Molecular systematics of Plethodon and Aneides (Caudata: Plethodontidae: Plethodontini): phylogenetic analysis of an old and rapid radiation

The closely related salamander genera Plethodon and Aneides (Plethodontidae) differ in morphology, behavior, and ecology. Although the systematics of these taxa has been the focus of much study, many details remain unresolved. To generate an hypothesis for the relationships among these taxa, I sequenced a segment of the mitochondrial protein-coding gene ND4 and portions of mitochondrial tRNAs. Taxa sampled were 5 species of Aneides, 7 species of western Plethodon, and 13 species of eastern Plethodon. Ensatina eschscholtzii was used as the outgroup. Phylogenetic analyses using maximum-parsimony, neighbor-joining, and maximum-likelihood consistently recovered some relationships. The eastern species of Plethodon are a robust, well-supported clade. Sister taxon relationships of P. elongatus and P. stormi, of P. dunni and P. vehiculum, and of A. hardii and the three west coast species of Aneides were also consistently resolved with good support. The monophyly of Aneides was only weakly supported in some analyses and there is no evidence for the monophyly of Plethodon or of the western species of Plethodon. Excluding the relatively distant outgroup, down-weighting saturated substitutions, and analyzing conserved data partitions did not yield additional resolution or support among the lineages of western Plethodon and Aneides. These results are consistent either with saturation of sequences, due to the age of the lineages, or with relatively rapid radiation. An old, rapid radiation is consistent with the results of previous studies. An analysis of current taxonomy within the phylogenetic framework presented here retains Aneides and recognizes Plethodon as a metataxon (indicated with an asterisk, Plethodon*).     

A molecular phylogenetic analysis of the family Rhacophoridae with an emphasis on the Asian and African genera

Using characters from mitochondrial DNA to construct maximum parsimony and maximum likelihood trees, we performed a phylogenetic analysis on representative species of 14 genera: 12 that belong to the treefrog family Rhacophoridae and two, Amolops and Rana, that are not rhacophorids. Our results support a phylogenetic hypothesis that depicts a monophyletic family Rhacophoridae. In this family, the Malagasy genera Aglyptodactylus, Boophis, Mantella, and Mantidactylus form a well-supported sister clade to all other rhacophorid genera, and Mantella is the sister taxon to Mantidactylus. Within the Asian/African genera, the genus Buergeria forms a well-supported clade of four species. The genera, except for Chirixalus, are generally monophyletic. An exception to this is that Polypedates dennysii clusters with species of Rhacophorus, suggesting that the taxonomy of the rhacophorids should be revised to reflect this relationship. Chirixalus is not monophyletic. Unexpectedly, there is strong support for Chirixalus doriae from Southeast Asia forming a clade with species of the African genus Chiromantis, suggesting that Chiromantis dispersed to Africa from Asia. Also, there is strong support for the sister taxon relationship of Chirixalus eiffingeri and Chirixalus idiootocus apart from other congeners.     

Utility of the white gene in estimating phylogenetic relationships among mosquitoes (Diptera: Culicidae)

The utility of a nuclear protein-coding gene for reconstructing phylogenetic relationships within the family Culicidae was explored. Relationships among 13 species representing three subfamilies and nine genera of Culicidae were analyzed using a 762-bp fragment of coding sequence from the eye color gene, white. Outgroups for the study were two species from the sister group Chaoboridae. Sequences were determined from clone PCR products amplified from genomic DNA, and aligned following conceptual intron splicing and amino acid translation. Third codon positions were characterized by high levels of divergence and biased nucleotide composition, the intensity and direction of which varied among taxa. Equal weighting of all characters resulted in parsimony and neighboring-joining trees at odds with the generally accepted phylogenetic hypothesis based on morphology and rDNA sequences. The application of differential weighting schemes recovered the traditional hypothesis, in which the subfamily Anophelinae formed the basal clade. The subfamily Toxorhynchitinae occupied an intermediate position, and was a sister group to the subfamily Culicinae. Within Culicinae, the genera Sabethes and Tripteroides formed an ancestral clade, while the Culex-Deinocerites and Aedes- Haemagogus clades occupied increasingly derived positions in the molecular phylogeny. An intron present in the Culicinae- Toxorhynchitinae lineage and one outgroup taxon was absent in the basal Anophelinae lineage and the second outgroup taxon, suggesting that intron insertions or deletions may not always be reliable systematic characters.      

DO LARVAL TRAITS RE‐EVOLVE? EVIDENCE FROM THE EMBRYOGENESIS OF A DIRECT‐DEVELOPING SALAMANDER,PLETHODON CINEREUS

Recent molecular phylogenies suggest the surprising reacquisition of posthatching metamorphosis within an otherwise direct-developing clade of lungless salamanders (family Plethodontidae). Metamorphosis was long regarded as plesiomorphic for plethodontids, yet the genus Desmognathus, which primarily includes metamorphosing species, is now nested within a much larger clade of direct-developing species. The extent to which the putative reacquisition of metamorphosis in Desmognathus represents a true evolutionary reversal is contingent upon the extent to which both larva-specific features and metamorphosis were actually lost during the evolution of direct development. In this study we analyze development of the hyobranchial skeleton, which is dramatically remodeled during salamander metamorphosis, in the direct-developing red-backed salamander, Plethodon cinereus. We find dramatic remodeling of the hyobranchial skeleton during embryogenesis in P. cinereus and the transient appearance of larva-specific cartilages. Hyobranchial development in this direct-developing plethodontid is highly similar to that in metamorphosing plethodontids (e.g., Desmognathus). The proposed reacquisition of hyobranchial metamorphosis within Desmognathus does not represent the "re-evolution" of a lost phenotype, but instead the elaboration of an existing developmental sequence.     

Molecular phylogeny of new world primates (Platyrrhini) based on beta2-microglobulin DNA sequences

Neotropical primates, traditionally grouped in the infraorder Platyrrhini, comprise 16 extant genera. Cladistic analyses based on morphological characteristics and molecular data resulted in topologic arrangements depicting disparate phylogenetic relationships, indicating that the evolution of gross morphological characteristics and molecular traits is not necessarily congruent. Here we present a phylogenetic arrangement for all neotropical primate genera obtained from DNA sequence analyses of the beta2-microglobulin gene. Parsimony, distance, and maximum likelihood analyses favored two families, Atelidae and Cebidae, each containing 8 genera. Atelids were resolved into atelines and pitheciines. The well-supported ateline clade branched into alouattine (Alouatta) and ateline (Ateles, Lagothrix, Brachyteles) clades. In turn, within the Ateline clade, Lagothrix and Brachyteles were well-supported sister groups. The pitheciines branched into well-supported callicebine (Callicebus) and pitheciine (Pithecia, Cacajao, Chiropotes) clades. In turn, within the pitheciine clade, Cacajao and Chiropotes were well-supported sister groups. The cebids branched into callitrichine (Saguinus, Leontopithecus, Callimico, Callithrix-Cebuella), cebine (Cebus, Saimiri), and aotine (Aotus) clades. While the callitrichine clade and the groupings of species and genera within this clade were all well supported, the cebine clade received only modest support, and the position of Aotus could not be clearly established. Cladistic analyses favored the proposition of 15 rather than 16 extant genera by including Cebuella pygmaea in the genus Callithrix as the sister group of the Callithrix argentata species group. These analyses also favored the sister grouping of Callimico with Callithrix and then of Leontopithecus with the Callithrix-Callimico clade.     

Pleistocene climatic fluctuations explain the disjunct distribution and complex phylogeographic structure of the Southern Red-backed Salamander, <Emphasis Type="Italic">Plethodon serratus</Emphasis>

The southeastern United States (U.S.) has experienced dynamic climatic changes over the past several million years that have impacted species distributions. In many cases, contiguous ranges were fragmented and a lack of gene flow between allopatric populations led to genetic divergence and speciation. The Southern Red-backed Salamander, Plethodon serratus, inhabits four widely disjunct regions of the southeastern U.S.: the southern Appalachian Mountains, the Ozark Plateau, the Ouachita Mountains, and the Southern Tertiary Uplands of central Louisiana. We integrated phylogenetic analysis of mitochondrial DNA sequences (1399 base pairs) with ecological niche modeling to test the hypothesis that climate fluctuations during the Pleistocene drove the isolation and divergence of disjunct populations of P. serratus. Appalachian, Ozark, and Louisiana populations each formed well-supported clades in our phylogeny. Ouachita Mountain populations sorted into two geographically distinct clades; one Ouachita clade was sister to the Louisiana clade whereas the other Ouachita clade grouped with the Appalachian and Ozark clades but relationships were unresolved. Plethodon serratus diverged from its sister taxon, P. sherando, ~5.4 million years ago (Ma), and lineage diversification within P. serratus occurred ~1.9–0.6 Ma (Pleistocene). Ecological niche models showed that the four geographic isolates of P. serratus are currently separated by unsuitable habitat, but the species was likely more continuously distributed during the colder climates of the Pleistocene. Our results support the hypothesis that climate-induced environmental changes during the Pleistocene played a dominant role in driving isolation and divergence of disjunct populations of P. serratus.     

CAN PARALLEL DIVERSIFICATION OCCUR IN SYMPATRY? REPEATED PATTERNS OF BODY‐SIZE EVOLUTION IN COEXISTING CLADES OF NORTH AMERICAN SALAMANDERS

A classic paradigm in evolutionary biology is that geographically isolated clades inhabiting similar selective regimes will diversify to create similar sets of phenotypes in different locations (e.g., similar stickleback species in different lakes, similar Anolis ecomorphs on different islands). Such parallel radiations are not generally expected to occur in sympatry because the available niche space would be filled by whichever clade is diversified first. Here, we document a very different pattern, the parallel evolution of similar body-size morphs in three sympatric clades of plethodontid salamanders ( Desmognathus, Plethodon, Spelerpinae) in eastern North America. Using a comprehensive, time-calibrated phylogeny of North American plethodontids from nuclear and mitochondrial DNA sequences, we show that these three clades have undergone replicated patterns of evolution in body size and that this parallel diversification occurred in broad-scale sympatry. At the local scale, we find that coexisting species from these clades are more similar in body size than expected under a null model in which species are randomly assembled into communities. These patterns are particularly surprising in that competition is known to be important in driving phenotypic diversification and limiting local coexistence of similar-sized species within these clades. Although parallel diversification of sympatric clades may seem counterintuitive, we discuss several ecological and evolutionary factors that may allow the phenomenon to occur.     

A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata)

We examine phylogenetic relationships among salamanders of the family Salamandridae using approximately 2700 bases of new mtDNA sequence data (the tRNALeu, ND1, tRNAIle, tRNAGln, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI genes and the origin for light-strand replication) collected from 96 individuals representing 61 of the 66 recognized salamandrid species and outgroups. Phylogenetic analyses using maximum parsimony and Bayesian analysis are performed on the new data alone and combined with previously reported sequences from other parts of the mitochondrial genome. The basal phylogenetic split is a polytomy of lineages ancestral to (1) the Italian newt Salamandrina terdigitata, (2) a strongly supported clade comprising the "true" salamanders (genera Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), and (3) a strongly supported clade comprising all newts except S. terdigitata. Strongly supported clades within the true salamanders include monophyly of each genus and grouping Chioglossa and Mertensiella as the sister taxon to a clade comprising Lyciasalamandra and Salamandra. Among newts, genera Echinotriton, Pleurodeles, and Tylototriton form a strongly supported clade whose sister taxon comprises the genera Calotriton, Cynops, Euproctus, Neurergus, Notophthalmus, Pachytriton, Paramesotriton, Taricha, and Triturus. Our results strongly support monophyly of all polytypic newt genera except Paramesotriton and Triturus, which appear paraphyletic, and Calotriton, for which only one of the two species is sampled. Other well-supported clades within newts include (1) Asian genera Cynops, Pachytriton, and Paramesotriton, (2) North American genera Notophthalmus and Taricha, (3) the Triturus vulgaris species group, and (4) the Triturus cristatus species group; some additional groupings appear strong in Bayesian but not parsimony analyses. Rates of lineage accumulation through time are evaluated using this nearly comprehensive sampling of salamandrid species-level lineages. Rate of lineage accumulation appears constant throughout salamandrid evolutionary history with no obvious fluctuations associated with origins of morphological or ecological novelties.     

Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data

Phylogenetic relationships were studied based on DNA sequences obtained from all recognized genera of the family Corvidae sensu stricto . The aligned data set consists 2589 bp obtained from one mitochondrial and two nuclear genes. Maximum parsimony, maximum-likelihood, and Bayesian inference analyses were used to estimate phylogenetic relationships. The analyses were done for each gene separately, as well as for all genes combined. An analysis of a taxonomically expanded data set of cytochrome b sequences was performed in order to infer the phylogenetic positions of six genera for which nuclear genes could not be obtained. Monophyly of the Corvidae is supported by all analyses, as well as by the occurrence of a deletion of 16 bp in the β-fibrinogen intron in all ingroup taxa. Temnurus and Pyrrhocorax are placed as the sister group to all other corvids, while Cissa and Urocissa appear as the next clade inside them. Further up in the tree, two larger and well-supported clades of genera were recovered by the analyses. One has an entirely New World distribution (the New World jays), while the other includes mostly Eurasian (and one African) taxa. Outside these two major clades are Cyanopica and Perisoreus whose phylogenetic positions could not be determined by the present data. A biogeographic analysis of our data suggests that the Corvidae underwent an initial radiation in Southeast Asia. This is consistent with the observation that almost all basal clades in the phylogenetic tree consist of species adapted to tropical and subtropical forest habitats.     

Toward understanding Anophelinae (Diptera,Culicidae) phylogeny: insights from nuclear single-copy genes and the weight of evidence

A phylogeny of the mosquito subfamily Anophelinae was inferred from fragments of two protein-coding nuclear genes, G6pd (462 bp) and white (801 bp), and from a combined data set (2,136 bp) that included a portion of the mitochondrial gene ND5 and the D2 region of the ribosomal 28S gene. Sixteen species from all three anopheline genera and six Anopheles subgenera were sampled, along with six species of other mosquitoes used as an outgroup. Each of four genes analyzed individually recovered the same well-supported clades; topological incongruence was limited to unsupported or poorly supported nodes. As assessed by the incongruence length difference test, most of the conflicting signal was contributed by third codon positions. Strong structural constraints, as observed in white and G6pd, apparently had little impact on phylogenetic inference. Compared with the other genes, white provided a superior source of phylogenetic information. However, white appears to have experienced accelerated rates of evolution in few lineages, the affinities of which are therefore suspect. In combined analyses, most of the inferred relationship were well-supported and in agreement with previous studies: monophyly of Anophelinae, basal position of Chagasia, monophyly of Anopheles subgenera, and subgenera Nyssorhynchus + Kerteszia as sister taxa. The results suggested also monophyletic origin of subgenera Cellia + Anopheles, and the white gene analysis supported genus Bironella as a sister taxon to Anopheles. The present data and other available evidence suggest a South American origin of Anophelinae, probably in the Mesozoic; a rapid diversification of Bironella and basal subgeneric lineages of Anopheles, potentially associated with the breakup of Gondwanaland; and a relatively recent and rapid dispersion of subgenus Anopheles.     

Molecular phylogenetics of the bee-eaters (Aves: Meropidae) based on nuclear and mitochondrial DNA sequence data

The bee-eaters (family Meropidae) comprise a group of brightly colored, but morphologically homogeneous, birds with a wide variety of life history characteristics. A phylogeny of bee-eaters was reconstructed using nuclear and mitochondrial DNA sequence data from 23 of the 25 named bee-eater species. Analysis of the combined data set provided a well-supported phylogenetic hypothesis for the family. Nyctiornis is the sister taxon to all other bee-eaters. Within the genus Merops, we recovered two well-supported clades that can be broadly separated into two groups along geographic and ecological lines, one clade with mostly African resident species and the other clade containing a mixture of African and Asian taxa that are mostly migratory species. The clade containing resident African species can be further split into two groups along ecological lines by habitat preference into lowland forest specialists and montane forest and forest edge species. Intraspecific sampling in several of the taxa revealed moderate to high (3.7-6.5%, ND2) levels of divergence in the resident taxa, whereas the lone migratory taxon showed negligible levels of intraspecific divergence. This robust molecular phylogeny provides the phylogenetic framework for future comparative tests of hypotheses about the evolution of plumage patterns, sociality, migration, and delayed breeding strategies.     

Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia)

A large‐scale phylogenetic study is presented for Cucujoidea (Coleoptera), a diverse superfamily of beetles that historically has been taxonomically difficult. This study is the most comprehensive analysis of cucujoid taxa to date, with DNA sequence data sampled from eight genes (four nuclear, four mitochondrial) for 384 coleopteran taxa, including exemplars of 35 (of 37) families and 289 genera of Cucujoidea. Maximum‐likelihood analyses of these data present many significant relationships, some proposed previously and some novel. Tenebrionoidea and Lymexyloidea are recovered together and Cleroidea forms the sister group to this clade. Chrysomeloidea and Curculionoidea are recovered as sister taxa and this clade (Phytophaga) forms the sister group to the core Cucujoidea (Cucujoidea s.n .). The nitidulid series is recovered as the earliest‐diverging core cucujoid lineage, although the earliest divergences among core Cucujoidea are only weakly supported. The cerylonid series (CS) is recovered as monophyletic and is supported as a major Cucujiform clade, sister group to the remaining superfamilies of Cucujiformia. Currently recognized taxa that were not recovered as monophyletic include Cucujoidea, Endomychidae, Cerylonidae and Bothrideridae. Biphyllidae and Byturidae were recovered in Cleroidea. The remaining Cucujoidea were recovered in two disparate major clades: one comprising the nitidulid series + erotylid series + Boganiidae and Hobartiidae + cucujid series, and the other comprising the cerylonid series. Propalticidae are recovered within Laemophloeidae. The cerylonid series includes two major clades, the bothriderid group and the coccinellid group. Akalyptoischiidae are recovered as a separate clade from Latridiidae. Eupsilobiinae are recovered as the sister taxon to Coccinellidae. In light of these findings, many formal changes to cucujiform beetle classification are proposed. Biphyllidae and Byturidae are transferred to Cleroidea. The cerylonid series is formally recognized as a new superfamily, Coccinelloidea stat.n. Current subfamilies elevated (or re‐elevated) to family status include: Murmidiidae stat.n. , Teredidae stat.n. , Euxestidae stat.n. , Anamorphidae stat.rev. , Eupsilobiidae stat.n. , and Mycetaeidae stat.n. The following taxa are redefined and characterized: Cleroidea s.n. , Cucujoidea s.n. , Cerylonidae s.n. , Bothrideridae s.n. , Endomychidae s.n. A new subfamily, Cyclotominae stat.n. , is described. Stenotarsinae syn.n. is formally subsumed within a new concept of Endomychinae s.n.     

Systematics of dusky salamanders, Desmognathus (Caudata: Plethodontidae), in the mountain and Piedmont regions of Virginia and North Carolina, USA

We analysed mitochondrial (cytochrome  b ) nucleotide sequences, nuclear allozyme markers, and morphometric characters to investigate species boundaries and phylogenetic relationships among dusky salamanders ( Desmognathus ) in the southern Blue Ridge and adjacent Piedmont Physiographic Provinces of Virginia and North Carolina. Our results revealed four distinct mitochondrial DNA clades that are also characterized by distinct allozyme markers. One clade consists of sequences derived from populations distributed from New England to south-western Virginia that are referable to Desmognathus fuscus Rafinesque, 1820, although there is considerable sequence and allozyme divergence within this clade. A second clade consists of sequences derived from populations referable to Desmognathus planiceps Newman, 1955, a form that we resurrect from its long synonymy under D. fuscus . Desmognathus planiceps and D. fuscus also differ in mandibular tooth shape. Two other cytochrome  b sequences recovered from populations along the Blue Ridge escarpment in southern Virginia are quite divergent from those of the previous two clades, and these populations may represent yet another distinct species. Sequences from a population in the Brushy Mountains in the Piedmont of northern North Carolina are similar to those of Desmognathus carolinensis . Population groupings indicated by allozyme data generally correspond to the cytochrome  b clades. Cryptic diversity in Appalachian desmognathan salamanders clearly requires further study. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 115–130.     

Plethodontid salamander mitochondrial genomics: A parsimony evaluation of character conflict and implications for historical biogeography

A new parsimony analysis of 27 complete mitochondrial genomic sequences is conducted to investigate the phylogenetic relationships of plethodontid salamanders. This analysis focuses on the amount of character conflict between phylogenetic trees recovered from newly conducted parsimony searches and the Bayesian and maximum likelihood topology reported by Mueller et al. (2004 ; PNAS, 101, 13820–13825). Strong support for Hemidactylium as the sister taxon to all other plethodontids is recovered from parsimony analyses. Plotting area relationships on the most parsimonious phylogenetic tree suggests that eastern North America is the origin of the family Plethodontidae supporting the “Out of Appalachia” hypothesis. A new taxonomy that recognizes clades recovered from phylogenetic analyses is proposed. © The Willi Hennig Society 2005.     

Molecular phylogenetics of the butterflyfishes (Chaetodontidae): taxonomy and biogeography of a global coral reef fish family

Marine butterflyfishes (10 genera, 114 species) are conspicuously beautiful and abundant animals found on coral reefs worldwide, and are well studied due to their ecological importance and commercial value. Several phylogenies based on morphological and molecular data exist, yet a well-supported molecular phylogeny at the species level for a wide range of taxa remains to be resolved. Here we present a molecular phylogeny of the butterflyfishes, including representatives of all genera (except Parachaetodon) and at least one representative of all commonly cited subgenera of Chaetodon (except Roa sensuBlum, 1988). Genetic data were collected for 71 ingroup and 13 outgroup taxa, using two nuclear and three mitochondrial genes that total 3332 nucleotides. Bayesian inference, parsimony, and maximum likelihood methods produced a well-supported phylogeny with strong support for a monophyletic Chaetodontidae. The Chaetodon subgenera Exornator and Chaetodon were found to be polyphyletic, and the genus Amphichaetodon was not the basal sister group to the rest of the family as had been previously proposed. Molecular phylogenetic analysis of data from 5 genes resolved some clades in agreement with previous phylogenetic studies, however the topology of relationships among major butterflyfish groups differed significantly from previous hypotheses. The analysis recovered a clade containing Amphichaetodon, Coradion, Chelmonops, Chelmon, Forcipiger, Hemitaurichthys, Johnrandallia, and Heniochus. Prognathodes was resolved as the sister to all Chaetodon, as in previous hypotheses, although the topology of subgeneric clades differed significantly from hypotheses based on morphology. We use the species-level phylogeny for the butterflyfishes to resolve long-standing questions regarding the use of subgenera in Chaetodon, to reconstruct molecular rates and estimated dates of diversification of major butterflyfish clades, and to examine global biogeographic patterns.     

Combined mitochondrial and nuclear sequences support the monophyly of forcipulatacean sea stars

Previous molecular phylogenetic analyses of forcipulatacean sea stars (Echinodermata: Asteroidea) have reconstructed a non-monophyletic order Forcipulatida, provided that two or more forcipulate families are included. This result could mean that one or more assumptions of the reconstruction method was violated, or else the traditional classification could be erroneous. The present molecular phylogenetic analysis included 12 non-forcipulatacean and 39 forcipulatacean sea stars, with multiple representatives of all but one of the forcipulate families and/or subfamilies. Bayesian analysis of approximately 4.2kb of sequence data representing seven partitions (nuclear 18S rRNA and 28S rRNA, mitochondrial 12S rRNA, 16S rRNA, 5 tRNAs and cytochrome oxidase I with first and second codon positions analyzed separately from third codon positions) recovered a consensus tree with three well-supported clades (78%-100% bootstrap support) that corresponded at least approximately to traditional taxonomic ranks: the superorder Forcipulatacea (Forcipulatida + Brisingida) + Pteraster, the Brisingida/Brisingidae and Asteriidae + Rathbunaster + Pycnopodia. When a molecular clock was enforced, the partitioned Bayesian analysis recovered the traditional Forcipulatacea. Five of six genera represented by two or more species were monophyletic with 100% bootstrap support. Most of the traditional subfamilial and familial groupings within the Forcipulatida were either unresolved or non-monophyletic. The separate partitions differed considerably in estimates of model parameters, mainly between nuclear sequences (with high GC content, low rates of sequence substitution and high transition/transversion rate ratios) and mitochondrial sequences.     

A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family

Phylogenetic analysis of 330 plastid matK gene sequences, representing 235 genera from 37 of 39 tribes, and four outgroup taxa from eurosids I supports many well-resolved subclades within the Leguminosae. These results are generally consistent with those derived from other plastid sequence data (rbcL and trnL), but show greater resolution and clade support overall. In particular, the monophyly of subfamily Papilionoideae and at least seven major subclades are well-supported by bootstrap and Bayesian credibility values. These subclades are informally recognized as the Cladrastis clade, genistoid sensu lato, dalbergioid sensu lato, mirbelioid, millettioid, and robinioid clades, and the inverted-repeat-lacking clade (IRLC). The genistoid clade is expanded to include genera such as Poecilanthe, Cyclolobium, Bowdichia, and Diplotropis and thus contains the vast majority of papilionoids known to produce quinolizidine alkaloids. The dalbergioid clade is expanded to include the tribe Amorpheae. The mirbelioids include the tribes Bossiaeeae and Mirbelieae, with Hypocalypteae as its sister group. The millettioids comprise two major subclades that roughly correspond to the tribes Millettieae and Phaseoleae and represent the only major papilionoid clade marked by a macromorphological apomorphy, pseudoracemose inflorescences. The robinioids are expanded to include Sesbania and members of the tribe Loteae. The IRLC, the most species-rich subclade, is sister to the robinioids. Analysis of the matK data consistently resolves but modestly supports a clade comprising papilionoid taxa that accumulate canavanine in the seeds. This suggests a single origin for the biosynthesis of this most commonly produced of the nonprotein amino acids in legumes.     

Molecular evolution of southern North American Cyprinidae (Actinopterygii), with the description of the new genus Tampichthys from central Mexico

Most of the recognized species of the genus Dionda inhabit drainages of the Gulf of Mexico from central Mexico to central Texas, USA, and have been considered a monophyletic group based on morphological, osteological, and allozyme investigations. Phylogenetic relationships of 15 species of Dionda and 34 species from closely related genera were inferred from one mitochondrial (cytb) and three nuclear gene sequences (S7, Rhodopsin, Rag1) totaling 4487 nucleotides. Separate analyses of all four genes yield congruent phylogenies; however the 15 putative species of Dionda evaluated were never recovered as a monophyletic group when species from nine related genera were included in the analyses. Among the ingroup taxa, one well-supported and highly divergent clade is consistently recognized and consists of six recognized and three undescribed northern species currently recognized in the genus Dionda. These nine species inhabit present or past tributaries of the Rio Grande basin of northern Mexico and southern USA, and were recovered as a basal clade in all analyses. Another large, also strongly supported clade, consisting of seven genera, include five southern recognized species currently in the genus Dionda, forming the sister group to the Codoma clade. These five species comprise the "Southern Dionda clade" and inhabit headwaters of the Pánuco-Tamesí drainage and some adjacent coastal rivers in the Tampico Embayment. The consistent and repeated identification of eight different clades recovered in most of the separate gene analyses strongly supports a division of the non-natural genus Dionda. A new genus, Tampichthys, is proposed for the clade of species endemic to east-central Mexico and formerly in Dionda. Tampichthys and the putative monotypic genus Codoma are more related to Mexican species of the genera Cyprinella and Notropis than to other species referred to Dionda sensu stricto.     

Higher-level phylogeny and morphological evolution of tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannida)

Despite increased understanding of higher-level relationships in passerine birds in the last 15 years, the taxonomic boundaries and phylogenetic interrelationships of the major groups of the Tyrannida (including the cotingas, manakins, tityrines, and tyrant flycatchers) remain unclear. Here, we present an analysis of DNA sequence data obtained from two nuclear exons, three introns, and one mitochondrial gene for 26 genera of Tyrannida and 6 tracheophone outgroups. The analysis resulted in well-supported hypotheses about the earliest evolution within Tyrannida. The Cotingidae, Pipridae, Tityrinae (sensu) [Prum, R.O., Rice, N.H., Mobley, J.A., Dimmick, W.W., 2000. A preliminary phylogenetic hypothesis for the cotingas (Cotingidae) based on mitochondrial DNA. Auk 117, 236-241], Tyrannidae, and the tyrannid subfamiles Tyranninae and Pipromorphinae (sensu) [Sibley, C.G., Monroe, B. L. Jr., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT] were all found to be reciprocally monophyletic (given the present taxon sampling). The Cotingidae and Pipridae form a clade that is the sister group to a well-supported clade including Oxyruncus, the Tityrinae, Piprites, and the Tyrannidae. Oxyruncus is the sister group to the Tityrinae, and Piprites is placed as the sister group to the Tyrannidae. The tyrannid subfamilies Tyranninae and Pipromorphinae are monophyletic sister taxa, but the relationships of Platyrinchus mystaceus to these two clades remains ambiguous. The presence of medial (=internal) cartilages in the syrinx is a synapomorphy for the Oxyruncus-Tityrinae-Piprites-Tyrannidae clade. Although morphological synapomorphies currently support the monophyly of both the Pipridae and the Cotingidae, convergences and/or reversals in morphological character states are common in Tyrannida. The relationship between Oxyruncus and the Tityrinae is congruent with additional syringeal synapomorphies and allozyme distance data. Accordingly, we propose the recognition the family Tityridae within the Tyrannida to include the genera Schiffornis, Laniisoma, Laniocera, Iodopleura, Xenopsaris, Pachyramphus, Tityra, and Oxyruncus.     

Phylogeny of the plant bug subfamily Mirinae (Hemiptera: Heteroptera: Cimicomorpha: Miridae) based on total evidence analysis

The first comprehensive phylogenetic analyses of the most diverse subfamily of plant bugs, Mirinae, is presented in this study, for 110 representative taxa based on total evidence analysis. A total of 85 morphological characters and 3898 bp of mitochondrial (16S, COI) and nuclear (18S, 28S) sequences were analysed for each partitioned and combined dataset based on parsimony, maximum likelihood and Bayesian inference. Major results obtained in this study include monophyly of the tribe Mecistoscelini. The largest tribe, Mirini, was recovered as polyphyletic, and Stenodemini was recovered as paraphyletic. The clade of Stenodemini + Mecistoscelini is the sister group of the remaining Mirinae. The monophyly of two complexes composed of superficially similar genera were tested; the Lygus complex was recovered as nonmonophyletic, and the Adelphocoris–Creontiades–Megacoelum complex was confirmed to be monophyletic. The generic relationships of the main clades within each tribe based on the phylogeny, as well as their supported morphological characters, are discussed.