DOI: 10.1126/science.1157704 , 1763 (2008); 320Science et al.Shannon J. Hackett, Evolutionary History A Phylogenomic Study of Birds Reveals Their www.sciencemag.org (this information is current as of June 27, 2008 ): The following resources related to this article are available online at http://www.sciencemag.org/cgi/content/full/320/5884/1763 version of this article at: including high-resolution figures, can be found in the onlineUpdated information and services, http://www.sciencemag.org/cgi/content/full/320/5884/1763/DC1 can be found at: Supporting Online Material http://www.sciencemag.org/cgi/content/full/320/5884/1763#otherarticles , 4 of which can be accessed for free: cites 24 articlesThis article http://www.sciencemag.org/cgi/collection/evolution Evolution : subject collectionsThis article appears in the following http://www.sciencemag.org/about/permissions.dtl in whole or in part can be found at: this article permission to reproduce of this article or about obtaining reprintsInformation about obtaining registered trademark of AAAS. is aScience2008 by the American Association for the Advancement of Science; all rights reserved. The title CopyrightAmerican Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by theScience o n J un e 27 , 2 00 8 w w w .s ci en ce m ag .o rg D ow nl oa de d fro m A Phylogenomic Study of Birds Reveals Their Evolutionary History Shannon J. Hackett,1* Rebecca T. Kimball,2*† Sushma Reddy,1* Rauri C. K. Bowie,1,3,4 Edward L. Braun,2 Michael J. Braun,5,6 Jena L. Chojnowski,2 W. Andrew Cox,2 Kin-Lan Han,2,5,6 John Harshman,1,7 Christopher J. Huddleston,5 Ben D. Marks,8 Kathleen J. Miglia,9 William S. Moore,9 Frederick H. Sheldon,8 David W. Steadman,10 Christopher C. Witt,8,11 Tamaki Yuri2,5 Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ~32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds. Although well studied, the evolutionaryrelationships among major avian groupsare contentious (1–6). Recovering deep evolutionary relationships in birds is difficult, probably reflecting a rapid divergence early in their evolutionary history (1–3, 7, 8) that has resulted in many distinctive, morphologically co- hesive groups (e.g., owls, parrots, and doves) with few, if any, extant intermediary forms linking them to other well-defined groups. This extreme radiation alsomakes it difficult to place fossil taxa, which further contributes to the difficulty in pre- cisely timing avian divergences (3, 9). Only two nodes at the base of the avian tree are consistently supported by both molecular and morphological phylogenetic studies (2–5, 10–14). The first divides the Paleognathae (ratites and tinamous) and Neognathae (all other birds), and the second splits the neognaths between the Galloanserae (chickens, ducks, and allies) and Neoaves (other neognaths). Although the Neoaves represents the majority of avian diversity (95% of extant species) and is the focus of most compar- ative studies, little consensus exists regarding rela- tionships within this clade (1–5, 8). The absence of intermediate forms linking well-defined groups, combined with the difficulty of resolving relation- ships, led to hypotheses that the base of Neoaves represents an unresolved evolutionary radiation (polytomy) (7, 8). Previous efforts to reconstruct these phylogenetic relationships have been limited by taxon sampling, the number of loci, and/or slowly evolving loci with limited power to re- solve short internodes [e.g., (3, 4, 10, 12, 14)]. Moreover, conflicting results have been obtained with morphology (13, 15), DNA-DNA hybridiza- tion (6), whole mitochondrial genomes (16–18), and different nuclear exon, ribosomal RNA, and intron sequences (1, 3, 4, 10, 12, 14). Phylogenomics is useful for resolving diffi- cult phylogenies and for verifying or overturning relationships created on the basis of single genes (19–21). We collected a large DNA sequence data set to address avian phylogenetic relation- ships from 171 species representing all but three nonpasserine families, all major passerine clades, and two crocodilian outgroups (22). Our alignment of 32 kb represents 19 nuclear loci located on 15 different chromosomes in the chicken genome (22), with introns (74%), coding exons (23%), and un- translated regions (UTRs) (3%). Data quality and sequence alignments were assessed before analy- ses (22).We analyzed the data using different optimali- ty criteria and distinct tree-search algorithms (22). Our sampling of many loci allowed us to as- sess whether relationships were supported by a sig- nal across the genome or were driven by a single locus.We (i) analyzed individual loci, (ii) conducted “gene-jackknifing” (excluding one locus at a time, then analyzing the remaining data) to determine whether conclusions were driven by a single locus, (iii) conducted a partitioned–maximum likelihood (ML) analysis (where each locus had a distinctive set of parameters), and (iv) coded the data as R (purine) or Y (pyrimidine) to avoid conclusions driven by base-compositional biases [e.g., (16)]. Analyses of individual loci showed that no single genewas able to recover all nodes identified with the concatenated data (Fig. 1). The low power of individual loci was themost pronounced in short and slowly evolving genes, which generally did not resolve any interordinal relationships (Fig. 1). Consistent with previous studies, we recov- ered genome-wide support for basal divergences between Paleognathae and Neognathae and between Galloanserae and Neoaves (Fig. 2) with robust support. The topology at the base of Neoaves, with extremely short internodes, indi- cated a rapid radiation (Fig. 3) that likely explains conflicts among previous studies. However, we consistently found several, well-supported, deep divisions within Neoaves (highlighted in different colors in Figs. 2 to 4). Our study (i) revealed robust higher-level groupings within Neoaves, (ii) suggested several previously unrecognized interordinal relation- ships, (iii) supported previously proposed clades, (iv) reinforced established relationships not con- sistently recovered in previous studies, and (v) found well-supported groupings at the tips of major clades. The results discussed below focus on groups that are found with multiple analytical methods and partitions and that exhibit strong support (ML bootstrap support ≥ 70%) (23). The largest clade in Neoaves was a well- supported land bird clade (green, node F, Fig. 2) (3) that contained the Passeriformes (perching birds, representing more than half of all avian species), which is allied with several morpholog- ically diverse orders. These included Piciformes (woodpeckers and allies), Falconiformes (hawks and falcons), Strigiformes (owls), Coraciiformes (kingfishers, hornbills, rollers, and allies), Psitta- ciformes (parrots), Coliiformes (mousebirds), and Trogoniformes (trogons). One of the most un- expected findings was the sister relationship between Passeriformes and Psittaciformes (node A, Fig. 2), with Falconidae (falcons) sister to this clade. This relationship varied slightly among analyses and gene-jackknifing (Fig. 1), yet the close relationship between passerines with par- rots and/or falcons appeared consistently. Sister to the land birds is the Charadriiformes (shorebirds, gulls, and alcids; yellow, node G, Fig. 2). This grouping seems to be driven pri- marily by the b-fibrinogen gene (FGB), because it was present in analyses of only this gene and disappeared when the gene was removed through jackknifing (Fig. 1). Regardless of the exact placement of the Charadriiformes in our analy- ses, we consistently support that this order is not basal within Neoaves (24) and thus refute the hypothesis that transitional shorebirds gave rise to all modern birds (7). Our phylogeny revealed a highly supported water bird clade (blue, node H, Fig. 2) (3, 14), including members of the Pelecaniformes (totipalmate birds), Ciconiifor- mes (storks and allies), Procellariiformes (tube- nosed birds), Sphenisciformes (penguins), and Gaviiformes (loons). Basal to the water birds were two clades of terrestrial and arboreal taxa 1Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA. 2Department of Zoology, University of Florida, Gainesville, FL 32611, USA. 3Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. 4Department of Science and Technology–National Research Foundation Centre of Excellence at the Percy FitzPatrick Institute, Department of Botany and Zoology, Stellenbosch University, Matieland 7602, South Africa. 5Department of Vertebrate Zoology, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA. 6Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA. 7Pepperwood Way, San Jose, CA 95124, USA. 8Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA. 9Department of Biological Sciences, Wayne State Uni- versity, 5047 Gullen Mall, Detroit, MI 48202, USA. 10Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. 11Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA. *These authors contributed equally to this work. †To whom correspondence should be addressed. E-mail: rkimball@ufl.edu www.sciencemag.org SCIENCE VOL 320 27 JUNE 2008 1763 REPORTS Fig. 1. Congruence of clades as determined from concatenated analyses and multiple data partitions. Nodes refer to groups in Fig. 2. Dark blue or dark gray cells indicate those with relationships present in maximum parsimony (MP) and ML [GARLI (31) and RAxML (32)] analyses (A) or in ML (B and C); light blue or light gray cells indicate relationships present with the exception of or inclusion of one taxon; and striped cells indicate relation- ships found by either GARLI or RAxML, but not both. The size of each data partition is listed below its name. (A) major partitions (BS, bootstrap support; dashes represent clades with less than 50% bootstrap support); (B) individual locus analyses; (C) gene-jackknifing analyses. n/a, not applicable. 27 JUNE 2008 VOL 320 SCIENCE www.sciencemag.org1764 REPORTS (node J, Fig. 2): Musophagiformes (turacos) and a clade (gray, node I, Fig. 2) including core Gruiformes (rails, cranes, and allies), Cuculifor- mes (cuckoos), and Otididae (bustards, which are typically considered as belonging toGruiformes). These latter relationships were also largely dependent on the presence of FGB (Fig. 1) and require further study to determine their validity. One of our most important findings was that several well-accepted orders were not mono- phyletic. Our analyses provided strong support that (i) Tinamiformes (tinamous) are found Sylvia Turdus Passer Ploceus Vidua Corvus Pipra Pitta Falco Alcedo Todus Bucco Capito Tockus Upupa Colius Tyto Strix Buteo Jacana Larus Turnix Acanthisitta Bombycilla Regulus Fringilla Picathartes Malurus Climacteris Menura Dendrocolaptes Scytalopus Grallaria Thamnophilus Mionectes Tyrannus Smithornis Sapayoa Alisterus Psittacula Micropsitta Chalcopsitta Platycercus Psittacus Cacatua Daptrius Herpetotheres Micrastur Cariama Momotus Brachypteracias Merops Galbula Megalaima Dryocopus Indicator Bucorvus Phoeniculus Pharomachrus Trogon Leptosomus Urocolius Phodilus Speotyto Gampsonyx Pandion Sagittarius Cathartes Sarcoramphus Arenaria Rostratula Pedionomus Thinocorus Dromas Burhinus Charadrius Phegornis Haematopus * * * * * * * * * * * * * * * * * * * * ** * * * * * * * * * * * * * * * * 60 98 54 67 81 77 73 64 69 * ** * * 98 98 * * * 71 85 * * * * ** * * 61 98 81 ** D B C A * * 98 96 96 * * Morus Ardea Gavia Grus Rallus Coua Treron Gallus Crax Anas Aythya Anser Rhea Anhinga Phalacrocorax Fregata Cochlearius Eudocimus Balaeniceps Scopus Pelecanus Ciconia Diomedea Oceanodroma Pelecanoides Puffinus Oceanites Eudyptula Corythaeola Tauraco Aramus Psophia Heliornis Sarothrura Himantornis Centropus Coccyzus Phaenicophaeus Cuculus Crotophaga Geococcyx Choriotis Eupodotis Opisthocomus Aegotheles Aerodramus Streptoprocne Hemiprocne Colibri Phaethornis Caprimulgus Eurostopodus Batrachostomus Podargus Nyctibius bracteatus Nyctibius grandis Steatornis Eurypyga Rhynochetos Columba Geotrygon Columbina Otidiphaps Mesitornis Monias Pterocles Syrrhaptes Phaethon lepturus Phaethon rubricauda Phoenicopterus Podiceps Alectura Megapodius Colinus Coturnix Rollulus Numida Biziura Malacorhynchus Oxyura Anseranas Chauna Apteryx Casuarius Dromaius Crypturellus Tinamus Eudromia Nothoprocta Struthio * ** * *72 68 * * ** * * 88 81 94 9889 86 * * * * * ** * * * * * 68 81 * * * * * 58 98 61 * * *66 * * * * * * * * * * * * * * 65 96 62 * * ** 98 98 99 60 97 Oscines Suboscines Psittaciformes Falconidae Strigiformes Accipitridae Cathartidae Charadriiformes Musophagiformes "Gruiformes" Cuculiformes Otididae Apodiformes Columbiformes Mesitornithidae Pteroclididae Phaethontidae Galliformes Anseriformes Tinamiformes Passeriformes Piciformes Coraciiformes Trogoniformes Coliiformes Struthioniformes Caprimulgiformes PelecaniiformesCiconiiformes Procellariiformes Gruiformes Gruiformes Sphenisciformes Gaviiformes Phoenicopteriformes Podicipediformes Cariamidae E F G H I J K L M N O P Q Coracias Fig. 2. ML analysis of the 19-locus data set (ln = –866017.07). ML bootstrap values > 70% from GARLI are indicated on the cladogram by thicker branches and are listed at nodes, with values of 100% designated by asterisks. Diamonds at nodes indicate congruence with MP analysis, and black vertical bars refer to ordinal designations (those that are dashed indicate paraphyly). The phylogenetic tree was rooted to crocodilian outgroups (not shown). Genera in bold are icertae sedis. Branch colors represent major clades supported in this study: land birds (green), charadriiforms (yellow), water birds (blue), core gruiforms and cuckoos (gray), apodiforms and caprimulgiforms (brown), galloanserae (orange), and paleognaths (purple). Large capital letters indicate groups discussed in the text and Fig. 1. www.sciencemag.org SCIENCE VOL 320 27 JUNE 2008 1765 REPORTS within Struithioniformes (ostriches and allies; purple, node Q, Fig. 2), (ii) Apodiformes (hum- mingbirds and swifts) are found within Capri- mulgiformes (nightjars and their allies; brown, node L, Fig. 2), and (iii) Piciformes are found with- in Coraciiformes (node C, Fig. 2). Typical Pele- caniformes and Ciconiiformes [sensu (13, 25)] were intermixed in a clade (Fig. 2) that excludes one traditional pelecaniform family: the Phaethon- tidae (tropicbirds). The Gruiformes represented at least four distinct clades in our tree (Fig. 4), de- pending on the circumscriptions of this order [reviewed in (6)]. Finally, Falconidae and Accipit- ridae (hawks and osprey) formed distinct clades in all analyses, rather than a monophyletic Falconi- formes (Fig. 2) (18). Several disparate taxa were robustly placed in our analyses. Cariamidae (seriemas) has tradi- tionally been classified as a gruiform, although convergence with Falconiformes was noted (6). We found strong support for placing Cariamidae within land birds near other raptorial groups. Leptosomus (cuckoo roller) is generally placed within Coraciiformes, though a relationship with Falconiformes has also been suggested (6). Our data set placed Leptosomus sister to a clade in- cluding Piciformes, Coraciiformes, and Trogoni- formes (node D, Fig. 2). Our results suggest resolution of some contro- versial groupings. For example, Cathartidae (New World vultures)—traditionally placed within Falconiformes—were previously allied with Cic- oniidae (storks) (6). However, our phylogeny demonstrated no affinity with storks [see also (3, 18, 26)] and instead strongly supported placement of Cathartidae within the land birds (usually with Accipitridae). We support that Turnix (buttonquail) belongs within the Charadriiformes (3, 4, 27) and that Podicipediformes (grebes) and Phoenicopteriformes (flamingos; node N, Fig. 2) (14) are sister taxa. Finally, we recovered a sister relationship between Rhynochetos (kagu) and Eurypyga (sunbittern) (node M, Fig. 2) (28): two monospecific and geographically disparate fam- ilies that grouped outside of the core Gruiiformes. The previously proposed division of Neoaves into Coronaves andMetaves is driven by two loci (4) in our analyses (Fig. 1) and may not represent the species tree. Many taxa assigned to Metaves are composed of small numbers of closely related extant species, including Mesitornithidae (mesi- tes), Phaethontidae, Pteroclididae (sandgrouse), and Columbiformes (pigeons and doves). The dif- ficulty in placing them may be driven by long, unbreakable branches leading to the tips (Fig. 3). The enigmaticOpisthocomus (hoatzin) still cannot be confidently placed, but some putative sister relationships can be rejected (29). Modern birds occupy a wide diversity of niches and exhibit a variety of behaviors. The broad structure of our phylogeny suggested di- versification along general ecological divisions, such as water birds, shorebirds, and land birds. However, adaptations to these environments clear- ly arose multiple times (4), because many aquatic birds were not part of the water bird clade (e.g., tropicbirds, flamingos, and grebes) and terrestrial birds were found outside of the land bird clade (e.g., turacos, doves, sandgrouse, and cuckoos). Our phylogeny also indicated several distinctive niches, such as nocturnal (owls, nightjars, and allies), raptorial (falcons, hawks, eagles, New World vultures, seriema, and owls), or pelagic (tubenosed birds, frigatebirds, and tropicbirds) lifestyles, have evolved multiple times. Further- more, our results reinterpret the evolution of various adaptations (e.g., the diurnal Apodifor- mes evolved from nocturnal/crepuscular Capri- mulgiformes, and flighted Tinamiformes arose within the flightless Struthioniformes) and bio- geographic patterns (e.g., the New Caledonian kagu and Neotropical sunbittern are sister taxa). Given the number of nonmonophyletic groups in our study, we compared our results with major classifications [supporting online mate- rial (SOM) text]. Unexpectedly, roughly the same percentage (35%) of orders defined by different classifications (13, 25, 30) was not monophyletic relative to the results of our study (Fig. 4). Some orders, such as Gruiformes and the broadly encompassing Ciconiiformes [sensu (30)], were particularly problematic. Other tra- ditional orders were not monophyletic be- cause of the exclusion or inclusion of one or a few taxa (e.g., placing Turnix within Cha- radriiformes contradicts all three classifica- tions). Only six orders were defined consistently across taxonomies and monophyletic in our study (Fig. 4). Given our results, conclusions from comparative studies that depended upon these classifications may need to be re-evaluated in light of this understanding of avian evolution. Deciphering the roots of the avian tree of life has been a lingering problem in evolu- tionary biology. The inclusion of multiple loci with diverse rates of evolution, particularly the large proportion of rapidly evolving in- trons, yielded a well-supported phylogenetic tree at multiple taxonomic depths. Although some higher-level avian relationships remain unresolved, simulations suggest that addition- al sequence data from rapidly evolving loci may resolve these remaining questions (1). It is also evident that future classifications will 0.1 Fig. 3. ML phylogram demonstrating the short internodes at the base of Neoaves and highlighting certain extreme examples of rate variation across avian lineages. Colors are as in Fig. 2. Scale bar indicates substitutions per site. Figure S1 shows the phylogram with taxon names. 27 JUNE 2008 VOL 320 SCIENCE www.sciencemag.org1766 REPORTS change dramatically, based on our phyloge- netic study, and that our results will stimulate comparative studies to address the growing number of questions regarding the evolution of birds. References and Notes 1. J. L. Chojnowski, R. T. Kimball, E. L. Braun, Gene 410, 89 (2008). 2. J. Cracraft et al., in Assembling the Tree of Life, J. Cracraft, M. J. Donoghue, Eds. (Oxford Univ. Press, New York, 2004), pp. 468–489. 3. P. G. P. Ericson et al., Biol. Lett. 2, 543 (2006). 4. M. G. Fain, P. Houde, Evolution Int. J. Org. Evolution 58, 2558 (2004). 5. J. Harshman, in Reproductive Biology and Phylogeny of Birds, B. G. M. Jamieson, Ed. (Science Publishers, Enfield, NH, 2007), pp. 1–35. 6. C. G. Sibley, J. E. Ahlquist, Phylogeny and Classification of Birds: A Study in Molecular Evolution (Yale Univ. Press, New Haven, CT, 1990). 7. A. Feduccia, Science 267, 637 (1995). 8. S. Poe, A. L. Chubb, Evolution Int. J. Org. Evolution 58, 404 (2004). 9. J. W. Brown, J. S. Rest, J. Garcia-Moreno, M. D. Sorenson, D. P. Mindell, BMC Biol. 6, 6 (2008). 10. A. L. Chubb, Mol. Phylogenet. Evol. 30, 140 (2004). 11. J. Cracraft, J. Clarke, in New Perspectives on the Origin and Early Evolution of Birds: Proceedings of the International Symposium in Honor of John H. Ostrom, J. Gauthier, L. F. Gall, Eds. (Yale Univ. Press, New Haven, CT, 2001), pp. 143–156. 12. J. G. Groth, G. F. Barrowclough, Mol. Phylogenet. Evol. 12, 115 (1999). 13. B. C. Livezey, R. L. Zusi, Zool. J. Linn. Soc. 149, 1 (2007). 14. M. van Tuinen, D. B. Butvill, J. A. W. Kirsch, S. B. Hedges, Proc. R. Soc. London Ser. B 268, 1345 (2001). 15. G. Mayr, J. Clarke, Cladistics 19, 527 (2003). 16. E. L. Braun, R. T. Kimball, Syst. Biol. 51, 614 (2002). 17. D. P. Mindell et al., Syst. Biol. 48, 138 (1999). 18. K. E. Slack, F. Delsuc, P. A. Mclenachan, U. Arnason, D. Penny, Mol. Phylogenet. Evol. 42, 1 (2007). 19. F. Delsuc, H. Brinkmann, H. Philippe, Nat. Rev. Genet. 6, 361 (2005). 20. E. Jiménez-Guri, H. Philippe, B. Okamura, P. W. H. Holland, Science 317, 116 (2007). 21. W. J. Murphy, P. A. Pevzner, S. J. O’Brien, Trends Genet. 20, 631 (2004). 22. Materials and methods are available as supporting material on Science Online. 23. D. M. Hillis, J. J. Bull, Syst. Biol. 42, 182 (1993). 24. T. Paton, O. Haddrath, A. J. Baker, Proc. R. Soc. London Ser. B 269, 839 (2002). 25. J. L. Peters et al., Check-list of Birds of the World, J. L. Peters et al., Eds. (Museum of Comparative Anatomy, Cambridge, MA, 1931 to 1979), vols. I to XV. 26. C. S. Griffiths, Auk 111, 787 (1994). 27. T. A. Paton, A. J. Baker, J. G. Groth, G. F. Barrowclough, Mol. Phylogenet. Evol. 29, 268 (2003). 28. J. Cracraft, Geobios Memoire Spec. 6, 25 (1982). 29. M. D. Sorenson, E. Oneal, J. García-Moreno, D. P. Mindell, Mol. Biol. Evol. 20, 1484 (2003). 30. C. G. Sibley, B. L. Monroe Jr., Distribution and Taxonomy of Birds of the World (Yale Univ. Press, New Haven, CT, 1990). 31. D. J. Zwickl, thesis, University of Texas at Austin (2006). 32. A. Stamatakis, Bioinformatics 22, 2688 (2006). 33. This work is a contribution of the Early Bird project, supported by NSF’s Assembling the Tree of Life program (DEB-0228675, DEB-0228682, DEB-0228688, and DEB-0228617). We thank the American Museum of Natural History, Australian National Wildlife Collection, Burke Museum of Natural History and Culture (University of Washington), Field Museum of Natural History, University of Kansas Natural History Museum and Biodiversity Center, L. Densmore private collection, Louisiana State University Museum of Natural Science, Marjorie Barrick Museum (University of Nevada, Las Vegas), Museum of Southwestern Biology (University of New Mexico), Museum of Vertebrate Zoology (University of California, Berkeley), Museum Victoria, National Museum of Natural History, San Francisco Zoological Garden, and Zoological Museum University of Copenhagen, as well as many different collectors for tissue samples (table S1). We appreciate support from D. Zwickl and R. Ree for analysis; the DePaul Bioinformatics Group, part of the Illinois Bio-grid at DePaul University, for access to their supercomputing facilities; and J. Bates, D. Levey, P. Makovicky, T. Schulenberg, and P. Soltis for comments. Z. Bear, N. Block, B. Burkley, M. Burns, Z. Burns, S. Coplowitz, R. Flynn, K. Hammons, V. Heimer-Torres, E. Sackett-Hermann, Fig. 4. Our phylogeny differs from and agrees with previous classifications. We merged well-supported (>70% bootstrap values) monophyletic clades at the tips with the same ordinal designation across all three classifications (e.g., 24 species called Passerines). Only higher relationships supported by bootstrap values >50% are shown. Colors are as in Fig. 2. Color bars to the right of the tree show membership in three different classifications: Peters’ (25) (left), Sibley and Monroe’s (30) (middle), and Livezey and Zusi’s (13) (right). Black text within the bars indicates monophyletic orders in our phylogeny, whereas white text within the bars indicates nonmonophyletic orders. Ordinal name codes: ANS (Anseriformes), APO (Apodiformes), APT (Apterygiformes), ARD (Ardeiformes), BAL (Balaenicipitiformes), BUC (Buceroti- formes), CAP (Caprimulgiformes), CAS (Casuariiformes), CHA (Charadriiformes), CIC (Ciconiiformes), CLM (Columbiformes), COL (Coliiformes), COR (Coraciiformes), CRA (Craciformes), CUC (Cuculiformes), FAL (Falconiformes), GAL (Galliformes), GAV (Gaviiformes), GLB (Galbuliformes), GRU (Gruiformes), MUS (Musophagiformes), OPI (Opisthocomiformes), PAS (Passeriformes), PEL (Pelecaniformes), PIC (Picifor- mes), POD (Podicipediformes), PRO (Procellariiformes), PSI (Psittaciformes), RAL (Ralliformes), RHE (Rheiformes), SPH (Sphenisciformes), STH (Struthioniformes), STR (Strigiformes), TIN (Tinamiformes), TRC (Trochiliformes), TRO (Trogoniformes), TUR (Turniciformes), and UPU (Upupiformes). www.sciencemag.org SCIENCE VOL 320 27 JUNE 2008 1767 REPORTS A. Hudson, S. Hunter-Smith, S. Kearney, L. Kimball, K. Rozofsky, J. Smith, and P. Tester provided assistance in the lab. Sequence accession numbers in GenBank are EU737149 to EU740386, EF521416 to EF521576, and EU302706 to EU302748. Supporting Online Material www.sciencemag.org/cgi/content/full/320/5884/1763/DC1 Materials and Methods SOM Text Figs. S1 to S3 Tables S1 to S3 References 12 March 2008; accepted 29 May 2008 10.1126/science.1157704 A Significant Upward Shift in Plant Species Optimum Elevation During the 20th Century J. Lenoir,1* J. C. Gégout,1 P. A. Marquet,2,3,4 P. de Ruffray,5 H. Brisse6 Spatial fingerprints of climate change on biotic communities are usually associated with changes in the distribution of species at their latitudinal or altitudinal extremes. By comparing the altitudinal distribution of 171 forest plant species between 1905 and 1985 and 1986 and 2005 along the entire elevation range (0 to 2600 meters above sea level) in west Europe, we show that climate warming has resulted in a significant upward shift in species optimum elevation averaging 29 meters per decade. The shift is larger for species restricted to mountain habitats and for grassy species, which are characterized by faster population turnover. Our study shows that climate change affects the spatial core of the distributional range of plant species, in addition to their distributional margins, as previously reported. Recent warming has induced biologicaland ecological responses from animalsand plants throughout the world (1–3). Consistent responses to global warming or “finger- prints” are apparent in the phenology and distri- bution of species (1–5). For plants, invertebrates, and vertebrates, climate change has strongly in- fluenced distribution and abundance at range mar- gins both in latitude (polar margins) (5–8) and in elevation (upper margins) (5, 9–11), and even in depth for marine fishes (8). Shifts at the upper edge of altitudinal range agree with the hypoth- esis of an upward trend to escape rising temper- atures (12–14). Changes in range limits, however, are just one, albeit important, expression of the likely consequences of climate change. More sub- tle changes within the ranges of species are also likely and, although poorly explored as yet, might have important ecological and evolutionary con- sequences. Assuming niche conservatism over evolutionary time (15), we tested for large-scale (across temperate and Mediterranean mountain forests in west Europe), long-term (over the 20th century), and multispecies (through an assem- blage of 171 species) climate-related responses in forest plant altitudinal distributions. We analyzed species responses by measuring shifts in the al- titudinal position of species’maximum probabil- ity of presence within their distribution, instead of focusing on distributional extremes. Addition- ally, we tested for the effect of ecological and life history traits on the magnitude of the response to climate warming (16). In particular, we tested whether species restricted to mountain areas (10–12, 17, 18) and/or fast generation times (19) are particularly sensitive to temperature changes. We studied species in forest communities found between lowland to the upper subalpine vegetation belt (0 to 2600m above sea level) over six mountain ranges in west Europe (the Western Alps, the Northern Pyrenees, the Massif Central, the Western Jura, the Vosges, and the Corsican range). Climatic change in France has been char- acterized by increases in average temperature of far greater magnitude than increases in the world mean annual temperature, of about 0.6°C over the 20th century (20), reaching up to 0.9°C (21) and even close to 1°C in the alpine region since the early 1980s (22). From two large-scale flo- ristic inventories (about 28,000 surveys) (23), we extracted two well-balanced subsamples, includ- ing 3991 surveys each, carried out across the studied mountain ranges (see fig. S1 for surveys location). The first subsample included surveys carried out before the mid-1980s (1905–1985), and the other one, after 1985 (1986–2005) (see fig. S2 for altitudinal distribution of surveys). We chose this temporal threshold because the anal- ysis of yearly mean surface temperature anom- alies between 1965 and 2005 shows that in 1986 the studied mountain ranges experienced a tem- perature regime shift (Fig. 1A), staying above the average baseline conditions. In contrast, analysis of annual precipitation anomalies between 1965 1AgroParisTech, UMR 1092, Laboratoire d'Etude des Ressources Forêt-Bois (LERFoB), 14 rue Girardet, F-54000 Nancy, France. 2Center for Advanced Studies in Ecology and Biodiversity (CASEB), Departamento de Ecologia, Pontificia Universidad Católica de Chile, Alameda 340 C.P. 6513677, Santiago, Chile. 3Institute of Ecology and Biodiversity (IEB), Casilla 653, Santiago, Chile. 4Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA. 5CNRS, Institut de Biologie Moléculaire des Plantes (IBMP), Université Louis Pasteur, 12 Rue du Général Zimmer, F-67084 Strasbourg Cedex, France. 6CNRS, UMR 6116, Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Faculté des Sciences de Saint Jérôme, case 461, F-34397 Marseille Cedex 20, France. *To whom correspondence should be addressed. E-mail: jonathan.lenoir@agroparistech.fr Fig. 1. Climatic trends from 1965 to 2006. (A) Yearly mean surface temperature anom- alies (using overall mean temperature as baseline) and (B) annual precipitation anom- alies (using overall mean annual precipita- tion as baseline) averaged for 73 elevation sites in the French mountains ranging in altitude from 10 to 2010m above sea level. Solid gray bars refer to positive anomalies, whereas open bars refer to negative ones. The solid curve is the smoothed average with use of a 10-year filter. The vertical dotted lines mark the split between the two studied periods. Data have been gathered from the French National Climatic Network (Météo-France). 27 JUNE 2008 VOL 320 SCIENCE www.sciencemag.org1768 REPORTS