Molecular phylogeny of plethodonine salamanders and hylid frogs: statistical analysis of protein comparisons.

The bootstrapping method of determining confidence in the topology of phylogenetic trees has been applied to electrophoretic protein data for two groups of amphibians: salamanders of two North American genera (Aneides and Plethodon) of the tribe Plethodontini and Holarctic hylid frogs. Some current methods of phylogenetic reconstruction for electrophoretic protein data have been evaluated by comparing the trees obtained from molecular data sets with available morphological data. Molecular data on the phylogenetic relationships of Aneides and Plethodon, data obtained from electrophoretic and immunological studies, indicate that Aneides probably was derived from western Plethodon subsequent to the separation of eastern and western Plethodon. Thus Plethodon very likely is a paraphyletic genus. The extremely low rate of morphological evolution in Plethodon compared with that in Aneides causes difficulty in indicating their evolutionary relationships taxonomically because there are no synapomorphic morphological characters that define either eastern or western Plethodon, whereas there are several for the genus Aneides. Thus molecular data alone probably indicate the evolutionary relationships of the species in these genera. Highton and Larson's (1979) arrangement of species of Plethodon into eight species groups is supported. The topologies of the unweighted pair-group method using arithmetic means (UPGMA) and distance Wagner trees were compared with independent morphological and molecular data on the relationships of the 28 plethodonine species. It was found that UPGMA trees indicate relationships that are more in agreement with other information than are those provided by distance Wagner trees. The use of the bootstrap technique indicates that the topologies of UPGMA trees are better supported statistically than are the topologies of distance Wagner trees. Moreover, different addition criteria produce a variety of distance Wagner trees with different topologies, each with several groupings that are not supported statistically. It is concluded that considerable caution should be used in interpreting the topology of distance Wagner trees. Very similar results were obtained with a second data set on 30 taxa of Holarctic hylid frogs. Trees obtained by the neighbor-joining method are more in agreement with UPGMA phenograms and other data, so this method of phylogenetic reconstruction may be useful to systematists not willing to assume constant rates of evolution.(ABSTRACT TRUNCATED AT 400 WORDS)     

Molecular phylogenetic analysis of the dragonfly genera Libellula, Ladona, and Plathemis (Odonata: Libellulidae) based on mitochondrial cytochrome oxidase I and 16S rRNA sequence data

Molecular phylogenetic relationships among members of the odonate genus Libellula (Odonata: Anisoptera: Libellulidae) were examined using 735 bp of mitochondrial COI and 416 bp of 16S ribosomal RNA gene sequences. Considerable debate exists over several relationships within Libellula, as well over the status of two putative genera often placed as subgenera within Libellula: Ladona and Plathemis. Parsimony and maximum-likelihood analyses of the separate and combined data sets indicate that Plathemis is basal and monophyletic and that Ladona is the sister clade to the remainder of Libellula sensu stricto (s.s.) (all species within the genus Libellula, excluding Plathemis and Ladona). Moreover, two European taxa, Libellula fulva and L. depressa, were found to occupy a sister group relationship within the Ladona clade. Relationships within Libellula s.s. are less well resolved. However, monophyletic lineages within the genus are largely consistent with morphologically based subgeneric classifications. Although tree topologies from each analysis differed in some details, the differences were in no case statistically significant. The analysis of the combined COI and 16S data yielded trees with overall stronger support than analyses of either gene alone. Several analyses failed to support the monophyly of Libellula sensu lato due to the inclusion of one or more outgroup species. However, statistical comparisons of topologies produced by unconstrained analyses and analyses in which the monophyly of Libellula was constrained indicate that any differences are nonsignificant. Based on morphological data, we therefore reject the paraphyly of Libellula and accept the outgroup status of Orthemis ferruginea and Pachydiplax longipennis.     

A multigenic perspective on phylogenetic relationships in the largest family of salamanders, the Plethodontidae

Despite several recent studies, the phylogeny of plethodontid salamanders is not yet fully resolved and the phylogenetic positions of several key genera, especially Aneides, Hemidactylium, Hydromantes and Karsenia, are contentious. Here we present a combined dataset of complete mitochondrial genomes and three nuclear loci for 20 species (16 genera) of plethodontids, representing all major clades in the family. The combined dataset without mitochondrial third codon positions provides a fully resolved, statistically well-supported tree. In this topology two major clades are recovered. A northern clade includes Aneides, Desmognathus, Ensatina, Hydromantes, Karsenia, Phaeognathus and Plethodon, with Plethodon being the sister taxon to the rest of the clade. Hydromantes and Karsenia are sister taxa, and Aneides is recovered as the sister taxon to Ensatina. Desmognathus+Phaeognathus form the sister taxon to Aneides+Ensatina. An eastern/southern clade comprises two subclades. One subclade, the spelerpines (Eurycea, Gyrinophilus, Pseudotriton, Stereochilus, Urspelerpes) is the sister taxon to a subclade comprising Hemidactylium, Batrachoseps and the tropical plethodontids (represented by Bolitoglossa, Nototriton and Thorius). In this topology Hemidactylium is well-supported as the sister taxon to Batrachoseps. Only when mitochondrial third codon positions are included using maximum likelihood analysis is Hemidactylium recovered as the sister taxon to Batrachoseps+tropical genera. Hypothesis testing of alternative topologies supports these conclusions. On the basis of these results we propose a conservative taxonomy for Plethodontidae.     

Molecular systematics and radiation of western North American nymphophiline gastropods

Three mitochondrial DNA (mtDNA) markers were used to infer the phylogenetic relationships of the morphologically diverse, species rich, and poorly understood western North American aquatic gastropod genus Pyrgulopsis (Hydrobiidae: Nymphophilinae). Sequences were obtained from 62 of 124 currently recognized species of Pyrgulopsis and representatives of four related genera of North American nymphophilines. Separate and combined analyses of the mtDNA datasets recovered a well supported clade composed of Pyrgulopsis and two other North American nymphophiline genera (Floridobia, Nymphophilus) consistent with the results of a prior study based on a single gene and with anatomical evidence suggesting that these taxa form a monophyletic group. Phylogenetic relationships among lineages of Pyrgulopsis were little resolved in our analyses and provided no obvious basis for splitting this large genus into multiple genera. The little differentiated Mexican genus Nymphophilus was consistently placed within Pyrgulopsis in our trees and is formally synonymized with it herein. Pyrgulopsis was also depicted as paraphyletic with respect to Floridobia in some of our trees while in others the latter was sister to a Nymphophilus + Pyrgulopsis clade. Based on these equivocal results and the morphological and geographical divergence of eastern North American Floridobia relative to Pyrgulopsis, we recommend that the former be maintained as a separate genus. The short, weakly supported branches within Pyrgulopsis and the noncongruence between our molecular phylogenetic hypotheses and geographical groupings of species are attributed to an early rapid diversification of the genus, perhaps triggered by the complex changes in western topography which occurred during the late Tertiary. Our results also indicate that penial morphologies used to define species groups of Pyrgulopsis have been subject to striking convergence throughout the West, suggesting another compelling facet of the radiation of these snails.     

Evolution of a Neotropical marine fish lineage (Subfamily Chaenopsinae, Suborder Blennioidei) based on phylogenetic analysis of combined molecular and morphological data

Phylogenetic relationships within tube blennies (Chaenopsinae) were reconstructed using Bayesian, maximum parsimony and likelihood analyses of multiple molecular markers (mitochondrial DNA: COI; nuclear DNA: TMO-4C4, RAG1, Rhodopsin, and Histone H3) and 148 morphological characters. This total-evidence based topology is well-resolved and congruent across analytical methods with strong support for the monophyly of the Chaenopsinae, all included genera and several internal nodes. A rapid radiation in the early evolution of chaenopsins is inferred from the relatively poor support values for relationships among basal lineages and their divergence into different habitats (rocky reefs, coral reefs and the reef/sand interface). Rates of molecular evolution in chaenopsins, as inferred by divergence among four putative transisthmian geminate species pairs, are rapid compared to other fishes. Conflicts among genetic markers and morphology are especially evident within the genus Coralliozetus, with different species relationships supported by morphology, TMO-4C4, and RAG1 plus Rhodopsin. This study hypothesizes a novel sistergroup relationship between Ekemblemaria and Hemiemblemaria, consistent with morphological, molecular and habitat use data. Our total evidence phylogenetic hypothesis indicates that previously hypothesized morphological characters supporting a close relationship between Hemiemblemaria and Chaenopsis plus Lucayablennius resulted from convergent evolution in these relatively free-swimming blennies.     

Ribosomal DNA evidence and disjunctions of western American Portulacaceae

Phylogenetic analysis of ribosomal DNA internal transcribed spacer sequences from 35 members of western American Portulacaceae plus seven Portulacaceae outgroups generally supports morphologically based interpretations of multiple intercontinental disjunctions. The data neither support nor refute monophyly of the western American group but strongly support a group comprising the western American taxa plus Phemeranthus, the only strictly American genus of the morphology-based eastern American/African group of Portulacaceae, along with the Australian genus Parakeelya. Support is strong for the monophyly of Calandrinia, Montiopsis, Lewisia, Claytonia, and Montia, along with a sister relationship of the last two. The data neither strongly support nor refute the morphologically based diagnosis of Cistanthe, but they strongly support a clade including the North American Cistanthe section Calyptridium and the South American Cistanthe sections Amarantoideae and Philippiamra. The internal transcribed spacer data fail to resolve the phylogenetic relationships among most of the western American lineages, suggesting either rapid radiation or, alternatively, erratic evolution of the internal transcribed spacer. The internal transcribed spacer and morphological evidence together suggest that in this group there have been 8-13 dispersal and colonization events across >2000 km (1 for every 15-26 extant species in this group). The internal transcribed spacer data document complex molecular evolutionary patterns, including strong substitution biases, among-site rate heterogeneity, positional bias for deamination-type substitutions, nonstationarity, and variable rates of insertion/deletion. Our phylogenetic conclusions, however, do not appear to be sensitive to these patterns.     

Molecular systematics and phylogeography of the Plethodon elongatus species group: combining phylogenetic and population genetic methods to investigate species history

Plethodon elongatus and P. stormi (Caudata: Plethodontidae) are Pacific Northwest endemic species which occur in northwestern California and southwestern Oregon. Studies on these salamanders have resulted in differing taxonomic conclusions, but the underlying historical hypotheses, at both inter- and intraspecific levels, have never been examined in a molecular framework. Here, representatives of 81 populations from throughout the range of both taxa are sequenced. Portions of three mitochondrial protein-coding genes (cytochrome b, NADH dehydrogenase subunit 4, and ATPase 6) were sequenced. Four haplotype groups with nonoverlapping geographical ranges were recovered in separate and combined analyses of the data. One clade corresponds to the distribution of P. stormi, while the remaining three comprise P. elongatus. Phylogenetic relationships among haplotype groups differ in separate analyses of the genes but converge on a well-supported topology, with P. elongatus and P. stormi as monophyletic sister taxa, in combined Maximum Parsimony and Maximum Likelihood analyses. Population genetic analyses of mismatch distributions and Tajima's D-statistic are consistent with range expansion for the largest clade within P. elongatus, covering the northern two-thirds of the species range. In contrast, the P. stormi haplotype clade and the P. elongatus clade from the southern third of the species range may have been relatively stable. Morphological boundaries between P. elongatus and P. stormi are largely congruent with mitochondrial DNA breaks and continued treatment as sister taxa is supported. Although mitochondrial DNA haplotype groups may reflect historical separation within P. elongatus, genetic barriers are incongruent with intraspecific patterns of morphological variation.     

Mitochondrial DNA phylogeny of North American field crickets: perspectives on the evolution of life cycles,songs, and habitat associations

North American field crickets (genus Gryllus) exhibit a diversity of life cycles, habitat associations, and calling songs. However, patterns of evolution for these ecological and behavioral traits remain uncertain in the absence of a robust phylogenetic framework. Analyses of morphological variation have provided few clues about species relationships in the genus Gryllus. Here we use comparisons of mitochondrial DNA restriction site maps for 29 individuals representing 11 species (including potential outgroups) to examine relationships among eastern North American field crickets. Initially chosen as likely outgroup taxa, the two European species of Gryllus do not obviously fall outside of an exclusively North American clade and (based on amount of sequence divergence) appear to have diverged from North American lineages at about the same time that major North American lineages diverged from each other. The egg-overwintering crickets comprise a strongly supported monophyletic group, but relationships among these three closely related species cannot be resolved. The mtDNA data are consistent with a single origin of egg diapause and do not support a model of recent life cycle divergence and allochronic speciation for Gryllus pennsylvanicus and G. veletis. The two crickets are not sister species, despite remarkable similarity in morphology, habitat, and calling song. This conclusion is consistent with published data on allozyme variation in North American field crickets. The habitat associations of eastern North American field crickets have been labile, but calling songs sometimes have remained virtually unchanged across multiple speciation events.     

Phylogeny, biogeography and taxonomy of the African wattle-eyes (Aves: Passeriformes: Platysteiridae)

The African wattle-eyes (genera Platysteira and Dyaphorophyia) comprise 10 species endemic to Africa. We analyzed both mitochondrial and nuclear DNA sequence data to test the monophyly of this group and its two genera, provide a preliminary assessment of species limits, and gain insight into the phylogeographic history of the wattle-eye radiation. Analyses based on mitochondrial ND2 sequences failed to recover wattle-eye monophyly, but the alternatives were not well-supported. In contrast, analyses of two nuclear introns (myoglobin intron-2 and beta-fibrinogen intron-5) recovered wattle-eye monophyly, as did combined analyses of mitochondrial and nuclear data. These analyses, however, did not support reciprocal monophyly of the two wattle-eye genera typically recognized, suggesting instead that Platysteira is nested within a paraphyletic Dyaphorophyia. The diversification of most wattle-eye species and many subspecies occurred through the divergence of allopatric populations well before the Pleistocene. Species and subspecies with disjunct distributions are typically characterized by deep genetic divergences, suggesting that many of these populations are evolutionary independent and could be recognized as additional phylogenetic species. In D. castanea and D. chalybea, for example, divergent haplotypes from geographically disjunct populations were paraphyletic with respect to those of D. tonsa and D. jamesoni, respectively. Similarly, Platysteira laticincta is highly divergent from its sister taxon P. peltata ( approximately 9.5% ND2 sequence divergence), consistent with species level recognition of this endangered species. In contrast, more broadly distributed taxa inhabiting a greater diversity of habitats (e.g., P. peltata and P. cyannea) show evidence of gene flow and connectivity among regions, suggesting that previously isolated populations expanded and fused into one another. Our study provides a framework for additional analyses of intraspecific phylogeography and species limits in these colorful birds.     

Phylogenetic relationships and ancestral areas of the bustards (Gruiformes: Otididae), inferred from mitochondrial DNA and nuclear intron sequences

The taxonomy of the bustards is poorly understood phylogenetically and has not been extensively evaluated using molecular methods. We sequenced part of the mitochondrial cytochrome b gene, the control region (central domain II), and an intron-exon crossing fragment of the nuclear chromo-helicase-DNA binding gene (CHD1) in 27 bustard taxa (including multiple subspecies) representing 11 genera and four gruiform outgroup species. Molecular datings suggest a Miocene origin for the family. Inferred phylogenetic relationships include the following: (i) the basal polytomy consists of 10 branches (mostly consistent with traditional genera), suggesting a rapid early radiation; (ii) sister relationships between several couplets of genera include Ardeotis with Neotis, Afrotis with Eupodotis (excluding E. rueppellii), Otis with Chlamydotis, and Houbaropsis with Sypheotides; (iii) the genus Eupodotis may be polyphyletic; and (iv) the currently delimited genera Ardeotis and Neotis do not form independent monophyletic lineages. Molecular evidence for the Afro-tropical origin of the Otididae is provided.     

Molecular phylogenetics, vocalizations, and species limits in Celeus woodpeckers (Aves: Picidae)

Species limits and the evolutionary mechanisms that have shaped diversification of woodpeckers and allies (Picidae) remain obscure, as inter and intraspecific phylogenetic relationships have yet to be comprehensively resolved for most genera. Herein, we analyzed 5020 base pairs of nucleotide sequence data from the mitochondrial and nuclear genomes to reconstruct the evolutionary history of Celeus woodpeckers. Broad geographic sampling was employed to assess species limits in phenotypically variable lineages and provide a first look at the evolution of song and plumage traits in this poorly known Neotropical genus. Our results strongly support the monophyly of Celeus and reveal several novel relationships across a shallow phylogenetic topology. We confirm the close sister relationship between Celeus spectabilis and the enigmatic Celeus obrieni, both of which form a clade with Celeus flavus. The Mesoamerican Celeus castaneus was placed as sister to a Celeus undatus-grammicus lineage, with the species status of the latter drawn into question given the lack of substantial genetic, morphological, and vocal variation in these taxa. We recovered paraphyly in Celeus elegans; however, this result appears to be the consequence of mitochondrial introgression from Celeus lugubris considering the monophyly of elegans at the ?-FIBI7 locus. A second instance of paraphyly was observed in Celeus flavescens with deep genetic splits and substantial phenotypic variation indicating the presence of two distinct species in this broadly distributed lineage. As such, we advocate elevation of Celeus flavescens ochraceus to species status. Our analysis of Celeus vocalizations and plumage characters demonstrates a pattern of lability consistent with a relatively recent origin of the genus and potentially rapid speciation history.     

Confrontation of morphological and molecular data: the Praomys group (Rodentia, Murinae) as a case of adaptive convergences and morphological stasis

Phylogenetic relationships in a group of 21 African rodent species designated as the Praomys group (Murinae) were investigated using morphological characters and sequence data from the complete mitochondrial cytochrome b gene and nuclear IRBP gene fragment (840bp). The molecular results confirm the monophyly of the Praomys group, including the species Malacomys verschureni, while the other Malacomys species appear very divergent. The basal relationships within the Praomys group are poorly resolved, suggesting a rapid radiation at about 7-9 million years ago based on genetic divergence rates calibrated from the fossil record. Discrepancies between molecular and morphological results probably reflect of numerous convergences as well as variations in the rates of morphological evolution among lineages. Reconstructions of the ancestral character states suggest a savannah origin for the Praomys group, along with some morphological traits conserved by stasis in savannah taxa. At the same time, forest taxa seem to be characterized by an accelerated morphological evolution, with acquisition of convergent adaptive characters.     

Phylogeographic analyses of a circumarctic coastal and a boreal lacustrine mysid crustacean, and evidence of fast postglacial mtDNA rates

Phylogeographic structures of two weakly dispersing Mysis sibling species, one with a circumarctic coastal, the other with a boreal lacustrine-Baltic distribution, were studied from mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. Mysis segerstralei showed high overall diversity and little phylogeographic structure across the Arctic, indicating late-glacial dispersal among coastal and lake populations from Alaska, Siberia and the north of Europe. A strongly divergent refugial lineage was however identified in Beringia. The boreal 'glacial relict'Mysis salemaai in turn displayed clear structuring among postglacially isolated Scandinavian lake populations. The inferred pattern of intralake mitochondrial DNA (mtDNA) monophyly in Scandinavia suggested relatively small population sizes and a remarkably fast postglacial mtDNA divergence rate (0.27% per 10 000 years). Nevertheless, the broader phylogeographic pattern did not support distinct eastern and western glacial refugia in Northern Europe, unlike in some other aquatic taxa. In all, the two species comprised three equidistant mitochondrial lineages (approximately 2% divergence), corresponding to M. salemaai, to the bulk of M. segerstralei, and to the Beringian M. segerstralei lineage. The lack of reciprocal monophyly of the two species in respect to their mitochondrial genealogy could indicate postspeciation mitochondrial introgression, also exemplified by an evidently more recent capture of M. segerstralei mitochondria in a Karelian population of M. salemaai. Overall, the data suggest that the continental boreal M. salemaai has a relatively recent ancestry in arctic coastal waters, whereas two other boreal 'glacial relict'Mysis sibling species in Europe (Mysis relicta) and North America (Mysis diluviana) have colonized inland waters much earlier (approximately 8% COI divergence).     

Inferences on the phylogeography of the fungal pathogen Heterobasidion annosum, including evidence of interspecific horizontal genetic transfer and of human-mediated, long-range dispersal

Fungi in the basidiomycete species complex Heterobasidion annosum are significant root-rot pathogens of conifers throughout the northern hemisphere. We utilize a multilocus phylogenetic approach to examine hypotheses regarding the evolution and divergence of two Heterobasidion taxa associated with pines: the Eurasian H. annosum sensu stricto and the North American H. annosum P intersterility group (ISG). Using DNA sequence information from portions of two nuclear and two mitochondrial loci, we infer phylogenetic relationships via parsimony, Bayesian and median-joining network analysis. Analysis of isolates representative of the entire known geographic range of the two taxa results in monophyletic sister Eurasian and North American lineages, with North America further subdivided into eastern and western clades. Genetically anomalous isolates from the Italian presidential estate of Castelporziano are always part of a North American clade and group with eastern North America, upholding the hypothesis of recent, anthropogenically mediated dispersal. P ISG isolates from Mexico have phylogenetic affinity with both eastern and western North America. Results for an insertion in the mitochondrial rDNA suggest this molecule was obtained from the Heterobasidion S ISG, a taxon sympatric with the P ISG in western North America. These data are compatible with an eastern Eurasian origin of the species, followed by dispersal of two sister taxa into western Eurasia and into eastern North America over a Beringean land bridge, a pattern echoed in the phylogeography of other conifer-associated basidiomycetes.     

Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data

Despite intensive morphological and molecular studies of Onagraceae, relationships within the family are not fully understood. One drawback of previous analyses is limited sampling within the large tribe Onagreae. In addition, the monophyly of two species-rich genera in Onagreae, Camissonia and Oenothera, has never been adequately tested. To understand relationships within Onagraceae, test the monophyly of these two genera, and ascertain the affinities of the newly discovered genus Megacorax, we conducted parsimony and maximum likelihood analyses with rbcL and ndhF sequence data for 24 taxa representing all 17 Onagraceae genera and two outgroup Lythraceae. Results strongly support a monophyletic Onagraceae, with Ludwigia as the basal lineage and a sister-taxon relationship between Megacorax and Lopezia. Gongylocarpus is supported as sister to Epilobieae plus the rest of Onagreae, although relationships within the latter clade have limited resolution. Thus, we advocate placement of Gongylocarpus in a monogeneric tribe, Gongylocarpeae. Most relationships within Onagreae are weakly resolved, suggesting a rapid diversification of this group in western North America. Neither Camissonia nor Oenothera appears to be monophyletic; however, increased taxon sampling is needed to clarify those relationships. Morphological characters generally agree with the molecular data, providing further support for relationships.     

Testing hypotheses of speciation in the Plethodon jordani species complex with allozymes and mitochondrial DNA sequences

Salamander populations of the Plethodon jordani species complex form a challenging system for applying the general lineage concept of species to diagnose population-level lineages. The present study reports and analyses mitochondrial-DNA haplotypes (∼1200 nucleotide bases from the genes encoding ND2, tRNA^Trp, and tRNA^Ala from 438 salamanders) from 100 populations representing six species of the P. jordani complex ( Plethodon amplus , Plethodon cheoah , Plethodon jordani , Plethodon meridianus , Plethodon metcalfi , and Plethodon montanus ) with comparative analyses of previously published allozymic data to reconstruct the evolutionary history of this group and to diagnose species lineages. Analyses of mitochondrial haplotypic data include nested-cladistic analysis of phylogeography, analysis of molecular variance, hierarchical analysis of nucleotide-diversity measures, and likelihood-based estimates of recent temporal changes in population size. New analyses of allozymic data include multidimensional scaling and principal component analyses, and both data sets are analysed and compared for congruent genetic structure using Mantel correlation tests. These analyses in combination identify the six named species as distinct evolutionary lineages despite sporadic genetic exchanges among them and some discordance between mitochondrial DNA and allozymic markers. Sexual isolation is not complete for any pair of these six species, but they replace each other geographically and appear to block the geographical spreading of their neighbours. The P. jordani complex is a strong study system for investigating the genetic and ecological processes responsible for vicariant speciation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 25–51.     

Phylogenetic relationships of the Dactyloa clade of Anolis lizards based on nuclear and mitochondrial DNA sequence data

The Dactyloa clade, one of two major subgroups of mainland Anolis lizards, is distributed from Costa Rica to Peru, including the Amazon region and the southern Lesser Antilles. We estimated the phylogenetic relationships within Dactyloa based on mitochondrial (ND2, five transfer-RNAs, COI) and nuclear (RAG1) gene regions using likelihood and Bayesian methods under different partition strategies. In addition, we tested the monophyly of five previously recognized groups within Dactyloa. The data strongly support the monophyly of Dactyloa and five major clades: eastern, latifrons, Phenacosaurus, roquet and western, each of which exhibits a coherent geographic range. Relationships among the five major clades are less clear: support for basal nodes within Dactyloa is weak and some contradictory relationships are supported by different datasets and/or phylogenetic methods. Of the previously recognized subgroups within Dactyloa, only the roquet series consistently passed the topology tests applied. The monophyly of the aequatorialis, latifrons (as traditionally circumscribed) and punctatus series was strongly rejected, and the monophyly of Phenacosaurus (as traditionally circumscribed) yielded mixed results. The results of the phylogenetic analyses suggest the need for a revised taxonomy and have implications for the biogeography and tempo of the Dactyloa radiation.     

Phylogeny and evolution of Cervidae based on complete mitochondrial genomes

Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.     

Generic delimitation and biogeography of Maianthemum and Smilacina (Ruscaceae sensu lato): preliminary results based on partial 3′ matK gene and trnK 3′ intron sequences of cpDNA

The controversy over generic delimitation between Maianthemum and Smilacina has been unresolved for almost two centuries. Distributions of the two genera in the Northern Hemisphere also provide an excellent opportunity to further understand the disjunct distribution patterns of the North Temperate Flora. To test the generic delimitation and to investigate biogeographic patterns, we sequenced the partial 3′ matK gene and trnK 3′ intron of chloroplast DNA for 38 accessions, representing three species of Maianthemum, seven species of Smilacina, and four outgroup taxa. Maximum parsimony and neighbor-joining trees showed reciprocal monophyly of the two genera with very weak bootstrap support for each genus. Within each genus, relationships among species were poorly resolved. Despite its low resolution, this study shows that eastern Asian species of Smilacina and Maianthemum are generally more closely related to eastern North American taxa than to western ones. More detailed sampling of Smilacina from different geographic regions, especially from the two centers of diversity (southeastern Asia and Mexico/Central America), and additional sequences from cpDNA, as well as from nuclear DNA, are needed to test the reciprocal monophyly of the two genera and also to understand current distributions of disjunct taxa.