A MOLECULAR PHYLOGENY AND NEW INFR ADANS. (LEGUMINOSAE-PAPILIONOID MORPHOLOGY AND HYPOTHE M. # T rden oi-c as, ifica Kew, Richmond, Surrey, TW9 3AB, United Kingdom; ∥Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Avenue W5 Norte, 70770-917 Brasília, DF, Brazil; and #Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisas, Rua Pacheco Leão, 915, ical distribution through multiple long-distance dispersal events, which were facilitated by the occurrence of cies are grown as ornamentals in botanical gardens and green- houses (e.g.,M. bennettii F.Muell.).Mucuna pruriens is of wide economic importance and is currently used in agriculture as for- age and green manure, for biological control, and as a coffee 3 Author for correspondence; current address: Department of Bot- any, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington DC 20013-7012 USA; e-mail: vatanparastm @si.edu. Int. J. Plant Sci. 177(1):76–89. 2016. q 2015 by The University of Chicago. All rights reserved. 1058-5893/2016/17701-0007$15.00 DOI: 10.1086/684131substitute (Duke 1981; Garcia and Fragoso 2003; Ortiz-Ceballos and Fragoso 2004; Ortiz-Ceballos et al. 2007a, 2007b). It also Manuscript received May 2015; revised manuscript received August 2015; electronically published November 24, 2015.seeds adapted to oceanic dispersal. Keywords: Fabaceae, long-distance dispersal, sea-drifted seeds, systematics. Introduction Mucuna Adans. (Phaseoleae–Leguminosae) has a pantropi- cal distribution and comprises approximately 105 species (Lackey 1981; Schrire 2005). The highest diversity of the ge- nus occurs in Asia (68 taxa), followed by Oceania (34 taxa), the Americas (25 taxa), and Africa (19 taxa). Some species are widely distributed, such as Mucuna sloanei Fawc. & Rendle, occurring in the Americas, Hawaii, and Africa; M. gigantea (Willd.) DC., in Africa, Asia, and the Pacific Islands; and M. pruriens (L.) DC. across the entire tropical region. A number of species are ecologically and economically important, and the genus displays a high level of morphological variation, espe- cially in its inflorescences, flowers, fruits, and seeds. Most species of Mucuna are lianas (except the African en- demic species M. stans Welw. ex Baker, which has a shrubby habit), and they are often an important component of tropical ecosystems. Because of their showy inflorescences, some spe- 1 The two lead authors contributed equally in developing this study and should both be considered first author. 2 Author for correspondence; e-mail: tmariamoura@gmail.com.Jardim Botânico, 22460-030 Rio de Janeiro, RJ, Brazil Editor: Patrick S. Herendeen Premise of research. The genus Mucuna has a pantropical distribution and comprises approximately 105 spe- cies, many of which show great economic value for forage, ornament, and medicine. To date, phylogenetic relationships within Mucuna have not been investigated using molecular data. The aim of this study was to build a phylogenetic framework forMucuna to address questions about its monophyly, infrageneric relationships, divergence times, and biogeography. Methodology. We sequenced plastid (trnL-F) and nuclear ribosomal (internal transcribed spacer) regions and applied Bayesian and maximum likelihood analyses. An ancestral area reconstruction coupled with a di- vergence time analysis was used to investigate the historical biogeography of the genus. Pivotal results. Our results show that Mucuna is a monophyletic genus and that subgenus Stizolobium is a monophyletic group within it. We present here the analyses and results that support the need to recircumscribe subgenus Mucuna and to segregate a small group of species with large fruits into a newly proposed subgenus (to be described formally elsewhere after additional investigations). Conclusions. On the basis of ancestral area reconstruction and divergence time analyses, we conclude that the genus Mucuna originated and first diversified in the Paleotropics around 29.2 Ma and achieved a pantrop-Tania M. Moura,1,2,* Mohammad Vatanparast,1,3,† Ana Marcelo F. Simon,∥ Vidal F. Mansano, *Comparative Plant and Fungal Biology Department, Royal Botanic Ga of Biology, Graduate School of Science, Chiba University, 1-33 Yay Vegetal, Instituto de Biologia, Universidade Estadual de Campin Barão Geraldo, 13083-862 Campinas, SP, Brazil; §Ident76 This content downloaded from 160.11 All use subject to University of Chicago Press TermsSYMPOSIUM PAPER AGENERIC CLASSIFICATION OF MUCUNA EAE) INCLUDING INSIGHTS FROM SES ABOUT BIOGEOGRAPHY G. A. Tozzi,‡ Félix Forest,* C. Melanie Wilmot-Dear,§ adashi Kajita,† and Gwilym P. Lewis* s, Kew, Richmond, Surrey, TW9 3AB, United Kingdom; †Department ho, Inage-ku, Chiba 263-8-522, Japan; ‡Departamento de Biologia Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, tion and Naming Department, Royal Botanic Gardens,1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). ENhas been used for the treatment of Parkinson’s disease (Naga- shayana et al. 2000; Singhal et al. 2003). Most species have pendant inflorescences; M. stanleyi C.T. White, endemic to New Guinea, is the only lianescent Mucuna with an erect inflorescence. Peduncles vary from a few centi- meters long (e.g., 5–18 cm long inM. sloanei) to approximately 2 m long (e.g., M. globulifera T. M. Moura, N. Zamora & A. M. G. Azevedo). The length of peduncle is partially associ- ated with the pollination system. Species with short-pedunculate inflorescences are mostly pollinated by birds; those with long- pedunculate inflorescences (over 1 m long) are usually pollinated by bats. The single lianescent species with an erect inflorescence is visited by and may be pollinated by a possum (H. Fortune- Hopkins, unpublished data). Inflorescences can be pseudorace- mose (e.g.,M. flagellipesVogel, fromAfrica); pseudopaniculate (e.g., M. paniculata Baker, from Madagascar); or umbelliform, in which all flowers are closely clustered at the inflorescence apex and where the floral internodes are so reduced as to not be evident (e.g., M. elliptica Ruiz & Pavon, from South Amer- ica). The species with pseudoracemose inflorescences are dis- tributed across the entire geographical range of the genus; those with pseudopanicles occur in the Paleotropics,whereas all the spe- cies with umbelliform inflorescences are found in the Neotropics (i.e.,M. argenteaT.M.Moura, G. P. Lewis&A.M. G. Azevedo, M. cajamarca T. M. Moura, G. P. Lewis & A. M. G. Azevedo, M. cuatrecasasii Hern. Cam. & C. Barbosa ex. L. K. Ruiz, M. elliptica, M. klitgaardiae T. M. Moura, G. P. Lewis & A. M. A. Azevedo, and M. pseudoelliptica T. M. Moura, G. P. Lewis & A. M. G. Azevedo). Two widely distributed species (M. sloanei and M. gigantea) have a reduced pseudoraceme in which the brachyblasts and pedicels are progressively shorter toward the inflorescence apex (rather than of uniform length). This has been described as pseudoumbellate by some authors (e.g., Wilmot- Dear 1990; Tozzi et al. 2005), although the internodes are clearly visible on the inflorescence rachis. Mucuna flowers show a remarkable variation in color of the corolla, ranging from white (e.g., M. klitgaardiae), cream (e.g.,Mucuna urens (L.) Medik.), or greenish (e.g.,M.monticola Zamora, T. M. Moura & A. M. G. Azevedo) to yellow (e.g., M. japira A. M. G. A. Tozzi, Agostini & Sazima), orange (e.g., M. rostrata Benth.), red (e.g., M. bennetti), purple (e.g., M. pru- riens), or almost black (e.g., M. hainanensis Hayata). The wing petals of the corolla can be either longer than the standard (e.g., M. mutisiana (Kunth) DC.) or shorter (e.g., M. holtonii (Kuntze) Moldenke). The flowers vary in size from 2.5 cm long (e.g., M. lane-poolei Summerh.) to 11 cm long (in M. cuatrecasasii). The morphology of the fruits also presents an important suite of taxonomic characters. The pod surface is sometimes or- namented by lamellae (in a transversal, longitudinal, oblique, or reticulate pattern) or ornamentation can be completely lacking. Most species have dehiscent fruits, but two (M. poggei Taub. and M. occidentalis T. M. Moura & G. P. Lewis, both endemic toAfrica) have indehiscent fruits. Some species have fruits shorter than 10 cm and contain approximately five seeds (e.g., M. pru- riens); other species have fruits 10–30 cm long, but they again contain approximately five seeds (e.g.,M.urens); in a third group of species, the fruits can be over 50 cm long and have up to 18 seeds MOURA ET AL.—MOLECULAR PHYLOG(e.g., M. macrocarpa Wall.). In addition, the seeds and hilum provide taxonomically informative characters. Seeds can be re- niform, discoid, or globose; the length of the hilum varies from This content downloaded from 160.11 All use subject to University of Chicago Press Terms3–7 mm in length (circling less than 20% of the seed circumfer- ence) to 8–9 cm in length (circling more than 50% of the seed circumference). On the basis of fruit and seed morphology, two subgenera have been traditionally recognized in Mucuna (Wilmot-Dear 1984):M. subg.Mucuna andM. subg. Stizolobium (P. Browne) Baker. Stizolobium P. Brownewas described by Browne (1756), and De Candolle (1825) later down-ranked it to a section of Mucuna, as M. sect. Stizolobium (P. Browne) DC. Currently, the infrageneric classification of Mucuna recognizes two sub- genera and no sections (Wilmot-Dear 1984, 1991). Neverthe- less, due to differences in fruit and seed shape and hilum length, some authors have treated Stizolobium as a distinct genus (e.g., Molina Rosito 1975; Stevens et al. 2001; Zamora 2010). Phylo- genetic studies are necessary to clarify this issue. Regional taxonomic studies have been published for the ge- nus Mucuna across its pantropical distribution range (Verd- court 1970, 1971, 1978, 1979a, 1979b, 1981; Wilmot-Dear 1984, 1987, 1990, 1991, 1992, 1993, 2008; Wiriadinata and Ohashi 1990; Du Puy et al. 2002; Tozzi et al. 2005; Ren and Wilmot-Dear 2010; Moura et al. 2012a, 2012b, 2013a, 2013b, 2013c, 2013d, 2013e, 2014, 2015; Moura and Lewis 2014; Zamora and Moura 2014), but there has been no global taxonomic survey to date. Moreover, a comprehensive phylo- genetic study of Mucuna has never been performed. A small number of broader phylogenetic studies have included only two or three species of Mucuna (e.g., Kajita et al. 2001; Ste- fanovíc et al. 2009; Lima 2011) and thus have not adequately covered the entire geographical range or morphological var- iation of the genus. Although these studies have highlighted the relationships between Mucuna and its closest allies, the monophyly of the genus and its infrageneric groups remains to be tested. In addition, the lack of a phylogenetic framework for Mucuna precludes more precise inference about the area of origin of the genus and possible dispersal routes across the tropics. In this study, we present a densely sampled phylogeny of Mucuna and try to answer the following taxonomic and bio- geographical questions: (1) Are the genus Mucuna and its pro- posed subgenera monophyletic? (2) What are the infrageneric relationships among Mucuna species? (3) Do pollination sys- tems or geographical ranges correlate to clades identified by the molecular phylogeny? (4) When and where did the genus originate, and what processes may have produced its current pantropical distribution? Material and Methods Taxon Sampling and DNA Extraction Sixty-three taxa were sampled for this study, including 47 of Mucuna and 16 representing outgroups. Due to the wide geo- graphical distribution of the genus, most of the samples used in this study came from herbarium collections. Material of a few species was collected in the field and stored in silica gel. Three sequences of Mucuna and nine outgroups were obtained fromGenBank. The range of morphological variation and wide Y AND CLASSIFICATION OF MUCUNA 77geographical distribution of Mucuna are represented in this study. A list of the species and specimens sampled is presented in the appendix. 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). contigs and edited using the program Geneious, version 7.1.7 (Biomatters, Aukland, New Zealand), or SeqScape, version NAFor internal transcribed spacer (ITS) analysis, 53 accessions of Mucuna from 45 taxa were sequenced, and for the trnL-F region, 48 accessions of 33 taxa were sequenced. Because it was impossible to sequence all the samples for both markers due to the high level of degradation of the DNA, we opted for sequencing as much as we could for each locus and then presenting the results separately. We also present a combined analysis for the species sequenced for both markers (34 acces- sions, 30 taxa). The DNA extraction from leaf tissue was conducted in three different laboratories: (1) the specimens from MO, UEC, and CEN herbaria were extracted at theMissouri Botanical Garden (St. Louis, MO) using MP FastDNA Green Spin Kit (MP Bio- medicals). After extraction, the DNA was cleaned by DNA Axigen AxyPrepPCR Clean-Up Kit; (2) the specimens from K, some from L, and GH herbaria were extracted in the Jodrell Laboratory, Royal Botanic Gardens, Kew, using the 2# cetyl- trimethylammonium bromide method (Doyle and Doyle 1987), and the DNA was cleaned by a cesium chloride-ethidium bro- mide gradient (1.55 g/mL) and a dialysis procedure to yield material suitable for long-term storage; (3) specimens from L were extracted at Chiba University (Chiba, Japan), using the DNeasy Plant Mini Kit (Qiagen) and following the man- ufacturer’s instructions with a modified protocol for herbarium materials. The concentration of genomic DNA was measured with a GeneQuant 100 electrophotometer (GE Healthcare, Life Sciences). Polymerase Chain Reaction (PCR) and Sequencing Two markers were used: the nuclear region ITS (White et al. 1990) and the plastid region trnL-F (Taberlet et al. 1991).When amplification of the ITS region failed, internal primers ITS2 and ITS3 (Baldwin 1992) were used to amplify the ITS region in two fragments in association with primers ITS5 and ITS4, respec- tively. Because the DNA obtained from the herbarium spec- imens is generally degraded, both regions were amplified and sequenced using internal primers for most of the samples. The PCR and sequencing steps were conducted in two laboratories: the Jodrell Laboratory, Royal Botanic Gardens, Kew, and the Department of Biology at Chiba University. For the analysis conducted in the Jodrell Laboratory, the PCR was performed in 25-mL-volume reactions with the following components: 1.0 mL template DNA; 22.5 mL of Reddy PCR Master Mix (2.5 mM MgCl2; Thermo Scientific, Waltham, MA); 0.5 mL of each primer (100 ng/mL); 5 mL of tricholse, bo- vine serum albumin, and tween; 1.0 mL of dimethyl sulfoxide. The same PCRmixwas used for both nuclear and plastid regions. The PCR conditions for both regions were an initial denatura- tion at 807C for 5 min, followed by 35 cycles of denaturation at 957C for 1 min, primer annealing at 487–507C for 1 min, and primer extension at 657C for 1 min; this was followed by a final extension step of 7 min at 647C. For some samples that were dif- ficult to amplify, the PCR conditions included a ramp of 0.37C/s, as described by Shaw et al. (2007). PCR products were checked on 1% agarose gel before being cleaned with QIAquick PCR purification kit (Qiagen). Cycle se- 78 INTERNATIONAL JOURquencing reactions were performed in 5-mL-volume reactions, using 0.3–1.0 mL of the PCR product, 0.25 mL BigDye, 1.5 mL BigDye Buffer, 1.5 mL double distilled water (ddH2O), and This content downloaded from 160.11 All use subject to University of Chicago Press Terms2.7 (Life Technologies, Applied Biosystems). A BLAST search (http://blast.ncbi.nlm.nih.gov/) was conducted for all sequences to check for possible contaminant DNA. Afterward, edited alignments were performed using the Clustal W (Larkin et al. 2007) and MUSCLE (Edgar 2004) programs using default set- tings with manual adjustments. We performed phylogenetic analyses using two different approaches: Bayesian inference (BI) and maximum likelihood (ML). The Bayesian analysis was performed using a Markov chain Monte Carlo (MCMC) method, as implemented in Mr- Bayes, version 3.2.2 (Ronquist et al. 2012). The best-fit model of DNA substitution for each molecular region was determined using MrModeltest, version 2.2 (Nylander 2004), and the Akaike information criterion (Akaike 1974). The GTR1 I1G and GTR1G models were selected as the “best model” for the ITS and trnL-F regions, respectively. For the combined anal- ysis, two partitions were defined corresponding to the plastid and nuclear regions. Two independent Metropolis-coupled MCMCs with incremental heating temperature of 0.25 were run for 50 million generations, with the parameters and the re- sulting phylogenetic trees being sampled every ten-thousandth generation. The analysis was repeated four times. The MCMC sampling was considered sufficient when the effective sampling size (ESS) for each parameter was higher than 200, as verified with Tracer, version 1.6 (Rambaut et al. 2014). A burn-in period0.75 mL of the same primer as for PCR (diluted to 10%). The cycle sequencing products were cleaned using Magnesil and the automated workstation BiomeK NX58 (Beckman Coulter). Complementary strands were sequenced on an ABI 3730 au- tomated sequencer (Applied Biosystems) and then assembled; software base-calling was verified using Sequencher 4.5 (Gene Codes, Ann Arbor, MI). At Chiba University, PCR reactions were performed in volumes of 10 mL containing 0.2 units of ExTaq (TaKaRa) or 0.25 units of MightyAmp DNA Polymerase (TaKaRa) and 0.2 mM deoxynucleotide triphosphates, 10# PCR buffer con- taining 1.5 mM magnesium chloride, 0.5–1 mM of each primer, and 20 ng of genomic DNA. The PCR conditions were as follows: 2 min for initial denaturation at 957C, followed by 35 amplification cycles of 45 s denaturation at 957C, 1 min anneal- ing at 567C, 1 min extension at 727C, and a final 10 min exten- sion at 727C. The PCR products were visualized on a 0.8% aga- rose gel. PCR products were purified using illustra ExoStar Enzymatic PCR and Sequencing Clean-Up Kit (GE Healthcare) according to themanufacturer’s instructions. The cycle sequenc- ing reactions were performed using the BigDye Terminator, ver- sion 3.1, Cycle Sequencing Kit (Applied Biosystems), and cycle sequencing products were purified using an ethanol precipita- tion method. All base sequences were determined using an ABI 3500 DNA sequencer (Applied Biosystems). Phylogenetic Analyses The sequences for all DNA regions were assembled into L OF PLANT SCIENCESof onemillion generations per runwas applied, and the remaining trees were used to reconstruct an “allcompat” consensus tree with posterior probabilities (PP) for each node. Members of tribe 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). erated Maximum Likelihood (RAxML), version 8.1.11 (Sta- Evolutionary Analysis Sampling Trees (BEAST), version 1.8.1 seolus vulgaris L., published in Lavin et al. (2005). To sum- marize plausible trees and to obtain a maximum clade credi- whereas in the ITS trees (fig. 4) and combined trees (fig. 1), it is sister to the Stizolobium clade. Given that some authors argue ENbility tree, the Tree Annotator program implemented in the BEAST package was used. Twenty-five percent of trees (i.e., 7500 trees) were excluded as burn-in from the subsequent calculations. Tracer, version 1.6 (Rambaut et al. 2014), was used to check the ESSs, convergence, and confidence intervals (CIs). The trees were visualized and edited using FigTree, ver- sion 1.4.2. Biogeographic Inferences To investigate the historical biogeography of Mucuna, we conducted ancestral state geographic distributions on phylo-(Drummond et al. 2012), using the combined matrix of ITS and trnL-F, applying the same partition delimitation and evo- lutionary models as those used for the MrBayes analysis. We used an uncorrelated relaxed molecular clock with a lognor- mal distribution of rates and a Yule speciation model (Yule 1925; Gernhard 2008). The analysis was run for 30 million generations, sampling one tree every one-thousandth genera- tion. As a calibration point, we applied a normal prior distri- bution (mean 5 standard deviationp39.752.0 Ma) to the root of the tree, based on the age estimate of the most recent common ancestor of Platycyamus regnellii Benth. and Pha-matakis 2014), which implements a rapid hill-climbing algo- rithm (Stamatakis 2006). Analyses were run for the best-scoring ML tree inferences under the GTR-GAMMAmodel. Rapid boot- strapping was performed with 1000 replications using the GTR- CAT estimation to assess branch support (Stamatakis 2006). To increase analysis speed, parallel versions of the RAXML, MPI/ Pthreads were used (Pfeiffer and Stamatakis 2010). Partition Homogeneity Test To assess congruence between the trnL-F and ITS data sets, we performed the incongruence length difference (ILD) test (Far- ris et al. 1994), implemented as a partition homogeneity test in PAUP*, version 4.0b10 (Swofford 2002). The test was conducted using a heuristic search with tree-bisection-reconnection branch- swapping algorithm and with invariant characters excluded (Cunningham 1997). Three random additions per replicate with a time limit of 10 min were selected to run 1000 homogeneity replicates. Divergence Time Analysis Estimates of divergence time were obtained using the Bayes- ian inference approach implemented in the package BayesianDesmodieae, as well asApios americanaMedik., were selected as outgroup taxa based on published phylogenies (Kajita et al. 2001; Schrire 2005; Stefanovíc et al. 2009). The ML analysis was performed using Randomized Axel- MOURA ET AL.—MOLECULAR PHYLOGgenetic trees using the Bayesian Binary MCMC (BBM) method implemented in the Reconstruct Ancestral State in Phylogenies (RASP) program, version 3.2 (Yu et al. 2015). We divided the This content downloaded from 160.11 All use subject to University of Chicago Press Termsthat combining different data sets (fig. 1) generally improves phylogenetic accuracy, to increase the resolution of our trees re- gardless of their incongruence (Cunningham 1997; Yoder et al. 2001), we decided to merge data sets and perform a combined analysis. The majority rule consensus tree resulting from the Bayes- ian analysis of the combined data set revealed that the genus Mucuna is monophyletic (fig. 1). Three main clades were re- solved, here named the core Mucuna clade (which includes the type species of Mucuna, M. urens), which thus represents Mucuna subg. Mucuna; the Stizolobium clade (which includes the species currently placed in M. subg. Stizolobium); and the Macrocarpa clade. Themain diagnostic characteristic of species in theMacrocarpa clade is the long pods, and therefore Macro-pantropical distribution of Mucuna into eight areas that were based on the presence of endemic species: North America, in- cluding Mexico (A), Asia (B), Central America (C), Papua New Guinea (D), South America (E), Africa (F), Pacific (G), andMadagascar (H). BBMcalculates the probabilities of ances- tral ranges using the probabilities for each unit area. A con- densed tree created by Tree Annotator from the output of the BEAST analysis on the basis of a combined data set of trnL-F and ITS was used. MCMC calculations were conducted with 2,000,000 generations and a sample frequency of 1000. We used a FixedJC (Jukes-Cantor)model with the number of chains equal to 10 and excluding 200 samples as burn-in using null root distribution. The maximum number of areas selected was six. Results Phylogenetic Analyses The aligned trnL-F matrix consisted of 1203 characters for 58 samples, including 48 ofMucuna (33 taxa) and 10 outgroup taxa; the aligned ITS matrix consisted of 902 characters for 62 samples, 53 of Mucuna (45 taxa), and nine outgroup taxa. For both markers, Mucuna was supported as monophyletic (figs. 4, 5). For the trnL-F marker, both subgenera tradition- ally recognized within Mucuna were also monophyletic (fig. 4), whereas Mucuna subg. Mucuna appeared as nonmonophyletic in the analysis based on the ITS marker (fig. 5). A third clade, here named the Macrocarpa clade, was revealed. The ILD analysis suggested that the trnL-F and ITS data sets are incongruent (P<0.003). This incongruence was also detected from visual inspection of trees derived from individ- ual independent analysis of the plastid and nuclear regions (figs. 4, 5). The incongruence observed is mainly related to the position of the Macrocarpa clade; otherwise, no incongru- ence was found and the topologies of the main clades from each region were congruent with support 10.7 posterior prob- ability and 170%bootstrap. In the trnL-F tree, theMacrocarpa clade (M. birdwoodiana, M. calophylla, M. macrocarpa, and M. sempervirens) is sister to the core Mucuna clade (fig. 5), Y AND CLASSIFICATION OF MUCUNA 79carpa is an appropriate name for the clade (T. M. Moura, un- published data). The results obtained from the ML analysis are in agreement with the Bayesian results (results not shown). 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). NA80 INTERNATIONAL JOURThe BEAST analysis based on the combined data set (fig. 2) estimated the stem age of Mucuna to be in the Oligocene to early Miocene (29.2 Ma; 95% CI, 18.1–39.1). The subgenus This content downloaded from 160.11 All use subject to University of Chicago Press TermsL OF PLANT SCIENCESEstimates of Divergence Times Mucuna (Mucuna clade) and the clade comprising the Stizo- lobium and Macrocarpa subclades began diversifying during Fig. 1 Fifty percent majority rule consensus tree resulting from Bayesian analysis of the combined data set of trnL-F and internal transcribed spacer (ITS) sequences for Mucuna species. The numbers above and below branches are posterior probabilities and bootstrap supports, respec- tively. Values !0.7 and !70% are not shown.the Miocene at 20.8 Ma (95% CI, 11.4–31.0) and 20.8 Ma (95% CI, 10.5–32.1), respectively. Additionally, diversifica- tion of subgenus Stizolobium (Stizolobium clade) and the Mac- 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). ENMOURA ET AL.—MOLECULAR PHYLOGbiguous, and five ancestral areas are possible, B (MPp37.7%), BF (MPp20%), AB (MPp7%), F (MPp6.3%), and BE (MPp 5.7%), with 23% ambiguity (fig. 3, node V). Node VI This content downloaded from 160.11 All use subject to University of Chicago Press TermsY AND CLASSIFICATION OF MUCUNA 81rocarpa clade occurred in the late tomiddleMiocene around 10.4 Ma (95% CI, 4.5–17.8) and 9.5 Ma (95% CI, 3.4–18.2), respectively (fig. 2). Our results suggest that the main diversifi- cation of the genus Mucuna occurred more recently, in the mid- dle to late Miocene and Pliocene. Biogeographic Inferences The ancestral geographic ranges obtained by BBM analysis (fig. 3) suggest that Mucuna originated in area B (Asia, node I) with a marginal probability (MP) of 91.5%. Subclade Mucuna (node II) and the subclade comprising the Macrocarpa and Stizolobium clades (node III) are also postulated to have an Asian origin with MPs of 95.9% and 85.4%, respectively. Al- though the Macrocarpa clade has an exclusively Asian origin (node IV, MPp97.6%), the Stizolobium clade (node V) is am- was inferred to be of South American (area E) origin with MPp73.5%, suggesting a dispersal event from Asia to the Neotropics. Discussion Phylogenetic Analyses Mucuna was recovered as monophyletic in all analyses and comprises three main clades, two of them corresponding to M. subg. Mucuna as traditionally circumscribed. However, the positionof theMacrocarpa cladevaries between theanalyses, sug- gesting that additional molecular data, coupled with a detailed morphological analysis, are needed to clarify this relationship. The Macrocarpa clade is characterized by species with long fruits (often 150 cm in length, containing up to 18 seeds), Fig. 2 Chronogram for the genus Mucuna, based on the concatenated matrices of trnL-F and internal transcribed spacer markers obtained with a BEAST analysis. The numbers at nodes refer to mean age of the nodes (Ma). Gray bars represent 95% confidence intervals for the es- timated mean dates. Qua: Quaternary, Plio: Pliocene.whereas the remaining species in the core Mucuna clade (i.e., excluding the Macrocarpa clade) have fruits up to 30 cm long that usually contain no more than five seeds. Members of the 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). NA82 INTERNATIONAL JOURseeds are reniform in outline (rather than round, as they are in the other two clades), and the hilum is shorter. Although all the taxa of subgenus Stizolobium cluster in a well-supported clade, This content downloaded from 160.11 All use subject to University of Chicago Press TermsL OF PLANT SCIENCESStizolobium clade (M. subg. Stizolobium) also have fruits up to 10 cm long that usually contain nomore than five seeds, but the the topology of the trees indicates that this group should be treated as a subgenus within Mucuna (Wilmot-Dear 1984, Fig. 3 Output of the Bayesian binary Markov chain Monte Carlo analysis from the RASP program, version 3.2 (Yu et al. 2015), showing ancestral geographic reconstructions at each node of the phylogenetic tree of Mucuna. The proportion of colors in circles at each node represents possible ancestral ranges, and letters in the centers of the circles show the most likely state of each node. Numbers on the horizontal axis cor- respond to the estimated ages (Ma) obtained from the BEAST analysis. Ap North America, Bp Asia, Cp Central America, Dp Papua New Guinea, E p South America, F p Africa, G p Pacific, and H p Madagascar. Black represents other ancestral ranges.1991; Moura et al. 2013b, 2014), instead of as an independent genus, as suggested by some authors (Molina Rosito 1975; Stevens et al. 2001; Zamora 2010). 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). ENMOURA ET AL.—MOLECULAR PHYLOGysis of the ITS marker failed to include M. calophylla as a member of the Macrocarpa clade, placing it instead as the sis- ter taxon to subgenus Stizolobium, although with low support This content downloaded from 160.11 All use subject to University of Chicago Press TermsY AND CLASSIFICATION OF MUCUNA 83As stated above, the Macrocarpa clade is morphologically coherent with respect to fruit morphology. Only the ML anal- (58%). Conversely, there is high support (99% bootstrap and 1 posterior probability support) in the combined ML and BI Fig. 4 Fifty percent majority rule consensus tree resulting from Bayesian analysis of the trnL-F marker for Mucuna species. The numbers above and below branches are posterior probabilities and bootstrap supports, respectively. Values !0.7 and !70% are not shown.analyses for a clade comprisingM.birdwoodiana,M. calophylla, M.macrocarpa, andM. sempervirens. Incongruency between the chloroplast DNA and ITS trees regarding the position of the 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). Fig. 5 Fifty percent majority rule consensus tree resulting from Bayesian analysis of the internal transcribed spacer (ITS) marker for Mucuna species. The numbers above and below branches are posterior probabilities and bootstrap supports, respectively. Values !0.7 and !70% are not shown.This content downloaded from 160.111.254.017 on January 29, 2016 09:08:15 AM All use subject to University of Chicago Press Terms and Conditions (http://www.journals.uchicago.edu/t-and-c). have almost pantropical distributions. The distribution of these species is hypothesized to be a result of dispersal of seeds that ENMacrocarpa clade (see above) and the observed variation in poly- ploidy level among individuals of M. sempervirens might be the result of incomplete lineage sorting and/or introgressive hybrid- ization (Maddison and Knowles 2006; Petit and Excoffier 2009) among species of the Macrocarpa, core Mucuna, and Stizolobium clades. The corolla color, the pollination systems, and the lamellate ornamentation of the pod surface were not found to be syna- pomorphies for any of the three major clades in the analyses. For example, M. nova-guineensis and M. bennettii, two red- flowered species fromOceania, are placed in the same subclade, whereas M. neocaledonica (from New Caledonia) and M. ros- trata (Neotropics), which have red, purplish-red, or orange flowers, are nested in different subclades. Similarly, M. japira (endemic to Brazil) and M. sloanei (widely distributed) both have yellow flowers but are not closely related. There is also no evident clustering of species with similar pollination systems. Species bearing long peduncles, which are characteristic of bat pollination, appear in different subclades. For example, in the clade formed byM. urens,M. flagellipes,M.mollis, M. rostrata, and M. japira, the first three species have long peduncles and are bat pollinated, whereas the other two species have short pe- duncles and are pollinated by birds. Likewise, in the clade com- prising M. argyrophylla, M. mutisiana, andM. sloanei, the first two species have long peduncles and are probably bat polli- nated, whereas M. sloanei has a short peduncle and is likely to be bird pollinated. Our results suggest that the pollination syn- drome and floral features have arisen in parallel multiple times during the evolutionary history ofMucuna, a trend that has been reported in other plant groups, such as Sinningeae (Gesne- riaceae; Perret et al. 2003) and Bignonieae (Bignoniaceae; Al- cantara and Lohmann 2010). The presence of lamellate orna- mentation on the pod surface is apparently not synapomorphic (e.g., M. argyrophylla, M. mollis, and M. gigantea, which lack ornamented pods, group into different subclades, together with species with ornamented fruit). No clustering of species on the basis of inflorescence type, namely, pseudoracemose, pseudo- paniculate, or pseudoumbellate, was observed, although the in- clusion of severalNeotropical pseudoumbellate species (M.argen- tea, M. cajamarca, M. cuatrecasasii, M. elliptica, M. klitgaardiae, and M. pseudoelliptica), which were not included in our study, would be needed to further support this finding. On the other hand, the types of fruit, seed, and seed hilum do provide tax- onomically informative characters that support our molecular findings. Biogeographic Inferences Present-day global legume distributions are most likely a combination of long-distance dispersal (LDD) and vicariance, based on the evidence from phylogenetic studies and fossil records (Schrire et al. 2005; Bessega et al. 2006). More impor- tantly, the transoceanic distribution of various crown clades of the legumes is considered to be the result of LDD, because the young ages estimated for most legume groups preclude vicari- ance as an explanation for their disjunct distributions (Lavin et al. 2004). According to our divergence time analysis using MOURA ET AL.—MOLECULAR PHYLOGBEAST, the genus Mucuna evolved sometime in the Oligocene to early Miocene (39.1–18.1 Ma), whereas the core Mucuna, Macrocarpa, and Stizolobium clades diversified in the Miocene This content downloaded from 160.11 All use subject to University of Chicago Press Termshave drifted by ocean currents, because Mucuna seeds have been found even along the coast of New Zealand (Mason 1961) and on beaches in Europe (Nelson et al. 2000). LDD plays an important role in the biodiversity and biogeography of a number of legume genera, including Apios (Li et al. 2014), Canavalia and Dalbergia (Vatanparast et al. 2011; Vatanparast et al. 2013), Lonchocarpus (Silva et al. 2012), Zornia (Fortuna- Perez et al. 2013), and members of tribe Fabeae (Schaefer et al. 2012) and indeed of legumes in general (Lavin et al. 2004; Pen- nington et al. 2006). Although our taxon sampling could be increased, our anal- yses showed that at least two dispersal events from the Paleo- tropics (Asia) to the Neotropics can be inferred. One dispersal event to Central America has led to a clade comprising M. sloanei, M. mutisiana, and M. argyrophylla, whereas another inferred dispersal event to South America has resulted in a clade comprisingM. urens, M. mollis, M. rostrata, andM. japira. For Africa, four dispersal events can be inferred. Although the Af- rican species of M. subg. Stizolobium (M. coriacea, M. poggei, M. pruriens, and M. stans) could have resulted from a single colonization from Asia, M. subg. Mucuna arrived on the Afri- can continentmultiple times:M. flagellipes fromSouthAmerica, M. gigantea from Asia, and M. sloanei from Central America (all by LDD). Mucuna manogarivensis, which is endemic to Madagascar, is sister to M. atropurpurea from Asia, but the ancestor of these two species appears to be Central Ameri- can (although this relationship received low support of PP; 0.53). The species from Oceania, M. nova-guineensis, M. ben- nettii, and M. mollissima, also have an origin in Asia (fig. 3), whereas the origin of M. diabolica (an Australian species) is uncertain. Conclusions Our results confirm that the genus Mucuna is monophyletic, as is the previously described subgenus Stizolobium. Mucuna subg. Mucuna contains two main clades, the core Mucuna clade and Macrocarpa clade. Although the position of the Macro- carpa clade is variable in our analyses, it is consistent in species content for both studied markers. The species of this clade are morphologically distinctive with respect to fruit type, but we are carrying out additional investigations before formally de- scribing a new subgenus. On the basis of the divergence time(fig. 2). Our results suggest that the genus Mucuna originated in Asia and has since undergone multiple colonization events into Africa and North, Central, and South America. Although the role of long-distance dispersal in the biogeography of land plants has generally been underestimated (Cain et al. 2000; Vatanparast 2010), when one considers the topology of our phylogenetic trees and ancestral area reconstruction, it is plau- sible that several LDD events underpin the pantropical distribu- tion of Mucuna across Asia, Africa, and the Americas. The ma- jority of extantMucuna species (180%) are restricted to a single continent, whereas some species, M. gigantea and M. sloanei, Y AND CLASSIFICATION OF MUCUNA 85analysis, we conclude that the genus Mucuna originated in the Paleotropics, in theOligocene to earlyMiocene, and gradually ex- panded its geographic range via a number of dispersal events into 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). GQ413945.1, trnL-F: JN402868.1. Desmodium uncinatum (Jacq.) DC., ITS: GQ413950.1. Erythrina fusca Lour., Brazil: cul- ; tr en ed h & .1. 404 : KT cya lvar i H cu Mucuna argyrophylla Standl., Mexico, M. Sousa 11399 (MO), IT ul KT 603 & 607G.P. Lewis & A.M.G. Azevedo., Colombia, B. Kats & A. van D DC., Ceylon, A. G. Robyns 7327 (K), ITS: KT696030, trnL-F: Janeiro Botanical Garden, T. M. Moura 996 (UEC), ITS: KT69 L.G. Saw (L 0462392), trnL-F: KT696088. M. biplicata Teijsm KT696089. M. birdwoodiana Tutcher, China, W. T. Tang 20tivated in Rio de Janeiro Botanical Gardens, ITS: KT729507 Moura 1004 (UEC), ITS: KT729508; trnL-F: KT729513. K (MO), trnL-F: KT696082. Kennedia nigricans Lindl., cultivat KT696083. Kennedia prostrata R. Br., Australia, R. J. Smit (Dum. Cours.) G. Don, ITS: GU572175.1, trnL-F: JN402793 archboldianus Merr. & L. M. Perry, New Guinea, M. Fallen Brazil: cultivated in Rio de Janeiro Botanical Gardens, trnL-F Platy Platycyamus regnellii Benth., Brazil, B. A. S. Pereira & D. A Brazil, E. Ule 9496 (K), trnL-F: KT696080. Platycyamus ule KT696081. MuRech., Fiji, W. Greenwood 1109 (K), ITS: KT696034. M. bracteat KT696090. M. bracteata DC. ex Kurz 02, Burma, G. B. Vogt 49 R. C. Ching 21690 (GH), ITS: KT696035, trnL-F: KT696092. M This content downloaded from 160.11 All use subject to University of Chicago Press TermsnL-F: KT729512. Erythrina speciosa Andrews, Brazil, T. M. nedia coccinea (Curtis) Vent., Australia, T. R. Lally 1568 in the United States, H. Van der Werff 8254 (MO), trnL-F: A. Shade 39 (K), trnL-F: KT696084. Lespedeza cuneata Lespedeza maritima Nakai, ITS: GU572190.1. Strongylodon (MO), ITS: KT696078. Strongylodon macrobotrys A. Gray, 696131. mus enga 2474 (K), KT696079. Platycyamus ulei Harms 44721, arms 45190, Peru, E. Meneces s.n. (MO 4268531), trnL-F: na S: KT696029, trnL-F: KT696085. M. argentea T. M. Moura, men AVD 265 (K), ITS: KT729509. M. atropurpurea (Roxb.) 696086. M. bennettii F. Muell., Brazil, cultivated in the Rio de 1, trnL-F: KT696087. M. biplicata Teijsm & Binn., Malaysia, Binn., Malaysia, C. Hansen 136 (K), ITS: KT696032, trnL-F: (MO), ITS: KT696033, trnL-F: KT729514. M. brachycarpaAfrica and via at least two dispersal events into the Neotropics. These findings suggest that long-distance oceanic dispersal of Mucuna seeds has had a central role in forming the present- day pantropical distribution of and diversification within the genus. Acknowledgments We thank Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil, and the Science without Borders Program for the postdoctoral scholarship to T.M.Moura (pro- cess 245590/2012-9); Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), Brazil (process 2012/04635-8), and Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Brazil (process E-26/110.331/2012), for fi- nancial support; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brazil, for T. M. Moura’s PhD scholarship; the ShirleyA.GrahamFellowship,Missouri Botan- ical Garden, to T.M.Moura; the Biologia Vegetal postgraduate program at Universidade Estadual de Campinas (UNICAMP), Brazil; the Royal Botanic Gardens, Kew; and the Missouri Bo- tanical Garden for support. We also thank Dra. Anete Pereira de Souza and Centro de Biologia Molecular e Engenharia Genética (CBMEG) Laboratory, Brazil, for support at the be- ginning of this study; the Jodrell Laboratory staff (Royal Bo- tanic Gardens, Kew), especially Edith Kapinos, Dion Devey, László Csiba, JimClarkson, and Tim Fulcher, for valuable tech- nical support; we thank the curators of the herbaria at K, L, and MO for providing DNA material; all researchers and friends that helped with laboratory activities, including DNA extraction and data analysis, particularly Ana Paula Fortuna Perez, André Simões, Anne Bruneau, David Bogler, Domingos Cardoso, Eve Lucas, Fiorella Fernanda Mazine Capelo, Helen Fortune-Hopkins, Laura Lima, Marcos José da Silva, Mariana de Oliveria Bünger, and Valentina D’Amico. M. Vatanparast thanks Tetsukazu Yahara and Shuichiro Tagane from Kyushu University for providing fresh material of Mucuna. M. Va- tanparast and T. Kajita were supported by a grant from the Environment Research and Technology Development Fund (S-9) of the Ministry of the Environment, Japan. We thank Dr. Benjamin Torke and one anonymous reviewer for con- structive comments on the first submitted draft of the paper and also Patrick Herendeen for his valuable editorial input. Appendix Voucher Information and GenBank Numbers Shown below are voucher information and GenBank numbers (trnL-F and ITS) for all specimens used in this study. Outgroups Apios americana Medik., ITS: AF467019.1, trnL-F: EU717312.1. Craspedolobium schochii Harms, China, A. Henry 9241-A (K), ITS: KT696028. Desmodium barbatum (L.) Benth., trnL-F: EU717290.1. Desmodium microphyllum (Thunb.) DC., ITS: 86 INTERNATIONAL JOURNAL OF PLANT SCIENCESa DC. ex Kurz, Thailand, E. F. Anderson 4108 (MO), trnL-F: 5 (K), trnL-F: KT696091. M. calophylla W. W. Sm., China, . championii Benth., Hong Kong, Hu & But 20316 (MO), 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). .n. trn 96 nth ilip s.n ert erd (MO), ITS: KT696044. M. interrupta Gagnep., ITS: AB775135.1. M. irritans Burtt Davy, Malawi, E. A. Banda et al. 3573 (MO), ITS: KT696045. M. japira A. M. G. Azevedo, K. Agostini & M. Sazima, Brazil, T. M. Moura 630 (UEC), ITS: ENKT696046, trnL-F: KT696101. M. klitgaardiae T. M. Moura, G.P. Lewis & A.M.G. Azevedo, Ecuador, B. Klitgaard 99502 (MO), ITS: KT696047. M. lamellata Wilmot-Dear, China, C. Ford 64 (K), ITS: KT696048, trnL-F: KT696102. M. lamellata Wilmot-Dear (as M. paohwashanica T. Tang & F. T. Wang), China, X. Q. Wang & Y. N. Xiong 001 (MO), ITS: KT696049, trnL-F: KT696103. M. macrocarpa Wall., China, G. Z. Li s.n. (MO), ITS: KT696050, trnL-F: KT696104. M. macrophylla Miq., Indonesia, F. J. A. J. Verheijen 1330/31 (L), ITS: KT696051. M. macropoda Baker f., Papua New Guinea, H. Hopkins s.n. (L), ITS: KT696052. M. manongarivensis Du Puy & Labat, Madagascar, L. Gautier et al. 3785 (MO), ITS: KT696053, trnL-F: KT696105. M. melanocarpa Hochst. ex A. Rich., Ethiopia, I. Friis, W. Abebe & E. Getachew 13442 (K), trnL-F: KT696106. M. mollis (Kunth) DC., Colombia, H. Murphy & E. Parra 684 (MO), ITS: KT696054, trnL-F: KT696107. M. mollissima Teijsm. & Binn. ex Kurz, Papua New Guinea, J. H. Waterhouse s.n. (K), ITS: KT696055, trnL-F: KT696108. M. mollissima Teijsm. & Binn. ex Kurz [as M. cyanosperma K. Schum.], Papua New Guinea, B. Eddie s.n. (K), ITS: KT696056, trnL-F: KT696109. M. monosperma (Roxb.) DC., ITS: AB775136.1. M. mutisiana (Kunth) DC., Colombia, J.H. Kirkbride Jr. 2555 (MO), ITS: KT696057, trnL-F: KT696110. M. neocaledonica Baker f., New Caledonia, G. McPherson 5261 (K), ITS: KT696058, trnL-F: KT696111. M. nova-guineensis Scheff., Papua New Guinea, W.N., Takeuchi (L 0254121), ITS: KT696059, trnL-F: KT696112. M. poggei Taub. 01, Malawi, R-Smith, Pope & Goyder 5836 (K), ITS: KT696060, trnL-F: KT696113. M. poggei Taub. 02, Zambia, D. K. Harder et al. 3073 (MO), trnL-F: KT696114. M. pruriens var. utilis (Wall. ex Wight) Baker ex Burck, cultivated in Brazil, T. M. Moura 994 (UEC), ITS: KT696063, trnL-F: KT696118. M. pruriens var. utilis (Wall. ex Wight) Baker ex Burck (as M. hassjoo (Piper & Tracy) Mansf.), Taiwan, M.T. Kao 10159 (MO), ITS: KT696062, trnL-F: KT729516. M. pruriens var. utilis (Wall. ex Wight) Baker ex Burck 31, Ecuador, Z. T. Almeida 002 (MO), ITS: KT696064. M. pruriens var. utilis (Wall. ex Wight) Baker ex Burck 32, Ecuador, Z. T. Almeida 002 (MO), ITS: KT696065. M. pruriens (L.) DC. var. pruriens, Venezuela, R. Ramirez 26 (MO), ITS: KT696061, trnL-F: KT729515. M. pruriens (L.) DC. 038, French Guiana, J. J. de Granville (U 013577), trnL-F: KT696115. M. pruriens (L.) DC. M7, Mexico, R. Duno de Stefano1830 (MO), trnL-F: KT696116. M. rostrata Benth., Brazil, M. Simon 1639 (CEN), ITS: KT696066, trnL-F: KT696120. M. rostrata Benth. 36, Peru, F. Woytkowski 5378 (MO), trnL-F: KT729517. M. samarensis Merr. 027, Philippines, C. E. Ridsdale (L 0396765), ITS: KT696067, trnL-F: KT696121. M. schlechteri Harms, New Guinea, R. D. Hoogland 4241 (GH), ITS: KT696068. M. sempervirens Hemsl., China, D.E. Boufford (L 0254117), ITS: KT696069, trnL-F: KT696122. M. sempervirens Hemsl., Asia, Hemsl s.n. (MO), trnL-F: KT696123. M. sloanei Fawc. & Rendle, Brazil, T. M. Moura 1005 (UEC), ITS: KT696070, trnL-F: KT696124. M. stanleyi C. T. White, Papua New Guinea, L. J. Brass 24277 (L), ITS: KT729511. M. stanleyi C. T. White 2, Papua New Guinea, Hopkins & Hopkins 1018 (K), ITS: KT696071. M. stans Welw. ex Baker, Tanzania, F. Furuya 95 (MO), ITS: KT696072, trnL-F: KT696125. M. stenoplax Wilmot-Dear, Thailand, S. Phusomsaeng & S. Pinnin 49 (K), trnL-F: KT696126. M. stenoplax Wilmot-Dear, Asia, T. Kajita s./n. (FU), ITS: KT696073, trnL-F: KT696127. M. stenoplax Wilmot-Dear 22, Thailand, J. F. Maxwell (L 0401600), trnL-F: KT696128. M. urens (L.) Medik., Brazil, T. M. Moura 629 (UEC), ITS: KT696074, trnL-F: KT696130. M. urens (L.) Medik. 39, Guyana, T. R. van Andel (U0085459), trnL-F: KT696129. M. warburgii K. Schum. & Lauterb., Papua New Guinea, S. Lenean 1443 (K), ITS: KT696075. Literature Cited Akaike H 1974 A new look at the statistical model identification. IEEE Trans Autom Control 19:716–723. Alcantara S, LG Lohmann 2010 Evolution of floral morphology and pollination system in Bignonieae (Bignoniaceae). Am J Bot 97:782– 796. Baldwin B 1992 Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. Mol Phylogenet Evol 1:3–16. Bessega C, JC Vilardi, O Saidman 2006 Genetic relationships among Browne P 1756 The civil and natural history of Jamaica in three parts. Osborne & Shipton, London. Cain ML, BG Milligan, AE Strand 2000 Long-distance seed dispersal in plant populations. Am J Bot 87:1217–1227. Cunningham CW 1997 Can three incongruence tests predict when data should be combined? Mol Biol Evol 14:733–740. De Candolle ACP 1825 Prodromus systematis naturalis regni vegeta- bilis 2. Treuttel & Würtz, Paris. Doyle JJ, JL Doyle 1987 A rapid DNA isolation procedure for smallKT696042,trnL-F: KT696100. M. hainanensis Hayata, ITS: GU217596.1. M. hainanensis Hayata (as M. nigricans (Lour.) Steud.), Taiwan, W. L. Wagner 6735 (K), ITS: KT696043. M. holtonii (Kuntze) Moldenke, Colombia, W. Devia et al. 2302ITS: KT696036. M. coriacea Baker, Zimbabwe, R. D. Barnes s ex Keuch., Australia, K. Kenneally 6391 (K), ITS: KT696038, A.M.G. Azevedo., Ecuador, M. Blanco 2532 (MO), ITS: KT6 ITS: KT696040, trnL-F: KT696095. M. flagellipes Vogel ex Be KT696041, trnL-F: KT696096. M. gigantea (Willd.) DC., Ph KT696097. M. gigantea (Willd.) DC. 19, Hawaii, G. Spence gigantea subsp. quadrialata (Baker) Verdc.], Kenya, S. H. Rob (Willd.) DC. [as M. gigantea subsp. quadrialata (Baker) V MOURA ET AL.—MOLECULAR PHYLOGAmerican species of the genus Prosopis (Mimosoideae, Leguminosae) inferred from ITS sequences: evidence for long-distance dispersal. J Biogeogr 33:1905–1915. This content downloaded from 160.11 All use subject to University of Chicago Press Terms(K), ITS: KT696037, trnL-F: KT696093. M. diabolica Backer L-F: KT696094. M. ecuatoriana T. M. Moura, G.P. Lewis & 039. M. elmeri Merr., Indonesia, Ambriansyah (L 0501638), ., Ghana, C. C. H. Jonkind & D. K. Abbin 1588 (MO), ITS: pines, C. E. Ridsdale (L 0460611), ITS: KT729510, trnL-F: . (MO), trnL-F: KT696098. M. gigantea (Willd.) DC. [as M. son & Q. Luke 5438 (MO), trnL-F: KT696099. M. gigantea c.], Kenya, S.A. Robertson & Q. Luke (72675MO), ITS: Y AND CLASSIFICATION OF MUCUNA 87quantities of fresh leaf tissue. Phytochem Bull 19:11–15. Duke JA 1981 Handbook of legumes of world economic importance. Plenum, New York. 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). NADu Puy DJ, J-N Labat, R Rabevohitra, J-F Villiers, J Bosser, J Moat 2002 The Leguminosae of Madagascar. Royal Botanic Gardens, Kew. Drummond AJ, MA Suchard, D Xie, A Rambaut 2012 Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29: 1969–1973. Edgar RC 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. Farris J, M Källersjö, A Kluge, C Bult 1994 Testing significance of incongruence. Cladistics 10:315–319. Fortuna-Perez A, M Silva, L Queiroz, G Lewis, A Simões, A Tozzi, T Sarkinen, A Souza 2013 Phylogeny and biogeography of the ge- nus Zornia (Leguminosae: Papilionoideae: Dalbergieae). Taxon 62: 723–732. Garcia JA, C Fragoso 2003 Influence of different food substrate on growth and reproduction of two tropical earthworm species (Pontoscolex corethrurus and Amynthas corticis). Pedobiologia 47: 754–763. Gernhard T 2008 The conditioned reconstructed process. J Theor Biol 253:769–778. Kajita T, H Ohashi, Y Tateishi, CD Bailey, JJ Doyle 2001 rbcL and legume phylogeny, with particular reference to Phaseoleae, Millet- tieae, and allies. Syst Bot 26:515–536. Lackey JA 1981 Tribe 10. Phaseoleae DC. Pages 301–327 in RM Polhill, PH Raven, eds. Advances in legume systematics, part 1. Royal Botanic Gardens, Kew. Larkin MA, G Blackshields, NP Brown, R Chenna, PA McGettigan, H McWilliam, F Valentin, IM Wallace, A Wilm, R Lopez 2007 Clustal W and Clustal X, version 2.0. Bioinformatics 23:2947– 2948. Lavin M, PS Herendeen, MF Wojciechowski 2005 Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the Tertiary. Syst Biol 54:575–594. Lavin M, BD Schrire, GP Lewis, RT Pennington, A Delgado-Salinas, M Thulin, CE Hughes, AB Matos, MF Wojciechowski 2004 Meta- community process rather than continental tectonic history better explains geographically structured phylogenies in legumes. Philos Trans R Soc B 359:1509–1522. Li J, J Jiang, H Stel, A Homkes, J Corajod, K Brown, Z Chen 2014 Phylogenetics and biogeography of Apios (Fabaceae) inferred from sequences of nuclear and plastid genes. Int J Plant Sci 175:764– 780. Lima LCP 2011 Estudos filogenéticos em Desmodium Desv. (Leguminosae–Papilionoideae) e revisão taxonômica das espécies ocorrentes no Brasil. Tese, Universidade Estadual de Feria de Santana, Feira de Santana. Maddison W, L Knowles 2006 Inferring phylogeny despite incom- plete lineage sorting. Syst Biol 55:21–30. Mason R 1961 Dispersal of tropical seeds by ocean currents. Nature 191:408–409. MolinaRositoA 1975 Enumeración de las plantas deHonduras. Ceiba 19:1–118. Moura TM, R Gereau, GP Lewis 2015 Mucuna mooneyi (Legumino- sae: Papilionoideae), a new species from Ethiopia. Kew Bull 70:32. doi:10.1007/s12225-015-9581-x. Moura TM, GP Lewis 2014 Taxonomic studies in theMucuna poggei complex (Leguminosae: Papilionoideae). Kew Bull 69:9544. doi:10 .1007/s12225-014-9544-7. Moura TM, GP Lewis, VF Mansano, AMGA Tozzi 2013c Three new species of Mucuna (Leguminosae: Papilionoideae: Phaseoleae) from South America. Kew Bull 68:143–150. ——— 2014 Taxonomic Studies in Mucuna Adans. (Leguminosae – Papilionoideae) from Peru. Syst Bot 39:884–896. 88 INTERNATIONAL JOURMoura TM, VF Mansano, R Gereau, AMGA Tozzi 2013e Mucuna jarocha (Leguminosae-Papilionoideae-Phaseoleae), a new species from Mexico. Phytotaxa 89:43–46. This content downloaded from 160.11 All use subject to University of Chicago Press TermsMoura TM, VF Mansano, BM Torke, GP Lewis, AMGA Tozzi 2013b A taxonomic revision of Mucuna (Fabaceae: Papilionoideae: Pha- seoleae) in Brazil. Syst Bot 38:631–637. Moura TM, BM Torke, VF Mansano, AMGA Tozzi 2012a A new combination for an endemic Hawaiian species of Mucuna (Legu- minosae: Papilionoideae), with a key to the Hawaiian taxa of the genus. Kew Bull 67:1–5. Moura TM, AMGA Tozzi, VF Mansano, GP Lewis 2013a Lecto- typification of names of Neotropical species of Mucuna (Legumi- nosae: Papilionoideae: Phaseoleae). Taxon 62:391–393. Moura TM, NA Zamora, GP Lewis, VF Mansano, AMGA Tozzi 2013d Mucuna globulifera (Leguminosae: Papilionoideae), a new species from Costa Rica, Panama and Colombia. Kew Bull 68:151– 155. Moura TM, NA Zamora, BM Torke, VF Mansano, AMGA Tozzi 2012b A new species of Mucuna (Leguminosae-Papilionoideae- Phaseoleae) from Costa Rica and Panama. Phytotaxa 60:1–8. Nagashayana N, P Sankarankutty, MR Nampoothiri, PK Mohan, KP Mohanakumar 2000 Association of L-DOPA with recovery fol- lowing Ayurveda medication in Parkinson’s disease. J Neurol Sci 176:124–127. Nelson CE, W Walsh, A Hathway, PH Oswald 2000 Sea beans and nickar nuts: a handbook of exotic seeds and fruits stranded on beaches in north-western Europe. BSBI Handbooks for Field Iden- tification. Botanical Society of the British Isles, London. Nylander JAA 2004 MrModeltest version 2. Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. Ortiz-Ceballos AI, C Fragoso 2004 Earthworm populations under tropical maize cultivation: the effect of mulching with velvet bean. Biol Fert Soils 39:438–445. Ortiz-Ceballos AI, C Fragoso, GG Brown 2007b Synergistic effect of a tropical earthwormBalanteodrilus pearsei and velvet beanMucuna pruriens var. utilis on maize growth and crop production. Appl Soil Ecol 35:356–362. Ortiz-Ceballos AI, JJ Peña-Cabriales, C Fragoso, GG Brown 2007a Mycorrhizal colonization and nitrogen uptake by maize: combined effect of tropical earthworms and velvet bean mulch. Biol Fert Soils 44:181–186. Pennington RT, JE Richardson, M Lavin 2006 Insights into the his- torical construction of species-rich biomes from dated plant phylog- enies, neutral ecological theory and phylogenetic community struc- ture. New Phytol 172:605–616. Perret M, A Chautems, R Spichiger, G Kite, V Savolainen 2003 Sys- tematics and evolution of tribe Sinningieae (Gesneriaceae): evidence from phylogenetic analyses of six plastid DNA regions and nuclear ncpGS. Am J Bot 90:445–460. Petit RJ, L Excoffier 2009 Gene flow and species delimitation. Trends Ecol Evol 24:386–393. Pfeiffer W, A Stamatakis 2010 Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code. Paper presented at IEEE Inter- national Symposium on Parallel and Distributed Processing, Atlanta, April 19–23. Rambaut A, MA Suchard, D Xie, AJ Drummond 2014 Tracer, ver- sion 1.6. http://beast.bio.ed.ac.uk/Tracer. Ren S, CM Wilmot-Dear 2010 Mucuna. Pages 207–218 in Z Wu, PH Raven, eds. Flora of China: Fabaceae. Missouri Botanical Gar- den, St. Louis. Ronquist F, M Teslenko, P van der Mark, DL Ayres, A Darling, S Höhna, BLarget, L Liu,MASuchard, JPHuelsenbeck 2012 MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542. Schaefer H, P Hechenleitner, A Santos-Guerra, M Menezes de Sequeira, RT Pennington, G Kenicer, MA Carine 2012 Systemat- L OF PLANT SCIENCESics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages. BMC Evol Biol 12:250. 1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c). Schrire BD 2005 Phaseoleae. Pages 393–431 in G Lewis, B Schrire, B Mackinder, M Lock, eds. Legumes of the world. Royal Botanic Gardens, Kew. Schrire BD, M Lavin, GP Lewis 2005 Global distribution patterns of the Leguminosae: insights from recent phylogenies. Biol Skr 55: 375–422. Shaw J, EB Lickey, EE Schilling, RL Small 2007 Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in Angiosperms: the tortoise and the hare III. Am J Bot 94:275–288. Silva MJ, LP de Queiroz, AMGA Tozzi, GP Lewis 2012 Phylogeny and biogeography of Lonchocarpus sensu lato and its allies in the tribe Millettieae (Leguminosae, Papilionoideae). Taxon 61:93–108. Singhal B, J Lalkaka, C Sankhla 2003 Epidemiology and treatment of Parkinson’s disease in India. Parkinsonism Relat Disord 9:105–109. Stamatakis A 2006 RAxML-VI-HPC: maximum likelihood-based phy- ——— 1971 Mucuna. Pages 561–571 in Flora of tropical east Africa, Leguminosae (part 4) subfamily Papilionoideae. Royal Botanic Gardens, Kew. ——— 1978 New taxa of Leguminosae from Papua New Guinea. Kew Bull 32:455–473. ——— 1979a A manual of New Guinea legumes. Botany Bulletin no. 11. Office of Forests, Lae, Papua New Guinea. ——— 1979b A note on Mucuna schlechteri Harms (Leguminosae- Papilionoideae-Phaseoleae). Kew Bull 34:521–525. ——— 1981 New taxa of Mucuna (Leguminosae-Phaseoleae) from East Africa and Australia. Kew Bull 35:743–752. White TJ, T Bruns, S Lee, J Taylor 1990 Amplification and direct se- quencing of fungal ribosomal RNA genes for phylogenetics. Pages 315–322 in MA Innis, DH Gelfand, JJ Sninsky, TJ White, eds. PCR protocols: a guide to methods and applications. Academic Press, MOURA ET AL.—MOLECULAR PHYLOGENY AND CLASSIFICATION OF MUCUNA 89logenetic analyses with thousands of taxa andmixedmodels. Bioinfor- matics 22:2688–2690. ——— 2014 RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. Stefanovíc S, BE Pfeil, JD Palmer, JJ Doyle 2009 Relationships among phaseoloid legumes based on sequences from eight chloroplast re- gions. Syst Bot 34:115–128. Stevens WD, C Ulloa, A Pool, OM Montiel Jarquin 2001 Flora de Nicaragua. Monogr Syst Bot Mo Bot Gard 85:i–xlii. Swofford D 2002 PAUP*: phylogenetic analysis using parsimony (*and other methods). http://paup.csit.fsu.edu/. Taberlet P, L Gielly, G Pautou, J Bouvet 1991 Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109. Tozzi AMGA, K Agostini, M Sazima 2005 A new species of Mucuna Adans. (Leguminosae, Papilionoideae, Phaseoleae) from southeast- ern Brazil, with a key to Brazilian species. Taxon 54:451–455. Vatanparast M 2010 Phylogeography of a pantropical plant with sea-drifted seeds; Canavalia rosea (Sw.) DC., (Fabaceae). PhD the- sis. Chiba University, Japan. Vatanparast M, BB Klitgård, FACB Adema, RT Pennington, T Yahara, T Kajita 2013 First molecular phylogeny of the pantrop- ical genus Dalbergia: implications for infrageneric circumscription and biogeography. S Afr J Bot 89:143–149. Vatanparast M, K Takayama, MS Sousa, Y Teteishi, T Kajita 2011 Origin of Hawaiian endemic species of Canavalia (Fabaceae) from sea-dispersed species revealed by chloroplast and nuclear DNA se- quences. J Jpn Bot 86:15–25. Verdcourt B 1970 Studies in the Leguminosae-Papilionoideae for the “Flora of Tropical East Africa.” Kew Bull 24:235–307.This content downloaded from 160.11 All use subject to University of Chicago Press TermsLondon. Wilmot-Dear CM 1984 A revision of Mucuna (Leguminosae-Phaseoleae) in China and Japan. Kew Bull 39:23–65. ——— 1987 A revision of Mucuna (Leguminosae-Phaseoleae) in the Indian subcontinent and Burma. Kew Bull 42:23–46. ——— 1990 A revision of Mucuna (Leguminosae-Phaseoleae) in the Pacific. Kew Bull 45:1–35. ——— 1991 A revision of Mucuna (Leguminosae-Phaseoleae) in the Philippines. Kew Bull 46:213–251. ——— 1992 A revision ofMucuna (Leguminosae-Phaseoleae) in Thai- land, Indochina and the Malay Peninsula. Kew Bull 47:203–245. ——— 1993 Anew species ofMucuna (Leguminosae-Phaseoleae) from Thailand, and a revised key to the species in Thailand, Indochina and the Malay Peninsula. Kew Bull 48:29–35. ——— 2008 Mucuna (Leguminosae) in Thailand. Thai Forest Bull (Bot) 36:114–139. Wiriadinata H, H Ohashi 1990 Four new species of Mucuna (Legu- minosae) of the Lesser Sunda Islands. J Jap Bot 65:97–108. Yoder A, J Irwin, B Payseur 2001 Failure of the ILD to determine data combinability for slow loris phylogeny. Syst Biol 50:408–424. Yu Y, AJ Harris, C Blair, X He 2015 RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography. Mol Phy- logenet Evol 87:46–49. Yule UG 1925 A mathematical theory of evolution, based on the conclusions of Dr. JCWillis, FRS. Philos Trans R Soc B 88:433–436. Zamora N 2010 Fabaceae. Pages 395–775 in BE Hammel, MH Grayum, C Herrera, N Zamora, eds. Manual de Plantas de Costa Rica. Vol 5. Monogr Syst Bot Mo Bot Gard 119:395–775. Zamora NA, TMMoura 2014 Mucuna tapantiana (Fabaceae: Faboi- deae: Phaseoleae), a new species from Costa Rica. Kew Bull 69:9490. doi:10.1007/S12225-014-9490-4.1.254.017 on January 29, 2016 09:08:15 AM and Conditions (http://www.journals.uchicago.edu/t-and-c).