Nuclear and mitochondrial DNA evidence of polyphyly in the avian superfamily Muscicapoidea

Nucleotide sequences of the nuclear c-mos gene and the mitochondrial cytochrome b and ND2 genes were used to assess the monophyly of Sibley and Monroe's [Distribution and Taxonomy of Birds of the World, Yale University Press, New Haven, 1990] Muscicapoidea superfamily. The relationships and monophyly of major lineages within the superfamily, as well as genera membership in major lineages was also assessed. Analyses suggest that Bombycillidae is not a part of Muscicapoidea, and there is strongly supported evidence to suggest that Turdinae is not part of the Muscicapidae, but is instead sister to a Sturnidae+Cinclidae clade. This clade is in turn sister to Muscicapidae (Muscicapini+Saxicolini). Of the 49 Turdinae and Muscicapidae genera that we included in our analyses, 10 (20%) are shown to be misclassified to subfamily or tribe. Our results place one current Saxicolini genus in Turdinae, two Saxicolini genera in Muscicapini, and five Turdinae and two Muscicapini genera in Saxicolini; these relationships are supported with 100% Bayesian support. Our analyses suggest that c-mos was only marginally useful in resolving these "deep" phylogenetic relationships.     

A comparative analysis of the upper thermal tolerance limits of eastern Pacific porcelain crabs, genus Petrolisthes: influences of latitude, vertical zonation, acclimation, and phylogeny

Marine intertidal organisms are subjected to a variety of abiotic stresses, including aerial exposure and wide ranges of temperature. Intertidal species generally have higher thermal tolerance limits than do subtidal species, and tropical species have higher thermal tolerance limits than do temperate species. The adaptive significance of upper thermal tolerance limits of intertidal organisms, however, has not been examined within a comparative context. Here, we present a comparative analysis of the adaptive significance of upper thermal tolerance limits in 20 congeneric species of porcelain crabs, genus Petrolisthes, from intertidal and subtidal habitats throughout the eastern Pacific. Upper thermal tolerance limits are positively correlated with surface water temperatures and with maximal microhabitat temperatures. Analysis of phylogenetically independent contrasts (from a phylogenetic tree on the basis of the 16s rDNA gene sequence) suggests that upper thermal tolerance limits have evolved in response to maximal microhabitat temperatures. Upper thermal tolerance limits increased during thermal acclimation at elevated temperatures, the amount of increase being greater for subtidal than for intertidal species. This result suggests that the upper thermal tolerance limits of some intertidal species may be near current habitat temperature maxima, and global warming thus may affect the distribution limits of intertidal species to a greater extent than for subtidal species.     

The diversification of the northern temperate woody flora – A case study of the Elm family (Ulmaceae) based on phylogenomic and paleobotanical evidence

Ulmaceae is a woody family widespread in northern temperate forests. Despite the ecological importance of this family, its phylogeny and biogeographic history are poorly understood. In this study, we reconstruct phylogenetic relationships within the family and infer spatio-temporal diversification patterns based on chloroplast genome (complete cpDNA) and nuclear ribosomal DNA sequences (nrDNA). The seven Ulmaceae genera are resolved in two main clades (temperate vs. tropical) by both cpDNA and nrDNA sequences. The temperate clade includes four genera, Hemiptelea, Zelkova, Planera, and Ulmus. The relationships among Planera and other genera are controversial because of inconsistent topologies between plastid and nuclear data. The tropical clade includes three genera ((Ampelocera, Phyllostylon), Holoptelea). Molecular dating and diversification analyses show that Ulmaceae originated in the Early Cretaceous (ca. 110–125 Ma) with the main lineages establishing from the Late Cretaceous to the early Eocene. The diversification rate slowed during the middle to the late Paleogene (ca. 23–45 Ma), followed by a rapid diversification of the East Asian temperate group in the Neogene, congruent with a global cooling event. The ancestral state optimization analysis suggests an East Asian origin of the temperate Ulmaceae clade during the Paleocene, which is consistent with the fossil record. Both phylogenomic and fossil evidence support East Asia as a center of origin and diversification for the temperate woody lineages.     

Phylogenetic inferences of Atelinae (Platyrrhini) based on multi-directional chromosome painting in Brachyteles arachnoides, Ateles paniscus paniscus and Ateles b. marginatus

We performed multi-directional chromosome painting in a comparative cytogenetic study of the three Atelinae species Brachyteles arachnoides, Ateles paniscus paniscus and Ateles belzebuth marginatus, in order to reconstruct phylogenetic relationships within this Platyrrhini subfamily. Comparative chromosome maps between these species were established by multi-color fluorescence in situ hybridization (FISH) employing human, Saguinus oedipus and Lagothrix lagothricha chromosome-specific probes. The three species included in this study and four previously analyzed species from all four Atelinae genera were subjected to a phylogenetic analysis on the basis of a data matrix comprised of 82 discrete chromosome characters. The results confirmed that Atelinae represent a monophyletic clade with a putative ancestral karyotype of 2n = 62 chromosomes. Phylogenetic analysis revealed an evolutionary branching sequence [Alouatta [Brachyteles [Lagothrix and Ateles]]] in Atelinae and [Ateles belzebuth marginatus [Ateles paniscus paniscus [Ateles belzebuth hybridus and Ateles geoffroyi]]] in genus Ateles. The chromosomal data support a re-evaluation of the taxonomic status of Ateles b. hybridus.     

Feeding behavior, toe count, and the phylogenetic relationships among alcedinine kingfishers (Alcedininae)

The pygmy kingfishers of the Old World tropics (Alcedininae) display a range of feeding behaviors, plumage types, and morphologies that have caused much taxonomic confusion in the group. We sequenced mitochondrial and nuclear genes to reconstruct a phylogenetic hypothesis for the subfamily, which was then used to examine the utility of common taxonomic characters. The phylogenetic hypothesis reveals multiple shifts between insectivory and piscivory, as well as homoplasy in bill color and plumage color. Piscivores and insectivores are interspersed across the tree, as are blue and rufous plumage types. It is apparent that reliance on these characters to delineate genera has resulted in classifications that do not describe natural groups. The sole taxonomic character examined that defines a natural division in the subfamily, toe count, is also the one generally dismissed as non-informative in the alcedinines, yet all species with a reduction in the number of toes form a clade. It is recommended that four genera be retained to describe the variation within pygmy kingfishers.     

Phylogeny and the modalities of acoustic diversification in extant Eneopterinae (Insecta, Orthoptera, Grylloidea, Eneopteridae)

Calling with a tegminal stridulatory apparatus is widespread in crickets. However, the evolution of cricket stridulums has been poorly studied and then only on the basis of prephylogenetic models, which are unable to account for the huge diversity recently documented for acoustic features in crickets. The present paper focuses on the evolution of acoustic devices in the subfamily Eneopterinae. This is the first attempt to reconstruct the phylogeny of a large and diverse cricket clade in order to analyze the evolution of emitting structures using precise homology statements. In the first step, we reconstruct the phylogeny of this clade using a morphological data set of 193 characters and 45 taxa. The resultant phylogeny supports the monophyly of the subfamily and that of the 13 genera represented by at least two species in our taxonomic sample. Phylogenetic relationships within the subfamily also support the definition of five tribes: Eurepini, Eneopterini, Nisitrini, Xenogryllini and Lebinthini. In the second step, the evolution of acoustic devices is studied by optimization of venation characters defined on precise homology statements. As hypothesized by previous authors, losses of acoustic communication occur independently in the course of eneopterine evolution; however, they happen abruptly with no intermediate state. Our results also document for the first time the modalities of forewing evolution: the diversification of male forewing venation originates from two processes, a continuous and regular modification process, responsible for slight venation change; and an irregular, more intense punctuated process, allowing the emergence of different venations. This diversification process with sudden changes could be related to the occurrence of acoustic novelties in advertisement calls.     

A comprehensive molecular phylogeny of tiger beetles (Coleoptera,Carabidae, Cicindelinae)

Tiger beetles are a remarkable group that captivates amateur entomologists, taxonomists and evolutionary biologists alike. This diverse clade of beetles comprises about 2300 currently described species found across the globe. Despite the charisma and scientific interest of this lineage, remarkably few studies have examined its phylogenetic relationships with large taxon sampling. Prior phylogenetic studies have focused on relationships within cicindeline tribes or genera, and none of the studies have included sufficient taxon sampling to conclusively examine broad species patterns across the entire subfamily. Studies that have attempted to reconstruct higher‐level relationships of Cicindelinae have yielded conflicting results. Here, we present the first taxonomically comprehensive molecular phylogeny of Cicindelinae to date, with the goal of creating a framework for future studies focusing on this important insect lineage. We utilized all available published molecular data, generating a final concatenated dataset including 328 cicindeline species, with molecular data sampled from six protein‐coding gene fragments and three ribosomal gene fragments. Our maximum‐likelihood phylogenetic inferences recover Cicindelinae as sister to the wrinkled bark beetles of the subfamily Rhysodinae. This new phylogenetic hypothesis for Cicindelinae contradicts our current understanding of tiger beetle phylogenetic relationships, with several tribes, subtribes and genera being inferred as paraphyletic. Most notably, the tribe Manticorini is recovered nested within Platychilini including the genera Amblycheila Say, Omus Eschscholtz, Picnochile Motschulsky and Platychile Macleay. The tribe Megacephalini is recovered as paraphyletic due to the placement of the monophyletic subtribe Oxycheilina as sister to Cicindelini, whereas the monophyletic Megacephalina is inferred as sister to Oxycheilina, Cicindelini and Collyridini. The tribe Collyridini is paraphyletic with the subtribes Collyridina and Tricondylina in one clade, and Ctenostomina in a second one. The tribe Cicindelini is recovered as monophyletic although several genera are inferred as para‐ or polyphyletic. Our results provide a novel phylogenetic framework to revise the classification of tiger beetles and to encourage the generation of focused molecular datasets that will permit investigation of the evolutionary history of this lineage through space and time.     

Phylogenetic relationships of tachinid flies in subfamily Exoristinae (Tachinidae: Diptera) based on 28S rDNA and elongation factor-1α

Abstract The phylogenetic relationships within the largest subfamily of Tachinidae, Exoristinae, were explored using nucleotide sequences of two genes (EF-1α and 28S rDNA). A total of fifty-five and forty-three taxa were represented in the analyses for each gene, respectively, representing forty-three genera. Neighbour joining, parsimony and maximum likelihood inference methods were employed to reconstruct phylogenetic relationships in separate analyses of each gene, and parsimony was used to analyse the combined dataset. Although certain taxa were highly mobile, phylogenetic reconstructions generally supported recent classification schemes based on reproductive habits and genitalia. Generally, the monophyly of Tachinidae and Exoristinae was supported. Tribes Winthemiini, Exoristini and Blondeliini were repeatedly constructed as monophyletic groups, with the former two clades often occupying a basal position among Exoristinae. Goniini and Eryciini generally clustered together as a derived clade within Exoristinae; however, they were never reconstructed as two distinct clades. These results suggest that the possession of unembryonated eggs is plesiomorphic within the subfamily and that there may have been multiple transitions between microtype and macrotype egg forms.     

Incomplete cryptic speciation between intertidal and subtidal morphs of Acrocnida brachiata (Echinodermata: Ophiuroidea) in the Northeast Atlantic

The brittle-star Acrocnida brachiata (Montagu) lives in sandy-bottom habitat of both intertidal and subtidal zones along the coasts of the northwestern Europe. An allozyme frequency-based survey (five enzyme loci) was combined with a mitochondrial (mt) COI haplotype analysis (598-bp sequences) on 17 populations to trace back past colonization pathways from the actual population structure of the species. Both genetic markers display a sharp genetic break between intertidal (clade I) and subtidal populations (clade S). This break corresponds to an allele frequency inversion at three enzyme loci (Hk, Pgm and Pgi) and a deep divergence of about 20% in mtCOI sequences between most of the intertidal populations and other samples. The geographic distribution of clade I seems to be more restricted than clade S as it is absent from the intertidal of the eastern English Channel and North Sea and may be replaced by clade S in south Brittany. Applying previously published rates of mutation, divergence between the two clades is estimated to pre-date 5 million years ago and may be due to allopatric speciation processes at the Mio-Pliocene transition. The occurrence of putative hybrids in a few localities, however, suggests incomplete cryptic speciation with secondary contact zones. The relative importance of colonization history vs. habitat specialization are discussed in the light of neutral evolution as tested from mtCOI gene sequences. While differential selection seems to have contributed little to the separation of the lineages, it may have played a role in the emergence of adaptive polymorphisms in the hybrid zone. Furthermore, congruent spatial patterns of differentiation were observed in both clades suggesting a recent increase in population size. These findings are in agreement with a recent expansion of the populations during or after the formation of the English Channel, from a southern refuge for the subtidal clade whereas the intertidal clade may have persisted further north. As previously suspected for a species with a very short pelagic larval phase, contemporary gene flow between distant or adjacent populations appears to be extremely reduced or even absent.     

Molecular phylogeny and evidence for an adaptive radiation of geophagine cichlids from South America (Perciformes: Labroidei)

Nucleotide sequences from the mitochondrial ND4 gene and the nuclear RAG2 gene were used to derive the most extensive molecular phylogeny to date for the Neotropical cichlid subfamily Geophaginae. Previous hypotheses of relationships were tested in light of these new data and a synthesis of all existing molecular information was provided. Novel phylogenetic findings included support for : (1) a 'Big Clade' containing the genera Geophagus sensu lato, Gymnogeophagus, Mikrogeophagus, Biotodoma, Crenicara, and Dicrossus; (2) a clade including the genera Satanoperca, Apistogramma, Apistogrammoides, and Taeniacara; and (3) corroboration for Kullander's clade Acarichthyini. ND4 demonstrated saturation effects at the third code position and lineage-specific rate heterogeneity, both of which influenced phylogeny reconstruction when only equal weighted parsimony was employed. Both branch lengths and internal branch tests revealed extremely short basal nodes that add support to the idea that geophagine cichlids have experienced an adaptive radiation sensu Schluter that involved ecomorphological specializations and life history diversification.     

Dracula ant phylogeny as inferred by nuclear 28S rDNA sequences and implications for ant systematics (Hymenoptera: Formicidae: Amblyoponinae)

Ants are one of the most ecologically and numerically dominant families of organisms in almost every terrestrial habitat throughout the world, though they include only about 1% of all described insect species. The development of eusociality is thought to have been a driving force in the striking diversification and dominance of this group, yet we know little about the evolution of the major lineages of ants and have been unable to clearly determine their primitive characteristics. Ants within the subfamily Amblyoponinae are specialized arthropod predators, possess many anatomically and behaviorally primitive characters and have been proposed as a possible basal lineage within the ants. We investigate the phylogenetic relationships among the members of the subfamily, using nuclear 28S rDNA sequence data. Outgroups for the analysis include members of the poneromorph and leptanillomorph (Apomyrma, Leptanilla) ant subfamilies, as well as three wasp families. Parsimony, maximum likelihood, and Bayesian analyses provide strong support for the monophyly of a clade containing the two genera Apomyrma+Mystrium (100% bpp; 97% ML bs; and 97% MP bs), and moderate support for the monophyly of the Amblyoponinae as long as Apomyrma (Apomyrminae) is included (87% bpp; 57% ML bs; and 76% MP bs). Analyses did not recover evidence of monophyly of the Amblyopone genus, while the monophyly of the other genera in the subfamily is supported. Based on these results we provide a morphological diagnosis of the Amblyoponinae that includes Apomyrma. Among the outgroup taxa, Typhlomyrmex grouped consistently with Ectatomma, supporting the recent placement of Typhlomyrmex in the Ectatomminae. The results of this present study place the included ant subfamilies into roughly two clades with the basal placement of Leptanilla unclear. One clade contains all the Amblyoponinae (including Apomyrma), Ponerinae, and Proceratiinae (Poneroid clade). The other clade contains members from subfamilies Cerapachyinae, Dolichoderinae, Ectatomminae, Formicinae, Myrmeciinae, and Myrmicinae (Formicoid clade).     

Infrafamilial Phylogeny of the Aquatic Angiosperm Podostemaceae Inferred from the Nucleotide Sequences of the matK Gene

Abstract: The infrafamilial relationships of Podostemaceae were deduced from nucleotide sequences of the chloroplast matK gene. The matK phylogenetic analyses show that Podostemaceae are composed of two major clades that correspond to the subfamily Tristichoideae sensu stricto and Weddellina and the subfamily Podostemoideae. Weddellina, which has long been recognized as a member of the Tristichoideae, is sister to the Podostemoideae, supporting the classification that recognized a third subfamily Weddellinoideae. Malaccotristicha malayana and Terniopsis sessilis form a basal clade in Tristichoideae sensu stricto. Tristichoideae show a high morphological diversity and, surprisingly, a close relationship exists between Dalzellia zeylanica and Indotristicha ramosissima, which remarkably differ in their body plans. A few genera defined by particular characters, such as Synstylis and Torrenticola, merge into clades of other larger genera. The Podostemoideae taxa studied are composed of two American clades, an Asian-Australian clade and a Madagascan clade, and may suggest that the subfamily perhaps originated in America and migrated to the Old World.     

Phylogeny of the Procyonidae (Mammalia: Carnivora): molecules, morphology and the Great American Interchange

The Procyonidae (Mammalia: Carnivora) have played a central role in resolving the controversial systematics of the giant and red pandas, but phylogenetic relationships of species within the family itself have received much less attention. Cladistic analyses of morphological characters conducted during the last two decades have resulted in topologies that group ecologically and morphologically similar taxa together. Specifically, the highly arboreal and frugivorous kinkajou (Potos flavus) and olingos (Bassaricyon) define one clade, whereas the more terrestrial and omnivorous coatis (Nasua), raccoons (Procyon), and ringtails (Bassariscus) define another clade, with the similar-sized Nasua and Procyon joined as sister taxa in this latter group. These relationships, however, have not been tested with molecular sequence data. We examined procyonid phylogenetics based on combined data from nine nuclear and two mitochondrial gene segments totaling 6534bp. We were able to fully resolve relationships within the family with strongly supported and congruent results from maximum parsimony, maximum likelihood, minimum evolution, and Bayesian analyses. We identified three distinct lineages within the family: a (Nasua, Bassaricyon) clade, a (Bassariscus, Procyon) clade, and a Potos lineage, the last of which is sister to the other two clades. These findings, which are in strong disagreement with prior fossil and morphology-based assessments of procyonid relationships, reemphasize the morphological and ecological flexibility of these taxa. In particular, morphological similarities between unrelated genera possibly reflect convergence associated with similar lifestyles and diets rather than ancestry. Furthermore, incongruence between the molecular supermatrix and a morphological character matrix comprised mostly of dental characters [Baskin, J.A., 2004. Bassariscus and Probassariscus (Mammalia, Carnivora, Procyonidae) from the early Barstovian (Middle Miocene). J. Vert. Paleo. 24, 709-720] may be due to non-independence among atomized dental characters that does not take into account the high developmental genetic correlation of these characters. Finally, molecular divergence dating analyses using a relaxed molecular clock approach suggest that intergeneric and intrageneric splits in the Procyonidae mostly occurred in the Miocene. The inferred divergence times for intrageneric splits for several genera whose ranges are bisected by the Panamanian Isthmus is significant because they suggest diversification well precedes the Great American Interchange, which has long been considered a primary underlying mechanism for procyonid evolution.     

Phylogenetic relationships of the carabid subfamily Harpalinae (Coleoptera) based on molecular sequence data

The carabid subfamily Harpalinae contains most of the species of carabid beetles. This subfamily, with over 19,000 species, radiated in the Cretaceous to yield a large clade that is diverse in morphological form and ecological habit. While there are several morphological, cytological, and chemical characters that unite most harpalines, the placement of some tribes within the subfamily remains controversial, as does the sister group relationships to this large group. In this study, DNA sequences from the 28S rDNA gene and the wingless nuclear protein-coding gene were collected from 52 carabid genera representing 31 harpaline tribes in addition to more than 21 carabid outgroup taxa to reconstruct the phylogeny of this group. Molecular sequence data from these genes, along with additional data from the 18S rDNA gene, were analyzed with a variety of phylogenetic analysis methods, separately for each gene and in a combined data approach. Results indicated that the subfamily Harpalinae is monophyletic with the enigmatic tribes of Morionini, Peleciini, and Pseudomorphini included within it. Brachinine bombardier beetles are closely related to Harpalinae as they form the sister group to harpalines or, in some analyses, are included within it or with austral psydrines. The austral psydrines are the sister group to Harpalinae+Brachinini clade in most analyses and austral psydrines+Brachinini+Harpalinae clade is strongly supported.     

Molecular phylogeny of the family Dicroglossidae (Amphibia: Anura) inferred from complete mitochondrial genomes

The fork-tongued frogs, members of the amphibian Order Anura, belong to the family Dicroglossidae and are one of the most diverse groups of Anuran frogs; however, their taxonomy and phylogeny remain controversial. In the present study, sixteen dicroglossine mitochondrial genomes representing nine dicroglossine genera and 23 other neobatrachian taxa, were used to reconstruct the phylogenetic relationships of the family Dicroglossidae using different partitioned maximum likelihood and partitioned Bayesian inference methods at both the nucleotide and amino acid levels. The sampled fork-tongued frogs form a strongly supported monophyletic group that is the sister taxon to another well-supported clade that includes representatives of the families Ranidae, Rhacophoridae, and Mantellidae. The monophyly of the subfamily Occidozyginae and Dicroglossinae was revealed with strong supports, and two major clades were supported within Dicroglossinae. The sister-group relationship between the genera Limnonectes and the tribe Paini was supported. In addition, a sister-group relationships between Fejervarya and Euphlyctis + Hoplobatrachus, between Quasipaa and Yerana, and between Feirana and Nanorana are well supported. Estimates of divergence times revealed the divergence of Dicroglossidae during the Late Upper Cretaceous to the Early Eocene, and diversification of the major dicroglossine genera from the Early Eocene to the Middle Miocene.     

Anatomy and phylogenetic analysis of the neotropical callichthyid catfishes (Ostariophysi, Siluriformes)

Based mainly on morphological characters, the phylogenetic relationships among genera and some species groups of the neotropical family Callichthyidae were examined. A study of the osteology of a generalized callichthyid, Callichthys callichthys (Linnaeus), with detailed comparisons among representatives of the remaining genera in the family, is presented and used as a basis for the phylogenetic analysis. A single most parsimonious tree supported the monophyly of the family Callichthyidae based on 28 derived features and the division of the family in the subfamilies Corydoradinae and Callichthyinae. In the subfamily Corydoradinae, the genus Aspidoras is the sister-group of the clade formed by Corydoras plus Brochis. Five derived features support the monophyly of this clade and four support the monophyly of Brochis. No characters, however, were found to support the genus Corydoras. In the subfamily Callichthyinae, Dianema and Hopbstemum are sister-taxa. Megalechis represents the sister-group of Dianema plus Hoplosternum and Lepthoplosternum represents the sister-group to Megalechis plus Dianema plus Hopbstemum. Finally, Callichthys is considered the least derived member of the subfamily, and is hypothesized as the sister-group of the remaining species. A key to all callichthyid genera is provided.     

Phylogenetic relationships within the New World subfamily Larreoideae (Zygophyllaceae) confirm polyphyly of the disjunct genus Bulnesia

The Larreoideae subfamily is the major representative of the family Zygophyllaceae in South America, where several of its members are common to dominant in arid regions of the Southern Cone. However, there are currently no phylogenetic analyses of the subfamily that may help to understand its origin and diversification. Additionally, there are taxonomic discrepancies around Bulnesia Gay (1845), one of its more important genera. Accordingly, we performed a phylogenetic analysis combining chloroplast (rbcL and trnL-F) and nuclear (ITS) DNA sequences. Bayesian and Parsimony analyses were performed to highlight the intergeneric relationships within Larreoideae. All genera with the exception of Bulnesia are monophyletic and we propose to redefine Bulnesia, dividing it in two genera. Furthermore, other taxonomic issues of the remaining genera are solved. This study represents the first approximation to clarify the phylogenetic relationships amongst all Larreoideae genera, producing a phylogenetic framework that can be used in future macro-ecological studies.     

Reconstructing the deep-branching relationships of the papilionoid legumes

Resolving the phylogenetic relationships of the deep nodes of papilionoid legumes (Papilionoideae) is essential to understanding the evolutionary history and diversification of this economically and ecologically important legume subfamily. The early-branching papilionoids include mostly Neotropical trees traditionally circumscribed in the tribes Sophoreae and Swartzieae. They are more highly diverse in floral morphology than other groups of Papilionoideae. For many years, phylogenetic analyses of the Papilionoideae could not clearly resolve the relationships of the early-branching lineages due to limited sampling. In the eight years since the publication of Legumes of the World, we have seen an extraordinary wealth of new molecular data for the study of Papilionoideae phylogeny, enabling increasingly greater resolution and many surprises. This study draws on recent molecular phylogenetic studies and a new comprehensive Bayesian phylogenetic analysis of 668 plastid matK sequences. The present matK phylogeny resolves the deep-branching relationships of the papilionoids with increased support for many clades, and suggests that taxonomic realignments of some genera and of numerous tribes are necessary. The potentially earliest-branching papilionoids fall within an ADA clade, which includes the recircumscribed monophyletic tribes Angylocalyceae, Dipterygeae, and Amburanae. The genera Aldina and Amphimas represent two of the nine main but as yet unresolved lineages comprising the large 50-kb inversion clade. The quinolizidine-alkaloid-accumulating Genistoid s.l. clade is expanded to include Dermatophyllum and a strongly supported and newly circumscribed tribe Ormosieae. Sophoreae and Swartzieae are dramatically reorganized so as to comprise monophyletic groups within the Core Genistoid clade and outside the 50-kb inversion clade, respectively. Acosmium is excluded from the Genistoids s.l. and strongly resolved within the newly circumscribed tribe Dalbergieae. By providing a better resolved phylogeny of the earliest-branching papilionoids, this study, in combination with other recent evidence, will lead to a more stable phylogenetic classification of the Papilionoideae.