provide an estimate of minimal age of the group it represents, but this estimate is imprecise and subject to bias. Ironically, a misunderstanding of such estimation contributed to early arguments concerning ?temporal incongruence? and against a theropod origin for birds (e.g. Brochu & Norell, 2000, 2001). Although the definitions of ?stem? and ?crown? groups are relatively simple (Meier & Richter, 1992), the former sharing conceptual roots with earlier terms of assumed or possible direct ancestry such as ?plesions? (Wiley, 1981), it seems that these designations carry important nomenclatural implications (Benton, 2000) and may impede the integration and interpretation of fossil and modern taxa by identical means. Where ancillary assumptions regarding local polarities and implications of ?stem-group? members are made in analyses based on narrow samples of taxa (e.g. Bour- don, 2005; Bourdon et al., 2005) or characters (e.g. Mayr, 2002a, 2003a, b, c, 2004e, 2005i; Mayr & Clarke, 2003; Mayr et al., 2003; Mayr & Ericson, 2004), or if the fossil material is of marginal quality (e.g. Mayr, 2002c, 2004e, 2005f), the differences between neonto- logical and palaeontological schools can be substan- tial. In many contexts, it appears virtually inescapable that ?stem-group? status implicitly conserves the notion of possible or likely ancestry relative to the corresponding crown-group, and thereby suggests an evolutionary role beyond mere cladistic position (e.g. successive sister-groups). Moreover, inclusion of a fossil in a ?stem-group? (Mayr, 2002c, 2005d) can lead to alternative analytical protocols, e.g. speculations of local polarities and sub- stitution of hypothesized instead of observable char- acter states to lend support to trees including mulitple fossils (e.g. Mayr, 2002c, 2004f, 2006a). The compara- tively well known Pseudasturidae ? formerly assigned to the Family Quercypsittacidae (Psittaciformes) by Mourer-Chauvir? (1992) ? were judged to combine ?intermediacy? in a number of characters purportedly diagnostic of psittaciforms with similarities to the ?Galbulae? (Piciformes), and were referred to the ordi- nal ?stem-group? of Psittaciformes by Mayr (2002c). Informal hypotheses of polarities in analyses of fossil birds ? e.g. by Mayr (2005i: characters 5 and 12), Mayr et al. (2003: characters 1, 6, 11, 29, 35 and 71), and Mayr & Ericson (2004: character 55) ? evidently intended to impose ?local? initial states in a particular context and often asserted in character descriptions (Mayr, 2002c), are innocuous if these are inferred from direct analysis rather than imposed based on precon- ceptions regarding a taxon. Evidently, however, in some cases states observed for given terminal taxa are replaced by states purportedly representative of ?stem- group? members (i.e. states hypothesized to be prede- cessors to those of taxa included in the corresponding ?crown group?). Examples of the latter ? confirmation of which requires character descriptions and the data matrix ? include characters 5, 9, 18, 26, 30 and 68 of Mayr et al. (2003). A related tradition of avian palaeontology is the imposition of intuitive trends that exceed the strict empirical content of available fossil material. For example, newly discovered fossils ? notably a ?stem- group hummingbird? (Eurotrochilus inexpectatus) from the early Oligocene of Germany of purportedly modern grade ? motivated Mayr (2003c, 2004d, 2005a, g) to enter the debate concerning the relationships of the Apodiformes. These efforts included a critique (Mayr, 2001f) of a description of a fossil taxon by Dyke (2001c), the attribution by Mayr (2004d) (based on limited taxonomic comparisons) of morphological spe- cializations both for hovering flight and for nec- tarivory to Eurotrochilus, and speculations on the earliest evidence of avian nectarivory and the coevo- lution of certain bird-pollinated angiosperms in the New World. Given the oversimplification of distribu- tions of characters, especially within the Apodiformes (Cohn, 1968; Karhu, 1992, 1999, 2001), and the wider controversy based on molecular data (Dumbacher et al., 2003; Thomassen et al., 2003, 2005; Chubb, 2004b), it is unfortunate that the characters included by Mayr (2001f, 2003c, 2004d, 2005g) totalled from 25 to 98, and failed to provide a synthesis of all relevant characters was not provided for relevant taxa prior to speculating regarding graded specializations and coevolutionary trends in the early Cenozoic. Plesiomorph or interordinal ?intermediate??: Perhaps the most prevalent idiosyncracy of palaeontological perspectives is the reputed importance of fossils as a source of phylogenetic ?bridges? between extant, com- paratively divergent lineages (Mayr, 2006b). However, neither the published record nor phylogenetic theory supports this notion, and the role of interordinal ?link- ing? lineages is at least as often revealed by extant taxa (Livezey, 1997a). The taxonomic history of Pres- byornis illustrates the potential that such expecta- tions may hold for phylogenetic placements of fossils with respect to modern higher-order groups. Wetmore (1926) originally described Presbyornis from a single element from the Eocene of western North America as a charadriiform, but later (with abundant additional material) it was asserted to be a ?transitional? shorebird and indicative of a close rela- tionship between Charadriiformes and Anseriformes (Olson & Feduccia, 1980a), the intuitive methods employed in the latter being criticized by Raikow (1981). More than a decade later and based on direct cladistic analysis of both Presbyornis and modern 50 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 taxa, the genus was determined to be a plesiomorphic anatoid (Ericson, 1997; Livezey, 1997a). Subsequently, Presbyornis (and synonyms) has been the genus of choice for referral of fossils from the Eocene of England (Harrison & Walker, 1976a), Eocene of Mon- golia (Kurochkin, 1988), Palaeocene of eastern North America (Olson, 1994; Ericson, 1997), Cretaceous of Antarctica (Noriega & Tambussi, 1995), late Palae- ocene of North America (Benson, 1999), and Creta- ceous of Mongolia (Kurochkin, Dyke & Karhu, 2002). An examination of the material upon which these referrals were made raises reasonable doubts as to diagnostic reliability, and reveals the role of the com- paratively well represented fossil Presbyornis as a palaeontological ?strange attractor? for other, variably preserved fossils of uncertain affinities. As the refer- rals of fossils to the early Anseriformes escalated, pur- ported allies of Presbyornis also increased in number and morphological diversity: Olson (1994) reported a ?giant? Presbyornis from the Palaeocene of eastern North America, Alvarenga (1999) referred a fossil from the mid-Tertiary of Brazil to the Anhimidae; Olson (1999b) phenetically allied Anatalavis from the London Clay to the modern Australian endemic Anseranatidae, a placement disputed by Dyke (2001b); Mourer-Chauvir? et al. (2004) allied Anser- pica from the Oligocene of Europe to the same family; and Clarke et al. (2005b) likened Vegavis (Cretaceous of Antarctica) to Presbyornis and referred the genus to the Anatoidea by a nested series of analyses of published data sets, by a method similar to that of supertrees. The saga of Presbyornis also extended to the inter- ordinal realm of fossil referrals, and provided insights into the alliance formerly alleged between Presbyornis and Phoenicopteridae by way of the poorly understood Juncitarsus (Olson & Feduccia, 1980a, b; Ericson, 1999), and thereby the subsequently proposed rela- tionship between Phoenicopteridae and Podicipedidae. In addition, Cheneval & Escuilli? (1992) cited similar- ities between grebes and the flamingo-like Palaelo- didae in the pelvic appendage ? the very class of characters considered by many of these authors to be prone to convergence and therefore unreliable in unit- ing grebes with loons. Nevertheless, Mayr (2004c: 140) considered the sister-group relationship between grebes and flamin- gos to be ?. . . one of the best supported higher-level clades within modern birds.? Mayr (2005a: 523) then suggested that the intermediacy of two skeletal fea- tures between Juncitarsus (Eocene of Wyoming) and the Palaelodidae (Oligocene of Europe), fossils tradi- tionally allied to the Phoenicopteridae, ?. . . provides a morphological link between Phoenicopteriformes and Podicipediformes.? As for the early inferences made for Presbyornis, to which Juncitarsus and phoenicop- terids were compared (Ericson, 1999), misclassifica- tion of fossils can lead to significant errors where informal phenetics and exceptional treatment of fossils are involved (Livezey, 1997a), problems not correctable by adoption of empirically depauperate taxonomic nomenclatures (e.g. ?stems? and ?crowns?) and contradictory views on the phylogenetic roles of fossil taxa. FOSSIL NEORNITHES: PRESERVATION AND OPPORTUNITIES Referrals, old and new: Despite the foregoing critique, well-preserved fossils can provide important insights into avian evolution, especially the Mesozoic origins of the group, and many potentially important fossils cur- rently have yet to be described (J. A. Clarke, pers. comm.) and are beyond the scope of the present work. Unfortunately, a majority of fossil Neornithes, both of Mesozoic (Hope, 2002) and Cenozoic age (Brodkorb, 1963, 1964, 1967, 1971b), were named based on mate- rial not permitting meaningful inclusion in a formal cladistic analysis of modern scale. Moreover, classifi- cations of many of these taxa were made phenetically, and with a marked tendency to refer new taxa to the modern taxon perceived to be most similar (Livezey & Martin, 1988; Livezey, 1997a, 2003c). Fortunately, increased use of cladistic analyses makes it likely that such records, especially those spanning the late Meso- zoic and early Cenozoic, will provide an increasingly refined palaeontological dimension to avian phyloge- netics. Given the limitations of direct diagnosis (Table 2) and the phenetics of seeking the best neornithine group in which to place a fossil (Livezey & Martin, 1988; Livezey, 1997a), what is the recommended means for evaluation of a new fossil with respect to the present data set? Two paths seem most informative at present: (i) unconstrained analysis of the present data set, appended with the codings for the fossil taxon, however incomplete (within reasonable limits of infor- mativeness); or (ii) analysis of the fossil taxon under a backbone-constraint for modern lineages (e.g. Figs 13? 18). The latter probably will prove optimal in those cases where missing data are especially numerous or where even higher-order affinities are indiscernible, and especially where both circumstances pertain. Tax- onomic groups of greatest diversity and quality of preservation hold the greatest potential for such insights, and these merit special emphasis here, espe- cially those broadly consistent with groupings inferred here and for groups having few modern members. Diversity, aquatic and terrestrial: Fossils have been referred, although not all by phylogenetic means, to all modern families of the Pelecaniformes: Phaethontidae HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 51 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 (Harrison & Walker, 1976b; Olson, 1983b, 1985; Mayr & Smith, 2002), Fregatidae (Olson, 1977), Fregatidae or Sulidae (Olson & Matsuoka, 2005), Sulidae (Olson & Rasmussen, 2001; Mayr, 2002d; Stucchi & Urbina, 2004), Pelecanidae (Olson, 1999a), Phalacrocoracidae (Mayr, 2001c) and Anhingidae (Alvarenga, 1995; Alva- renga & Guilherme, 2003; Mourer-Chauvir? et al., 2004). In addition, the controversially referred Plo- topteridae (Mayr, 2004b) have increased in palaeodi- versity (Olson & Hasegawa, 1979, 1996; Olson, 1980; Goedert, 1988). Less well justified is the putative membership of a group of widespread, fossil, pseudo- denticulate birds ? Odontopterygiformes (Owen, 1873; Howard, 1957; Goedert, 1989; Averianov et al., 1991; Zusi & Warheit, 1992; Gonz?lez-Barba et al., 2002) ? for which a modest analysis mustered marginal sup- port as an alternative sister-group to the Anseriformes (Bourdon, 2005). The Coliiformes, Trogoniformes, Coraciiformes and Piciformes merit renewed examination as these groups (e.g. Bucconidae sensu lato, including Pri- mobucconidae), as well as specimens of uncertain affinity (Olson, 1992b), also have received multiple new fossil referrals (Harrison, 1982a; Mayr, 2000c) ? including Trogoniformes (Mourer-Chauvir?, 1980; Mayr, 1998a, 1999a, 2001b, 2003b), Coliiformes (Olson & Houde, 1989; Houde & Olson, 1992; Mayr & Peters, 1998; Mayr, 2000b, 2001a, 2005d, e; Dyke & Water- house, 2000; Kristoffersen, 2001; Mayr & Mourer- Chauvir?, 2004), Coraciiformes (Olson, 1976, 1992b; Mourer-Chauvir?, 1985; Mayr & Mourer-Chauvir?, 2000; Mayr, Mourer-Chauvir? & Weidig, 2004b) and Piciformes (Mayr, 2001d, 2005h, i). Broadly delimited zygodactyl taxa (Feduccia & Martin, 1976; Mayr, 1998c, 2001e, 2004e, 2005h, i) complete the apparent palaeodiversity of ?higher? landbirds (Fig. 18), and con- trasts with modern passeriform dominance (Mane- gold, Mayr & Mourer-Chauvir?, 2004). The Psittaciformes, at least the modern members of which are anatomically distinctive, have attracted a number of newly described fossils, some of which obscure this distinctness (Mayr, 2002c), and thus the order has undergone pronounced extensions of its palaeodistributional limits (Harrison, 1982b; Mourer-Chauvir?, 1992; Mayr & Daniels, 1998; Stidham, 1998; Dyke & Mayr, 1999; Brochu & Norell, 2000; Dyke & Cooper, 2000; Mayr, 2001g, 2002c; Mayr & G?hlich, 2004; James, 2005). The uniquely apomorphic form of the crania of some taxa in this order is so extreme (Smith, 1975) as to pose challenges of comparability, and many modern mem- bers also manifest distinctly modified pectoral gir- dles and apomorphic pelvic skeletons (Smith, 1975; Livezey & Zusi, 2006). However, some fragments controversially referred to this clade are of potential relevance to the origins of modern orders and the K? T boundary (Stidham, 1998 vs. Dyke & Mayr, 1999), and merit reassessment. SPATIOCHRONOLOGICAL DIMENSIONS OF PHYLOGENETICS Preservation and inferred distribution: A traditional referral of issues of ?deep time? to palaeontology (Brochu et al., 2004) evidently reflects, in part, the rapidity with which fossil evidence was conjoined with modern phylogenetics for the calibration of geological time with phylogenetic hypotheses. Palaeocalibration of ages provided by fossil records in combination with models of molecular phylogenetics predictably turns on taxonomic groups possessed of rich, accurately aged fossils and reliable phylogenies. These cross-disciplinary works progressed (perhaps too) rapidly toward attempts at global treatments of Neornithes that were influenced by undue inclusion of fossils of unreliable identity and age. In addition, the early spate of efforts favoured classes of models (e.g. Markovian) that facilitate minimization or ?smoothing? of discrepancies between calibrations and branching patterns as opposed to realistic incorporation of het- erogeneous evolutionary rates (Sheldon et al., 2000; Brochu & Norell, 2001; Van Tuinen & Hedges, 2001; Dyke, 2003; Pol et al., 2004; Van Tuinen & Dyke, 2004; Van Tuinen et al., 2006). The latter, often underappre- ciated, reality reflects the likelihood of preservation and a negative skewness of such records expected to be inversely correlated with body size and related het- eroscedasticity that is directly correlated with geolog- ical age. These palaeontological issues are confounded by unrealistic assumptions of molecular trees and models in which the fossil data are incorporated. Not surprisingly, informativeness of such exercises to date has been limited ? i.e. modern orders have been inferred to have very early origins (Pereira & Baker, 2006a: table 1; Van Tuinen et al., 2006: tables 1, 2). Nevertheless, a phylogenetic hypothesis of high sup- port and resolution (Figs 10?18) is an essential start- ing point ? one, however, conditional on independent testing and augmentation. Another precondition of success, aside from well-documented fossil records (e.g. Clarke et al., 2003), is use of realistic assump- tions regarding molecular evolution where calibration of ages of divergence events is among the objectives (Pereira & Baker, 2006a). Calibration of time: Failure to verify the existence of a molecular ?clock? notwithstanding (Garc?a-Moreno, 2004), an endeavour of particular interest regards bringing to bear the calibration of geological time ? the ?time axis? of Benton (1996) ? through phylogenetically placed fossil taxa, thereby estimating a minimal age of corresponding nodes in a phylogeny and recavering the temporal pattern of avian diversification (Hedges 52 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 et al., 1996; Mindell et al., 1996; Miyaki et al., 1998; Cooper & Penny, 1997; Kumar & Hedges, 1998; Sep- kowski, 1999; Waddell et al., 1999; Cracraft, 2001). Direct use of stratigraphic data for inference of trees by means of parsimony or ?stratocladistics? has been criticized on several methodological grounds, and is especially inappropriate for the sparse avian fossil record (Fisher, 1992; Huelsenbeck & Rannala, 2000). Well-supported phylogenies for molecular models are critical for extrapolations of evolutionary rates from fossil-based point-estimates of geological age (Marshall, 1990; Springer, 1995; Arbogast et al., 2002; Broham et al., 2002; Smith & Peterson, 2002; Broham, 2003; Brochu, Sumrall & Theodor, 2004; Van Tuinen & Hedges, 2004). Disagreements among calibrations to date are consistent with evidence for significant vari- ation among rates of evolution (Thorne, Kishno & Painter, 1998; Johnson & Cicero, 2004; Cicero & Johnson, 2006; Zink & Klicka, 2006), the effects of out- groups (Waddell et al., 1999), initial estimates of which (e.g. Shields & Wilson, 1987) continue to be used. Other problems stem from the limited suitabil- ity of stratigraphic data in phylogenetic contexts (Huelsenbeck & Rannala, 2000), and effects of topo- logical aspects of trees (Pol et al., 2004). The continued controversy concerning the position of the Passeri- formes relative to other Neoaves (especially Fig. 10) ? considered by many to reflect effects of outgroup and relative evolutionary rates of mtDNA ? presents a critical issue for attempts at calibrations more precise than Mesozoic vs. Cenozoic origins (Stanley & Crac- raft, 2002; Cracraft et al., 2004; Pereira & Baker, 2006a, b; Slack et al., 2006a). Accordingly, the prospect of using currently avail- able palaeontological data to calibrate evolutionary rates is disconcerting, regardless of the phylogenetic framework conjoined, principally because of a paucity of fossils that are reliably classified and of precise age (Hope, 2002; Livezey, 2003c). However, the existence of avian lineages in the late Mesozoic has been substan- tiated directly by palaeontological evidence (Olson, 1992a; Dalla Vecchia & Chiappe, 2002; Grellet-Tinner & Norell, 2002; Schweitzer et al., 2002). For example, the estimated origin of megapodiid galliforms in the Cretaceous (Pereira & Baker, 2006b) agrees well with estimates for the comparably ancient Anseriformes. Special attention relates to the oldest fossil record for a member of the Neornithes, increasingly with respect to hypotheses of descent relative to massive faunal upheavals following the K?T boundary (Feduc- cia, 1977c, 1995; Olson & Feduccia, 1980a; Olson & Parris, 1987; Paton et al., 2002, 2003). Despite consid- erable effort, few points of agreement among phyloge- netic calibration of rates and fossil records have been achieved (Benton, 1999, 2001; Dyke & Mayr, 1999; Van Tuinen & Hedges, 2001). In part, disagreements reflect variable reliances on assumpitions of ?clock-like? mole- cular evolution (Helm-Bychowski & Wilson, 1986; Van Tuinen & Hedges, 2001; Van Tuinen & Hadly, 2004). The unrealistic assumption of ?clock-like? molecular change (Brochu et al., 2004) has led to diverse means of ?correction? or analytical adjustments (Mooers & Harvey, 1994; Sanderson, 1997; Mindell et al., 1998; Bleiweiss, 1998c; Ho et al., 2005), increased sampling of fossils (Springer, 1995; Smith & Peterson, 2002; Garc?a-Moreno, 2004; Pereira & Baker, 2006a, b), incorporation of multiple ?clocks? (Van Tuinen & Dyke, 2004) and relaxation of estimators through Bayesian methods (Yang & Rannala, 2006). For example, Mayr (2002c) stated that the earliest passeriform is no older than the early Oligocene, whereas Cracraft et al. (2004) inferred the order to have originated prior to the K?T boundary, a discrep- ancy of magnitude likely to weaken associated calibra- tions. Recent attempts to bracket times of avian cladogenesis by Dyke & Van Tuinen (2004: fig. 3) based on the few widely accepted higher-order rela- tionships necessarily encompassed relatively few major lineages of birds, whereas a priority accorded expanded taxonomic samples led Van Tuinen et al. (2006) to accept calibrations based on many fossils classified from the literature, relationships derived from the phenetics of DNA hybridization, and a null model incorporating questionable assumptions con- cerning molecular evolution (Pereira & Baker, 2006b) and a basal polytomy for Neoaves. Palaeobiogeography and the spatial dimension: There is considerable optimism bestowed upon fossil taxa for the reconstruction of historical biogeography (Olson, 1985; Carroll, 1997). Southern-hemispheric patterns interpreted in terms of tectonic fragmentation and movements are manifested in the literature of avian systematics (Glenny, 1954; Cracraft, 1973b, 1975, 1976c, 1982c; Hedges et al., 1996; de Kloet & de Kloet, 2005). Realistic reconstructions of historical biogeo- graphy require effects of vicariance events within con- tinents ? e.g. mountainous uplifts or glaciation ? as a secondary class of abiotic antecedants of phylogenetic diversification (Ploeger, 1968; Cracraft, 1982c, d). Of greater empirical substance for Aves, perhaps, are inferences of historical vicariance, notably those forti- fied by robust phylogenetic analyses and showing con- gruent geographical patterns. Most important of these for birds is the recurrent pattern of southern origins among many lineages, collectively suggestive of a crit- ical role for Gondwana in early avian origins and diver- sification and most strikingly coincident with the K?T boundary (Cracraft, 2001). Patterns consistent with southern genesis are especially compelling in light of a biased tendency for migratory habit to counter northern?southern hemispheric patterns relative to HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 53 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 those of eastern?western hemispheres (B?hning- Gaese, Gonz?lez-Guzm?n & Brown, 1998). Taxa for which circumstantial evidence of this kind is consis- tent with southern-hemispheric origins (Cracraft, 1973b), include: Ratitae (Cracraft, 1974a; Haddrath & Baker, 2001), Anseriformes (Livezey, 1986, 1997a, 1998a), Galliformes (Dyke et al., 2003), Sphenisci- formes (Cracraft, 1988; Cracraft & Mindell, 1989; Harrison et al., 2004), Gruiformes (Cracraft, 1973a, 1982b; Livezey, 1998b), Psittaciformes (Cracraft, 1988; Cracraft & Mindell, 1989; Miyaki et al., 1998; de Kloet & de Kloet, 2005), Trochilidae (Bleiweiss, 1998d) and suboscine Passeriformes (Ericson, Johansson & Parsons, 2000; Irestedt et al., 2001, 2002; Ericson et al., 2002a, b, 2003b; Barker et al., 2002, 2004; Edwards & Boles, 2002; Yuri & Mindell, 2002; Ericson & Johansson, 2003; Chubb, 2004b). The Palaearctic understandably dominated palaeo- geographical hypotheses in the early 20th century, especially for fossils from the late Cenozoic (Ploeger, 1968). The prevalence of terrestrial groups during the Palaeogene considered ?basal? to the Passeriformes (i.e. branching from the lineage culminating in the Passe- riformes and its sister-group) prompted Mayr (2005a) to suggest that the former taxa may have occupied ?passeriform? niches prior to the Oligocene. This hypothesis should be amenable to testing by morpho- logical comparisons but is contingent on the resolution of debated dates of origin of the Passeriformes (Boles, 1995, 1997; Cracraft et al., 2004; Mayr & Manegold, 2004). Among the avian clades most frequently cited with respect to adaptive radiation, key innovation, ontogenetic underpinnings and sheer diversity ? phenomena of prime interest (Starck, 1969; Smith, 1994) ? are the Apodiformes and Passeriformes. Accordingly, the Apodiformes (especially the Trochil- idae) attracted substantial anatomical (Cohn, 1968; Karhu, 1992, 1999, 2001) and phylogenetic study (Dyke, 2001c; Mayr, 2001f, 2003c, 2004d, 2005a, g; Thomassen et al., 2003, 2005; Chubb, 2004b). The Passeriformes, however, hold a position of unique diversity ? comprising 60% of extant Aves (Cracraft et al., 2004) and unmatched global distribution (Fitzpatrick, 1988; Kochmer & Wagner, 1988), evolutionary success (Raikow, 1986, 1988; Vermeij, 1988) and adaptation (Baum & Larson, 1991). Evolutionary radiations and the K-T controversy: Such palaeogeographical patterns have shed light on the theory of ?adaptive radiation? (Gould & Eldredge, 1977; Eldredge & Cracraft, 1980; Levinton, 1988; Eldredge, 1989; Valentine, 1990; Jablonski, 2000; Schluter, 2000), ?explosive radiation? (Feduccia, 1980, 1995, 1996, 2003; Sheehan & Fastovsky, 1992; Cooper & Penny, 1997; Kardong & Zweers, 1997; Cooper & Fortey, 1998), and ?mass extinction? (Jablonski, 2005) of Aves around the K?T boundary. Other biogeograph- ical hypotheses of significance relate cladogenetic pat- terns and faunal diversity to tectonic movements (Hedges et al., 1996; Craw, Grehan & Heads, 1999; Humphries & Parenti, 1999), and trans-Gondwanan dispersal (Cracraft, 1973b, 1975, 1976c, 1982b, c, 2001). In particular, the Charadriiformes have been the focus of substantial, speculative scenarios regarding a special evolutionary role involving multiple avian groups and major extinctions. The notion that ?shore- birds? are fundamental to an understanding of avian evolution across the K?T boundary (Olson & Feduccia, 1980a, b) is no longer considered promising, and was based in part on a preconception of Charadriiformes as phenotypic intermediates bridging higher-order avian groups (Zweers & Vanden Berge, 1997a, b; Zwe- ers, Vanden Berge & Berkhoudt, 1997; Dyke et al., 2002; Paton et al., 2002). Quantitative estimation of rates of evolutionary change (Rodriguez-Trelles, Tarrio & Ayala, 2002) ? given robust phylogenies (Marshall, 1990) and ade- quate fossil records (Sepkowski, 1999) ? have fostered more detailed hypotheses of phylogenetic bottlenecks and ?explosive? radiation near the K?T boundary (Feduccia, 1995, 2003; but see Stanley & Cracraft, 2002). However, there is growing evidence, at least based on Bayesian analyses of data largely or entirely from the mitochondrial genome, that most or all neornithine orders date from the late Cretaceous (Grellet-Tinner & Norell, 2002; Schweitzer et al., 2002; Dalla Vecchia & Chiappe, 2002; Pereira & Baker, 2006b; Slack et al., 2006a, b; Van Tuinen et al., 2006). If accurate, despite the vulnerability of such data to suboptimal rooting, this record undermines early anticipations of K?T boundary effects in mod- ern orders and an evolutionary timespan in which major divergences of neornithine lineages would extend through the early and middle Cenozoic. Expectations for avian fossils of such antiquity are correspondingly conservative, and although fossils of such age potentially offer new calibration points for early avian lineages, there is diminished hope for points of calibration bearing on the relative antiquity of modern (super)orders of birds or precise molecular estimates of associated evolutionary rates character- istic of phylogenetic lineages. PRIORITIES FOR FUTURE INVESTIGATION Current points of irresolution: Based on the present analysis (Figs 1?8) and other studies during recent decades (Figs 10?18), the area of primary ignorance for avian phylogenetics is the heretofore refractory groupings within the Neoaves, with principal prob- lems being the highest-level nodes (notably the posi- 54 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 tion of the Passeriformes within this group) and the comparatively routine but significant work of phylog- eny within orders and families (Fig. 11; Appendix 1). Optimism remains justified, however, with new genes and molecular signal of scale higher than simple sequences and indels under exploration (e.g. retro- posons). Reliance solely on a single scale of homology, e.g. the indels upon which Fain & Houde (2004) pro- posed largely hemisperically concordant ?Metaves? and ?Coronaves?, is herein inferred to be nomina nuda (Appendix 1). This fixation on single-scale molecular analyses justifiably led Harshman et al. (2006: 42) to ask: ?Can four million bases [nucleotides] resolve the [avian] tree?? Fortunately, there are a number of anatomical fields of study that remain virtually untouched in modern phylogenetic contexts (Livezey & Zusi, 2001, 2006), a circumstance of hope in light of the palaeontological discoveries that will necessitate refinement of these and refined anatomical complexes coded (e.g. os palatinum of Archaeopteryx; Mayr et al., 2005; Zusi & Livezey, 2006). Several episodes of avian phylogeny were incom- pletely resolved in the present analysis (Figs 12?18), and will require significantly intensified sampling of taxa to solve: ? Positions of Aepyornithiformes and Dinornithi- formes relative to extant ratites (Fig. 13). ? Resolution of genera within the Phasianoidea (Fig. 13). ? Resolution of the positions of the Psittaciformes and Columbiformes (Figs 16, 17). ? Determination of the relationships among several poorly resolved nodes involving the traditional Charadriiformes and Gruiformes, within the ?central? Charadriiformes (Fig. 15), for which alternative pro- posals continue to appear (Simmons et al., 2004; Van Tuinen et al., 2004; Paton & Baker, 2006; Pereira & Baker, 2006a), a task likely to require inclusion of rich suites of such integumentary characters as the natal integument for reconstruction of deeper nodes, and aspects of the definitive externum for resolution of shallower nodes (Jehl, 1968, 1971; Livezey, 1991, 1995b, c, d, 1996a, b, c, 1997c). ? Confirmation of relationships of the families of Caprimulgiformes (Fig. 17). ? Resolution of the trichotomy among the Coracii- formes, Piciformes and Passeriformes (Figs 17, 18), and resolution of subordinal and familial phylog- eny within the Passeriformes, and affirming the position of the Passeriformes relative to other Neoaves. ? Make available an empirically grounded platform for finer-scale analyses of single orders or families of Neornithes as an alternative to the classical litera- ture or the ?tapestry? by Sibley & Ahlquist (1990), with priority accorded to comparatively old, multifa- milial orders (e.g. Galliformes, Procellariiformes) or traditionally challenging groups (e.g. Pelecanimor- phae). ? Phylogenetic integration of well-preserved fossils into the phylogeny, both serving as additional taxa for resolution or revision of groups and as points of cali- bration of (minimal) ages of lineages of which these are members. An especially rewarding class of study awaits opti- mization of life-historical attributes at the present phylogenetic scale, attributes such as sexual dimor- phism, parental care and reproductive parameters (Wyles, Kunkel & Wilson, 1983; Winkler & Sheldon, 1993; Wesolowski, 1994; Wimberger & de Queiroz, 1996; Figuerola, 1999; Geffen & Yom-Tov, 2001; Tullberg, Ah-King & Temrin, 2002; Roulin, 2004; Pereira & Baker, 2005; Ekman & Ericson, 2006) as a starting point for more detailed studies in evolution- ary biology. This area of study can advance only with: (i) use of well-resolved, robustly supported phyloge- nies, often not feasible (e.g. Cubo, 2003); and (ii) refinement of methods for optimization a posteriori of attributes, including where phylogenies include poly- tomies (Saunders, Smith & Campbell, 1984; Temrin & Sill?n-Tullberg, 1994, 1995; Omland, 1997a, b; Ligon, 1999; Richardson et al., 1999). An unfortunate aspect of such methods has been revealed by a number of optimizations that relied on the phenetics of Sibley & Ahlquist (1990), ostensibly as it was the only hypothesis of adequate taxonomic breadth for the desired survey (e.g. Van Tuinen et al., 2006). Attributes so assessed include body mass (Mau- rer, 1998), wing length (McCall, Nee & Harvey, 1998) and correlates of flightlessness (Cubo & Arthur, 2001). Most such published surveys have recovered signifi- cant patterns in selected morphological attributes despite the virtually universal view that the quasi- phylogeny that was used is unreliable. This incongru- ity indicates that apparent significance of optimiza- tions is essentially meaningless, but more importantly provided a fortuitous insight that statistically signifi- cant patterns can emerge from inaccurate phyloge- netic hypotheses and that it may be prudent to adopt more conservative critical values for tests of this nature. Until more discriminating methods are avail- able, significance in this context should not be assessed against a null model of random change but instead against randomized evolution with varied descent or reserved for comparisons between phylogenies. Broadened phylogenetic horizons: Philippe & Laurent (1998) entitled their paper with a challenge of undis- puted cogency: ?How good are deep phylogenetic HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 55 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 trees?? An expansion of phylogenetics of the Theropoda and Dinosauria is well underway, how- ever, and will be central to a robust foundation for avian phylogeny, including significant implications for ?global? homology and anatomical nomenclature. This exploration should lead to phylogenetic hypothe- ses among Vertebrata of increasing scale, especially in light of character analyses already accomplished for non-avian Tetrapoda (Benton & Clark, 1988; Evans, 1988; Nielsen, 1995; Zardoya & Meyer, 1996; Laurin & Reisz, 1997; Philippe & Laurent, 1998; Zardoya et al., 1998; Xia, Xie & Kjer, 2003; Suzuki, Laskowski & Lee, 2004; Hill, 2005). Similar explora- tions among deep roots by molecular and morpholog- ical means also hold promise for the phylogenetic resolution of an expanded ?super-clade? of Reptilia and allied Tetrapoda (Benton, 1990; Graybeal, 1994; Kumazawa & Nishida, 1995; Mindell et al., 1999; Ruta, Coates & Quicke, 2003), including (sub)fossil taxa to the degree permitted by remains (Handt et al., 1994; Taylor, 1996) and logistic limits on life- historical data available for fossil taxa. In contrast to issues of quality of the fossil record (Wagner, 2000a) and limits on signal recoverable from fossils (Wagner, 2000b), potential for neontological study remains underexplored, especially that involving soft-tissue anatomical systems (W?gele, 1995). In light of the evident attraction of probabilistic reconstructions, phylogenetics may benefit most from an expansion of Bayesian methods to address prob- lems of incomplete data (Gelman & Xiao-Li, 2004), robustness of estimates (Insua & Ruggeri, 2000) and refined optimization, including (quasi-)likelihood methods, both parametric and non-parametric (Heyde, 1997; Beiko et al., 2006; Anisimova & Gas- cuel, 2006). In both major classes of probabilistic mod- els, renewed attention is justified to the analytical properties of branching processes (Harris, 1963; Ath- reya & Jagers, 1997; Kimmel & Axelrod, 2002; Hac- cou, Jagers & Vatutin, 2005), for which statistical methods have been elaborated only recently. In a prob- lem of this unprecedented scale, it is critical for mod- ern systematists to exploit a diversity of sources of data as a means to effect even-handed assessments of historical pattern. An overview of the literature (Figs 1?10) reveals that much remains to be accomplished in avian phy- logenetics. Significant advances principally lie in studies of great taxonomic scale and diverse support that target nodes of ordinal and higher taxonomic scales of Neoaves, in conjunction with a solution of the persistent disputes among morphological, mitoge- nomic and nuclear findings. In combination with incorporation of additional, evolutionarily conserva- tive characters of soft anatomy (Oliveira et al., 2004) and karyotypes (Shetty, Griffin & Graves, 1999; Burt, 2002), the methods of ?total-evidence? analyses hold promise for phylogenetic scales and calibration of ages previously not feasible (Stanley & Cracraft, 2002; Baker & Gatesy, 2002; Cracraft et al., 2004; Yang & Rannala, 2006), a potential not without early tests (e.g. Kennedy & Page, 2002) and new method- ological challenges (Baker et al., 1998; Ballard et al., 1998; Bang, Schultz & DeSalle, 2002; Bininda- Emonds et al., 2002). ACKNOWLEDGEMENTS This research was supported by National Science Foundation (NSF) grant BSR-9396249 to Livezey (PI/PD), NSF grant DEB-9815248 to B.C.L. (co-PI/PD) and R.L.Z. (co-PI), NSF grant TOL-0228604 to the Tree-of-Life group for the phylogeny of Theropoda (Livezey, co-PI), and National Museum of Natural His- tory grant RI-85337000 to R.L.Z. We thank the follow- ing individuals for granting and facilitating access to specimens or for special preparation of specimens in their institutions: G. Graves, S. Olson, R. Banks, J. Dean and F. Grady at National Museum of Natural History, Smithsonian Institution, Washington, DC; S. Rogers at Carnegie Museum of Natural History, Pitts- burgh, PA; J. Cracraft, G. Barrowclough and M. Norell at American Museum of Natural History, New York, NY; R. Payne and J. Hinshaw at University of Michi- gan, Museum of Zoology, Ann Arbor, MI; J. V. Remsen at Museum of Natural Science, Louisiana State Uni- versity, Baton Rouge, LA; P. Currie at Royal Tyrrell Museum of Palaeontology, Drumheller, AB, Canada; S. Chapman and A. Milner at British Museum (Natural History), London, UK; R. Prys-Jones and J. Cooper at Natural History Museum, Tring, UK; E. Pasquet, C. Lef?vre, D. Gouget and M. V?ran at Mus?um National d?Histoire Naturelle, Paris, France; D. Unwin at Hum- boldt-Universit?t, Berlin, Germany; G. Mayr at Fors- chungsinstitut Senckenberg, Frankfurt, Germany; H. Mayr at Bayerische Staatssammlung f?r Pal?ontolo- gie und Geology, Munich, Germany; G. Viohl at Jura- Museums, Eichst?tt, Germany; J. Sanz and F. Ortega at Universidad Auton?ma de Madrid, Madrid, Spain; W. Longmore and L. Christidis at Museum Victoria, Melbourne, Australia; P. Murray at Museum of Cen- tral Australia, Alice Springs, Australia; A. Tennyson and S. Bartle at National Museum of Natural History (Te Papa Tongarewa), Wellington, New Zealand; and P. Scofield and H. Schlumpf at Canterbury Museum, Christchurch Univeristy, Christchurch, New Zealand. We are grateful to M. C. McKitrick for granting access to unpublished myological data on Charadriiformes, P. Murray for access to unpublished material on Dromor- nithidae, and S. Olson for unpublished notes on Ste- atornis; K. M?ller for his generous assistance with use 56 B. C. LIVEZEY and R. L. 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Netherlands Journal of Zoology 47: 255?287. Zweers GA, Vanden Berge JC. 1997b. Birds at geological boundaries. Zoology 100: 183?202. Zweers GA, Vanden Berge JC, Berkhoudt H. 1997. Evolu- tionary patterns of avian trophic diversification. Zoology 100: 25?57. APPENDIX 1 The following proposal for a higher-order classification of Class Aves is intended to encode natural groups as recovered in the foregoing phylogenetic analysis of the companion morphological data (Livezey & Zusi, 2006). Procedures of phylogenetic classification followed Wiley (1981) and Cracraft (1974b, 1978). We avoided the current divergence between rank-free Phylocode and traditional Linnean formats, as well as the palae- ontological penchant for ?stem? and ?crown? groups. The four principles considered here were: (i) hierarchical grouping by phylogenetic relationship; (ii) preference to familiar, available taxa; (iii) preference given to names based on included type genera, where all other considerations are equal; and (iv) coordination of taxonomic ranks by similar emendation of names. Higher-order group names were chosen to conform most closely with others published comparatively recently and conformal with several conventions: (i) incertae sedis (indicative of unconfirmed monophyly and/or content); and (ii) sedis mutabilis, where a taxon comprises three or more members of equal rank (i.e. lineages in polytomy). Among Neornithes, the sequencing convention (Wiley, 1981) was used only for ordinal ranks for some taxa traditionally considered to be Gruiformes. The comparatively simplified phylogeny upon which this classification is based is depicted in Figure 11. Exemplary taxa (often nominate genera) actually coded and analysed are shown explicitly in trees (Figs 13?18), and the higher-order taxa (mostly fami- lies) that correspond to the exemplars appear in the fol- lowing classification. Families included in higher taxa are limited largely to those represented by exemplars analysed, e.g. two subfamilies of Anatidae as opposed to all recognized by Livezey (1997b). This convention is most notable with respect to the exceptionally diverse and minimally represented Passeriformes and embrac- ing superorder. However, inclusion of comparatively recently recognized family group names within two orders of Superorder Psittacimorphae (Psittaciformes and Columbiformes), not represented among exem- plars, was intended to counter under-representation of non-passeriform clades as well as to accommodate uncertainty of phylogenetic placement of exemplary genera with respect to recognized (sub)families. No protocol for derivation of taxa of higher rank has been codified; a recent attempt was that by Sibley et al. (1988, 1990). The proposal made here is but one of many alternatives, including 150 years of provi- sional classifications. Although the ?sequence conven- tion? might be applied to the very highest taxonomic ranks, we elected to retain distinct, dichotomous taxa to draw attention to these highest-order ranks within Neornithes; this permits hierarchical clarity, but it also results in some redundancy of higher-order names (Table 2). However, the convention was applied to names for some ranks listed prior to the Neornithes ? parvclasses, sections, etc. (cf. Ratitae). We chose to use historical names over proliferation of new (semi)synonyms to preserve taxonomic history and despite the fact that this perpetuated some names of variably different content and inappropriate etymol- ogy and diagnosis (as understood by the original authors of these taxa). In some cases, acceptable taxa for some highest-order ranks were not found, and in these few instances new taxa were proposed, e.g. Ter- restrornithes, and hyphenates of several others. Among several frequently cited, 19th-century authors of higher-order taxa, two ? Rafinesque (1815) and Leach (1820) ? were disqualified following the adjudication of most modern systematists (Bock, 1994). We avoided group names of strongly militaristic overtones, e.g. the ?brigades? and ?legions? of Gadow (1893). We found the compendia by Lambrecht (1933), Wetmore (1930, 1960), Mayr (1958), Storer (1960a, 88 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 1971b), Brodkorb (1963, 1964, 1967, 1971b, 1978), Sib- ley et al. (1988, 1990) and Sibley & Ahlquist (1972, 1990) to be critical for ascertainment of taxonomic authorships. Many taxa named by Stresemann (1959) or delimited by Verheyen (1961) also were adopted. Full citations of references for higher-order taxa were not included herein for the sake of brevity. For taxa of rank greater than ordinal, we adopted, where possible, the system of suffixes proposed by Sibley et al. (1988, 1990) and Sibley & Ahlquist (1990). Given the dubious comparability of taxonomic ranks of higher-order names, we elected to forego annotation of taxa of supraordinal rank with the conventional specification of ?new rank? in this proposal. The higher-order names given in bold type reflect inferred groupings, and although beyond the ranks of pervue by the ICZN, we provide diagnostic and sup- portive characters for these taxa (Table 2; Livezey & Zusi, 2006), whether new or conserved from historical works. The latter basis was preferred for naming higher-order groups, with inexactitude of content con- ceded as in such names used by Clarke & Norell (2002). For example, the content of an established name (e.g. Ornithurae) implicitly is defined herein (i.e. sensu present study). Taxonomy bearing on outgroup taxa (i.e. those preceeding Neornithes) are considered espe- cially tentative. A minor point of contention is the posi- tion of Lithornis (Houde, 1988), a relative to palaeognathous Neornithes, inferred to be the sister- group of Tinamidae by Clarke & Norell (2002) and Clarke (2004), but inferred to be the sister-group of Neornithes by Clarke & Chiappe (2001), Leonard et al. (2005) and the present analysis (Fig. 12). Should a sis- ter-group relationship between Lithornis and modern palaeognathous taxa be favoured, Panpalaeog- nathae Gauthier and de Queiroz, 2001 is available for the clade comprising both groups. Use of the tradi- tional, higher-order taxon Carinatae Merrem, 1813, was precluded by provisional monophyly of Hesperor- nis and Ichthyornis in the present study (see also Rees & Lindgren, 2005), avoiding as well the implication of the name with respect to secondary obsolesence or loss of the carina sterni among Neornithes (Livezey, 2003a). Supraordinal names proposed herein were intended to follow the convention of seniority of taxa and (to a lesser degree) included type family, as is typical of lower-scale taxa. Three important higher-order syn- onyms are: Neoaves Sibley et al., 1988, senior to Plethornithes Groth & Barrowclough, 1999 (avail- ability questionable in present context), and distinct from Eoaves Sibley et al., 1988. There are also, two taxa ? ?Cracrafti? and ?Conglomerati? ? informally pro- posed as alternatives by Slack et al. (2006a). Unused herein is the potentially useful higher-order name Euornithes Sereno, 1999. Gaviomorphae replaced Colymbimorphae (Gadow, 1893) by revision of the former type genus Colymbus. We also replaced the senior, unfamiliar Dypsporomorphae Ogilvie- Grant, 1898, with the more familiar derivation Pelecanimorphae. Similar reasoning led to the suppression of Aetomorphae (Huxley, 1864) by Falconimorphae (Seebohm, 1890), the latter derived from an included ordinal taxon, but junior to the less representative alternative of Strigimorphae (Wagler, 1830). Uniform emendation of superorders was not imposed herein for non-Neornithes. The importance of dichotomy among higher-order names of comparable rank for comparability with the phyloge- netic tree resulted in redundancy of supraordinal names for some clades, e.g. Subdivision Dendrorni- thes comprises a single Section Raptores, which in turn comprises a single Superorder Raptoromor- phae. Antiquity of historical, higher-order taxa often resulted in minor differences in content ? e.g. Anom- alogonates Garrod, 1874 optimally should exclude the Cuculiformes for consistency with the myological diagnosis implied by the name. Further study will probably subdivide Superorder Passerimorphae so as to comprise the Superorder Coracomorphae Huxley, 1867 and Superorder Passerimorphae (Linnaeus, 1758), the latter to com- prise Piciformes and Passeriformes (cf. Manegold, 2005). Within the Passeriformes, the most suspicious anomaly in the present analysis was that of Menura; broader samples may justify its transfer to the Passe- rida, and thereby the first subordinal taxon instead may comprise the Acanthisittidae (Barker et al., 2002, 2004; Ericson et al., 2002a, b), representatives of which were not available for analysis here. Principally because of limitations on available specimens, delegation of ordinal rank to the extinct elephant-birds (Aepyornithiformes) was favoured marginally over inclusion at lower rank within the Struthioniformes. A detailed classification of Order Anseriformes, including fossil taxa, was presented by Livezey (1997b), and a preliminary classification of the traditionally delimited Gruiformes, significantly revised by the present analysis relative to that pro- posed by Livezey (1998b), which tentatively recog- nized monophyly of the traditional order. (Sub)fossil taxa are plausible candidates for inclusion as sequen- tial sister-groups of Galloanseromorphae (Diatr- ymidae, Gastornithidae and Dromornithidae) or membership within the Galliformes (Sylviornithidae) or Anseriformes (e.g. Mourer-Chauvir? & Balouet, 2005) and are included based on published description (e.g. Cracraft, 1968; Livezey, 1997a) and cursory examinations. Material essential for rigorous diagno- sis is rare or lacking, but we considered provisional hypotheses to indicate groupings likely but as yet undemonstrated by formal analysis preferable in such cases to no inference presented at all. HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 89 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Subclass Avialae Gauthier, 1986 [Infraclass Alvarezsauria (Bonaparte, 1991)] Infraclass Aves Linnaeus, 1758 Parvclass Palaeoaves; new name Superorder Archaeornithes Gadow, 1893 Order Archaeopterygiformes F?rbringer, 1888 Family Archaeopterygidae Huxley, 1872 Order Confuciusornithiformes (Chiappe et al., 1999) Family Confuciusornithidae Hou et al., 1995 Superorder Euenantiornithes Walker, 1981; incertae sedis Order Rahonaviformes; new name Family Rahonavidae; new name Order Apsaraviformes; new name Family Apsaravidae; new name Parvclass Ornithurae Haeckel, 1866 Superorder Odontoholomorphae (Stejneger, 1885) Order Hesperornithiformes (F?rbringer, 1888) Family Hesperornithidae Marsh, 1872 Order Ichthyornithiformes (Marsh, 1873) Family Ichthyornithidae (Marsh, 1873) Parvclass Eoaves Sibley et al., 1988; incertae sedis Order Lithornithiformes Houde, 1988 Family Lithornithidae Houde, 1988 Parvclass Neornithes Gadow, 1893 Cohort Palaeognathae Pycraft, 1900 Subcohort Crypturi Goodchild, 1891 Superorder Dromaeomorphae (Huxley, 1867) Order Tinamiformes (Huxley, 1872) Family Tinamidae Gray, 1840 Subcohort Ratitae Merrem, 1813 [Superorder Apterygimorphae; incertae sedis] Order Apterygiformes (Haeckel, 1866) Family Apterygidae Gray, 1840 Order Dinornithiformes (Gadow, 1893) [Family Anomalopterygidae (Archey, 1941)] [Family Dinornithidae (Owen, 1843)] Superorder Casuariimorphae; new taxon Order Casuariiformes (Forbes, 1884) Family Casuariidae Kaup, 1847 Family Dromaiidae Richmond, 1908 Superorder Struthionimorphae; new taxon Order Aepyornithiformes (Newton, 1884) Family Aepyornithidae Bonaparte, 1853 Order Struthioniformes (Latham, 1790) Family Struthionidae Vigors, 1825 Family Rheidae (Bonaparte, 1853) Cohort Neognathae Pycraft, 1900 Subcohort Galloanserae Sibley & Ahlquist, 1990 Superorder Galloanserimorphae (Sibley et al., 1988) Order Galliformes (Temminck, 1820) Suborder Craci Sibley et al., 1988; incertae sedis Superfamily Megapodioidea (Lesson, 1831) Family Megapodiidae Lesson, 1831 [Family Sylviornithidae Mourer-Chauvir? & Balouet, 2005] 90 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Superfamily Cracoidea (Vigors, 1825) Family Cracidae Vigors, 1825 Suborder Phasiani (Vigors, 1825) Superfamily Meleagridoidea (Gray, 1840) Family Meleagrididae Gray, 1840 Superfamily Phasianoidea (Vigors, 1825); sedis mutabilis Family Phasianidae (Vigors, 1825); sedis mutabilis (Sub)Family Tetraonidae Vigors, 1825 Subfamily Perdicinae (Bonaparte, 1838) Subfamily Odontophorinae Gould, 1844 Subfamily Phasianinae Vigors, 1825 Subfamily Numidinae Reichenbach, 1850 [Order Dromornithiformes F?rbringer, 1888] Family Dromornithidae Vigors, 1825 [Order Diatrymiformes (Shufeldt, 1913)] Family Diatrymidae Shufeldt, 1913 Order Anseriformes (Wagler, 1831) Suborder Anhimae Wetmore & Miller, 1926 Family Anhimidae Stejneger, 1885 Suborder Anseres Wagler, 1831 Superfamily Anseranatoidea (Sclater, 1880) Family Anseranatidae Sclater, 1880 Superfamily Anatoidea (Vigors, 1825) [Family Presbyornithidae Wetmore, 1926] Family Anatidae (Vigors, 1825) Subfamily Anserinae Vigors, 1825 Subfamily Anatinae (Vigors, 1825) Subcohort Neoaves Sibley et al., 1988 Division Natatores Baird, 1858 Subdivision Pygopodo-tubinares; new taxon Superorder Gaviomorphae; new taxon Order Gaviiformes Wetmore & Miller, 1926 Family Gaviidae Allen, 1897 Order Podicipediformes (F?rbringer, 1888) Family Podicipedidae Bonaparte, 1831 Superorder Procellariimorphae (F?rbringer, 1888) Order Sphenisciformes Sharpe, 1891 Family Spheniscidae Bonaparte, 1831 Order Procellariiformes F?rbringer, 1888 Suborder Pelecanoidi (Gray, 1871) Family Pelecanoididae Gray, 1871 Suborder Procellarae (Gadow, 1893) Superfamily Oceanitoidea (Huxley, 1868) Family Oceanitidae Forbes, 1882 Superfamily Procellarioidea (F?rbringer, 1888) Family Procellariidae Vigors, 1825 Subfamily Procellariinae (Vigors, 1825) Subfamily Pachyptilinae (Oliver, 1930) Family Diomedeidae Gray, 1840 Subdivision Stegano-grallatores; new taxon Superorder Pelecanimorphae Huxley, 1867 [Order Odontopterygiformes (Spulski, 1910)] Family Odontopterygidae Lambrecht, 1933 Order Balaenicipitiformes (Sclater, 1924) Suborder Balaenicipites (Sclater, 1924) HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 91 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Family Balaenicipitidae (Sclater, 1924) Order Pelecaniformes Sharpe, 1891 Suborder Phaethontes (Sharpe, 1891) Family Phaethontidae Brandt, 1831 Suborder Steganopodes (Chandler, 1916) Infraorder Fregatides (Sharpe, 1891) Superfamily Fregatoidea (Garrod, 1874) Family Fregatidae Garrod, 1874 Infraorder Pelecanides (Sharpe, 1891) Parvorder Pelecanida (Sharpe, 1891); new rank Family Pelecanidae Vigors, 1825 Parvorder Sulida (Reichenbach, 1849); new rank Superfamily Suloidea (Reichenbach, 1849) Family Sulidae Reichenbach, 1849 Superfamily Phalacrocoracoidea (Bonaparte, 1854) Family Phalacrocoracidae (Bonaparte, 1854) Family Anhingidae Ridgway, 1887 Superorder Ciconiimorphae (Garrod, 1874) Order Ciconiiformes Garrod, 1874 Suborder Scopi (Bonaparte, 1853) Family Scopidae (Bonaparte, 1853) Suborder Ciconiae (Bonaparte, 1874) Superfamily Ciconioidea (Sundevall, 1836) Family Ciconiidae Sundevall, 1836 Family Phoenicopteridae Bonaparte, 1838 Superfamily Threskiornithoidea (Richmond, 1917) Family Threskiornithidae Richmond, 1917 Family Plataleidae (Bonaparte, 1838) Order Ardeiformes (Wagler, 1831) Family Cochleariidae Ridgway, 1887 Family Ardeidae Vigors, 1825 Subfamily Botaurinae Bock, 1956 Tribe Botaurini (Bock, 1956) Tribe Tigriornithini Bock, 1956 Subfamily Ardeinae (Vigors, 1825) Tribe Nycticoracini Bock, 1956 Tribe Ardeini Bock, 1956 Division Terrestrornithes; new taxon Subdivision Telmatorae (Lowe, 1931) Superorder Charadriimorphae Huxley, 1867 Order Gruiformes (Bonaparte, 1854) Suborder Cariamae (Wagler, 1830) Infraorder Otides Sibley et al., 1988 Family Otididae Gray, 1840 Infraorder Cariamides (F?rbringer, 1888) Superfamily Cariamoidea (Gray, 1853); sedis mutabilis [Family Bathornithidae Wetmore, 1933] Family Cariamidae Bonaparte, 1853 [Family Phorusrhacidae (Ameghino, 1899)] Suborder Eurypygae (F?rbringer, 1888) Infraorder Eurypygides Sibley et al., 1988 Family Eurypygidae Selby, 1840 Infraorder Rhynochetides Sharpe, 1891 Family Rhynochetidae Newton, 1868 92 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Family Aptornithidae Bonaparte, 1856 Suborder Grues Bonaparte, 1854 Superfamily Psophioidea (Bonaparte, 1831) Family Psophiidae Bonaparte, 1831 Superfamily Gruoidea (Vigors, 1825) Family Aramidae Bonaparte, 1854 Family Gruidae Vigors, 1825 Order Turniciformes (Huxley, 1868); incertae sedis Family Turnicidae (Gray, 1840) Family Mesitornithidae Wetmore, 1960 Order Ralliformes (Reichenbach, 1854) Family Heliornithidae Gray, 1841 Family Rallidae (Reichenbach, 1854) Order Charadriiformes (F?rbringer, 1888) Suborder Pedionomae (Gadow, 1893) Family Pedionomidae Gadow, 1893 Suborder Parrae (Gadow, 1893) Family Jacanidae Stejneger, 1885 Family Rostratulidae Ridgway, 1919 Suborder Limicolae (Beddard, 1898) Infraorder Dromaides (Sharpe, 1891) Family Dromadidae Gray, 1840 Infraorder Scolopacides (Strauch, 1978) Superfamily Thinocoroidea (Gray, 1845) Family Thinocoridae (Gray, 1845) Superfamily Scolopacoidea (Vigors, 1825) Family Scolopacidae Vigors, 1825 Family Phalaropodidae Bonaparte, 1831 Infraorder Charadriides (Huxley, 1867); incertae sedis Superfamily Charadrioidea (Vigors, 1825) Family Charadriidae Vigors, 1825 Superfamily Glareoloidea (Brehm, 1831) Family Glareolidae Brehm, 1831 Subfamily Glareolinae Brehm, 1831 Subfamily Cursoriinae Gray, 1840 Superfamily Burhinoidea (Mathews, 1912) Family Burhinidae Mathews, 1912 Superfamily Haematopoidea (Bonaparte, 1838) Family Haematopidae Bonaparte, 1838 Subfamily Haematopodinae (Bonaparte, 1838) Subfamily Ibidorhynchinae Bonaparte, 1856 Family Recurvirostridae (Bonaparte, 1831) Subfamily Recurvirostrinae Bonaparte, 1831 Subfamily Himantopodinae Reichenbach, 1849 Tribe Himantopodini Sibley et al., 1988 Tribe Cladorhynchini; new taxon Suborder Lari Sharpe, 1891; incertae sedis Infraorder Chionidides Sharpe, 1891 Family Chionididae Lesson, 1828 Infraorder Alcides (Sharpe, 1891) Family Alcidae (Vigors, 1825) Infraorder Larides (Sharpe, 1891) Superfamily Laroidea (Bonaparte, 1831) Family Stercorariidae Gray, 1870 Family Laridae (Bonaparte, 1831) Subfamily Larinae Bonaparte, 1831 HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 93 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Subfamily Sterninae Bonaparte, 1838 Superfamily Rynchopoidea (Bonaparte, 1838) Family Rynchopidae (Bonaparte, 1838) Subdivision Dendrornithes (Verheyen, 1961) Section Raptores Baird, 1858 Superorder Falconimorphae (Seebohm, 1890) Order Falconiformes Seebohm, 1890 [Suborder Teratornithi (Miller, 1909)] Suborder Cathartae (Coues, 1824) Family Cathartidae (Lafresnaye, 1839) Suborder Accipitres (Vieillot, 1816) Infraorder Serpentariides (Seebohm, 1890) Family Sagittariidae Finsch & Hartlaub, 1870 Infraorder Falconides (Sharpe, 1874) Superfamily Falconoidea (Vigors, 1824) Family Falconidae Vigors, 1824 Subfamily Falconinae Vigors, 1824 Subfamily Polyborinae Lafresnaye, 1839 Family Pandionidae Sclater & Salvin, 1873 Superfamily Accipitroidea (Vieillot, 1816) Family Accipitridae (Vieillot, 1816) Subfamily Accipitrinae (Vieillot, 1816) Subfamily Gypaetinae (Vieillot, 1816) Order Strigiformes (Wagler, 1830) Family Tytonidae (Mathews, 1912) Subfamily Tytoninae Mathews, 1912 Subfamily Phodilinae Beddard, 1898 Family Strigidae (Gray, 1840) Section Anomalogonates Garrod, 1874 Subsection Coccyges Huxley, 1867; incertae sedis Superorder Cuculimorphae Sibley et al., 1988 Order Opisthocomiformes (L?Herminer, 1837) Family Opisthocomidae Swainson, 1837 Order Cuculiformes (Wagler, 1830) Suborder Musophagi Seebohm, 1890 Family Musophagidae Bonaparte, 1831 Suborder Cuculi Wagler, 1830 Family Cuculidae Vigors, 1825; sedis mutabilis Subfamily Neomorphinae Shelley, 1891 Subfamily Centropodinae Horsfield, 1823 Subfamily Crotophaginae Swainson, 1837 Subfamily Cuculinae (Vigors, 1825) Subfamily Phaenicophacinae (Horsfield, 1822) Superorder Psittacimorphae (Huxley, 1867); incertae sedis Order Psittaciformes (Wagler, 1830); sedis mutabilis Family Nestoridae (Bonaparte, 1850) Family Psittacidae (Illiger, 1811) Family Cacatuidae Gray, 1840 Family Loriinidae Selby, 1836 Order Columbiformes (Garrod, 1874) Suborder Pterocletes (Boucard, 1876) Family Pteroclidae Bonaparte, 1831 Suborder Columbae (Latham, 1790) Family Columbidae (Illiger, 1811) Subfamily Columbinae (Illiger, 1811) Subfamily Didunculinae Gray, 1848 94 B. C. LIVEZEY and R. L. ZUSI ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Subfamily Gourinae Gray, 1840 Family Raphidae Wetmore, 1930 Subsection Incessores Baird, 1858 Superorder Cypselomorphae Huxley, 1867 Order Caprimulgiformes (Ridgway, 1891) Suborder Aegotheli Sibley et al., 1988 Family Aegothelidae (Bonaparte, 1853) Suborder Caprimulgi Ridgway, 1881; sedis mutabilis Family Caprimulgidae Vigors, 1825 Family Nyctibiidae (Chenu & Des Murs, 1851) Family Podargidae (Gray, 1840) Family Steatornithidae (Gray, 1846) Order Apodiformes Peters, 1940 Suborder Hemiprocni; new taxon Family Hemiprocnidae Oberholser, 1906 Suborder Apodi (Peters, 1940) Family Apodidae (Hartert, 1897) Subfamily Cypselinae Bonaparte, 1838 Subfamily Apodinae Hartert, 1897 Family Trochilidae Vigors, 1825 Subsection Trogones; new name Superorder Trogonomorphae; new taxon [Order Sandcoleiformes Houde & Olson, 1992] Family Sandcoleidae Houde & Olson, 1992 Order Coliiformes (Murie, 1872) Family Coliidae (Swainson, 1836) Order Trogoniformes Wetmore & Miller, 1926 Family Trogonidae Lesson, 1828 Subsection Pico-clamatores; new name Superorder Passerimorphae Sibley et al., 1988; sedis mutabilis Order Coraciiformes Forbes, 1884 Suborder Bucerotes F?rbringer, 1888 Infraorder Upupides (Seebohm, 1890) Family Upupidae Bonaparte, 1831 Family Phoeniculidae Sclater, 1924 Infraorder Bucerotides (F?rbringer, 1888) Family Bucerotidae (Gray, 1847) Suborder Halcyones (Forbes, 1884) Superfamily Motmotoidea (Gray, 1840) Family Motmotidae Gray, 1840 Superfamily Alcedinoidea (Stejneger, 1885) Family Todidae Vigors, 1825 Family Alcedinidae (Bonaparte, 1831) Subfamily Alcedininae Bonaparte, 1831 Subfamily Halcyoninae (Vigors, 1825) Suborder Coracii (Forbes, 1884) Infraorder Meropides (F?rbringer, 1888) Family Meropidae Vigors, 1825 Infraorder Coraciides (Wetmore & Miller, 1926) Superfamily Coracioidea (Vigors, 1825) Family Coraciidae Vigors, 1825 Superfamily Leptosomatoidea (Bonaparte, 1850) Family Leptosomatidae Bonaparte, 1850 Family Brachypteraciidae (Sharpe, 1892) Order Piciformes (Meyer & Wolf, 1810) Suborder Galbulae (F?rbringer, 1888) HIGHER-ORDER PHYLOGENY OF MODERN BIRDS 95 ? 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1?95 Family Galbulidae Bonaparte, 1831 Family Bucconidae Boie, 1826 Suborder Pici (Meyer & Wolf, 1810) Superfamily Capitonoidea (Bonaparte, 1840) Family Capitonidae Bonaparte, 1840 Family Rhamphastidae Vigors, 1825 Superfamily Picoidea (Vigors, 1825) Family Indicatoridae Swainson, 1837 Family Picidae Vigors, 1825 Subfamily Jynginae Bonaparte, 1838 Subfamily Picinae Bonaparte, 1838 Order Passeriformes (Linnaeus, 1758) Suborder Menurae (Sharpe, 1891) Family Menuridae (Lesson, 1828) Suborder Passeres Linnaeus, 1758 Infraorder Tyrannides Sibley et al., 1988 Family Tyrannidae Vigors, 1825 Family Pittidae Swainson, 1831 Infraorder Passerides (Linnaeus, 1758) Parvorder Corvida Sibley et al., 1988 Family Ptilinorhynchidae Gray, 1841 Family Corvidae Vigors, 1825 Parvorder Passerida Sibley et al., 1988 Family Bombycillidae Swainson, 1831 Family Paridae Vigors, 1825 Family Passeridae Illiger, 1811