Molecular systematics of the western rattlesnake, Crotalus viridis (Viperidae), with comments on the utility of the D-loop in phylogenetic studies of snakes.

Crotalus viridis, the western rattlesnake, ranges throughout western North America and has been divided into at least eight subspecies. However, the validity of and relationships among these subspecies and the monophyly of C. viridis as a whole are questionable. We used mitochondrial DNA sequence data from the D-loop region and ND2 gene to examine the relationships among 26 populations of C. viridis and to test the monophyly of this species. These data were analyzed separately and combined using maximum-likelihood and maximum-parsimony. The C. viridis group was monophyletic in all combined analyses, consisting of two strongly divergent clades. We recommend that these clades be recognized as two distinct evolutionary species: C. viridis and C. oreganus. Crotalus viridis should be restricted to the subspecies viridis and nuntius and the remaining subspecies be assigned to the species C. oreganus. Our data do not allow strong evaluation of the validity of the subspecies. We found that the ND2 gene had greater sequence divergences among closely related individuals than the D-loop region, but this relationship reversed at higher levels of divergence. This pattern is apparently due to: (1) ND2 third positions evolving faster than the D-loop but becoming saturated at higher levels of divergence, and (2) the D-loop evolving faster than ND2 second (and possibly first) positions. Our results suggest that the ND2 gene is preferable for examining intraspecific relationships and the D-loop may better resolve relationships between species of snakes. The latter result is contrary to the common perception of the phylogenetic utility of the D-loop. Another unusual result is that the 145 bp spacer region, adjacent to the 5' end of the light strand of the D-loop, provides greater phylogenetic resolution than the 1030 bp D-loop.     

Patchy distributions belie morphological and genetic homogeneity in rosy-finches

DNA sequence data often appear to contradict low-level avian taxonomy, which is usually based on patterns of external phenotypic similarity. We examined such an apparent contradiction in the Nearctic rosy-finches. On the basis of several phenotypic characters the finches were divided into three species congeneric with three Asian species. When Nearctic taxa were analyzed in a principal components analysis, 66.9% of phenotypic variation was explained by differences between the Bering Sea and continental populations, sexual dimorphism and a latitudinal cline. Our phylogenetic analysis of mitochondrial ND2 sequences revealed four clades among six species of rosy-finches. Three clades corresponded to three Asian species. The fourth clade included all three Nearctic species. Their haplotypes were not reciprocally monophyletic and the combined genetic variability of all Nearctic taxa was lower than in two of their Asian congeners. A Z-specific intron (ACO1I9) and an autosomal coding locus (MC1R) provided little additional phylogenetic information, most likely because of the longer coalescence times relative to ND2. Phylogeographic analyses of ND2 data revealed significant gene flow among neighboring localities regardless of their taxonomic assignment. Our analyses showed that DNA and phenotypic data are not in conflict, but rather complement each other, and together help clarify species limits. Our data are consistent with a single species in North America, not three.     

Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.     

Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree

It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1 kb of mtDNA (12S rRNA, 16S rRNA, ND1, ND2, ND4, Cyt b, and associated tRNA genes), and >2.2kb from three nuclear genes (RAG-1, BDNF, and GAPD) for most taxa. We conduct separate and combined phylogenetic analyses of these data using maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic relationships inferred from the mtDNA data are congruent with previous mtDNA analyses based on fewer characters and provide strong support for most branches. However, we detected strong incongruence between the mtDNA and nuclear data using comparisons of branch support and Shimodaira-Hasegawa tests, with the (P. platyrhinos+P. goodei) clade identified as the primary source of this conflict. Our analysis of a P. mcalliixP. goodei hybrid suggests that this incongruence is caused by reticulation via introgressive hybridization. Our preferred phylogeny based on an analysis of the combined data (excluding the introgressed mtDNA data) provides a new framework for interpreting character evolution and biogeography within Phrynosoma. In the context of this improved phylogeny we propose a phylogenetic taxonomy highlighting four clades: (1) Tapaja, containing the viviparous short-horned lizards P. ditmarsi, P. hernandesi, P. douglasii, and P. orbiculare; (2) Anota, containing species with prominent cranial horns (P. solare, P. mcallii, and the P. coronatum group); (3) Doliosaurus, containing three species lacking antipredator blood-squirting (P. modestum, P. platyrhinos, and P. goodei); and (4) Brevicauda, containing two viviparous species with extremely short tails that lack blood-squirting (P. braconnieri and P. taurus).     

形目15种鸟类线粒体ND6基因序列差异及其系统进化关系

采用PCR和质粒克隆测序方法 ,首次获得形目 15种鸟类线粒体基因组的ND6基因全长 5 2 2bp的序列。经对位排列 ,序列间未见有插入和缺失 ,共有 2 16个变异位点 ,种间序列差异为 5 17%～ 19 92 %。以白鹳为外群 ,用NJ法构建 15种鸟类的进化关系树。研究结果表明 :构建的系统树将形目 15种鸟类分为 2个支系。第 1支系包括蒙古沙、环颈、灰斑和反嘴鹬。第 2支系包括红脚鹬、林鹬、青脚鹬、翘嘴鹬、翻石鹬、大滨鹬、尖尾滨鹬、斑尾塍鹬、中杓鹬、大杓鹬和白腰杓鹬 ,其中鹬属的 3个种和杓鹬属的 3个种分别组成一个单系 ;翘嘴鹬和翻石鹬、大滨鹬和尖尾滨鹬分别聚为姊妹群 ,表现出较近的亲缘关系 ;斑尾塍鹬独立分支出来。分子证据提示 :鹬科中的塍鹬属、科中的斑属应提升为亚科分类阶元 ;反嘴鹬与科鸟类亲缘关系较近 ,组成一个单系 ,将其归入科下属的一个类群更为合理 ,与核型研究结果及Sibley新分类体系的观点相一致 [动物学报 49(1) :6 1～ 6 7,2 0 0 3]。     

Mitochondrial phylogeny of the Chrysisignita (Hymenoptera: Chrysididae) species group based on simultaneous Bayesian alignment and phylogeny reconstruction

The ignita species group within the genus Chrysis includes over 100 cuckoo wasp species, which all lead a parasitic lifestyle and exhibit very similar morphology. The lack of robust, diagnostic morphological characters has hindered phylogenetic reconstructions and contributed to frequent misidentification and inconsistent interpretations of species in this group. Therefore, molecular phylogenetic analysis is the most suitable approach for resolving the phylogeny and taxonomy of this group. We present a well-resolved phylogeny of the Chrysis ignita species group based on mitochondrial sequence data from 41 ingroup and six outgroup taxa. Although our emphasis was on European taxa, we included samples from most of the distribution range of the C. ignita species group to test for monophyly. We used a continuous mitochondrial DNA sequence consisting of 16S rRNA, tRNA(Val), 12S rRNA and ND4. The location of the ND4 gene at the 3' end of this continuous sequence, following 12S rRNA, represents a novel mitochondrial gene arrangement for insects. Due to difficulties in aligning rRNA genes, two different Bayesian approaches were employed to reconstruct phylogeny: (1) using a reduced data matrix including only those positions that could be aligned with confidence; or (2) using the full sequence dataset while estimating alignment and phylogeny simultaneously. In addition maximum-parsimony and maximum-likelihood analyses were performed to test the robustness of the Bayesian approaches. Although all approaches yielded trees with similar topology, considerably more nodes were resolved with analyses using the full data matrix. Phylogenetic analysis supported the monophyly of the C. ignita species group and divided its species into well-supported clades. The resultant phylogeny was only partly in accordance with published subgroupings based on morphology. Our results suggest that several taxa currently treated as subspecies or names treated as synonyms may in fact constitute separate species. Our study provides a solid basis for further systematic investigations of this enigmatic insect group.     

Rostral horn evolution among agamid lizards of the genus Ceratophora endemic to Sri Lanka.

The first phylogenetic hypothesis for the Sri Lankan agamid lizard genus Ceratophora is presented based on 1670 aligned base positions (472 parsimony informative) of mitochondrial DNA sequences, representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Phylogenetic analysis reveals multiple origins and possibly losses of rostral horns in the evolutionary history of Ceratophora. Our data suggest a middle Miocene origin of Ceratophora with the most recent branching of recognized species occurring at the Pliocene/Pleistocene boundary. Haplotype divergence suggests that an outgroup species, Lyriocephalus scutatus, dates at least to the Pliocene. These phylogenetic results provide a framework for comparative studies of the behavioral ecological importance of horn evolution in this group.     

Out of Asia: natricine snakes support the Cenozoic Beringian Dispersal Hypothesis

Based on a combination of six mitochondrial gene fragments (12S RNA, cyt b, ND1, ND2, ND4 and CO1) and one nuclear gene (c-mos) from 22 genera we infer phylogenetic relationships among natricine snakes and examine the date and area of origin of these snakes. Our phylogenetic results indicate: (1) the subfamily Natricinae is strongly supported as monophyletic including a majority of extant genera, and a poorly known and previously unassigned species Trachischium monticola, (2) two main clades are inferred within Natricinae, one containing solely taxa from the Old World (OW) and the other comprising taxa from a monophyletic New World (NW) group with a small number of OW relatives. Within the first clade, the genera Xenochrophis and Amphiesma are apparently not monophyletic. Divergence dating and ancestral area estimation indicate that the natricines originated in tropical Asia during the later Eocene or the Oligocene. We recover two major dispersals events out of Asia, the first to Africa in the Oligocene (28 Ma) and the second to the Western Palearctic and the New World at 27 Ma. This date is consistent with the dispersal of numerous other OW groups into the NW.     

Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear beta-fibrinogen intron 7 to carnivores

The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear beta-fibrinogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; approximately 3750 bp) and combined mt and nuclear data (nine genes; approximately 6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manul within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear beta-fibrinogen intron 7.     

Hiding deep in the trees: discovery of divergent mitochondrial lineages in Malagasy chameleons of the Calumma nasutum group

WE CONDUCTED A COMPREHENSIVE MOLECULAR PHYLOGENETIC STUDY FOR A GROUP OF CHAMELEONS FROM MADAGASCAR (CHAMAELEONIDAE: Calumma nasutum group, comprising seven nominal species) to examine the genetic and species diversity in this widespread genus. Based on DNA sequences of the mitochondrial gene (ND2) from 215 specimens, we reconstructed the phylogeny using a Bayesian approach. Our results show deep divergences among several unnamed mitochondrial lineages that are difficult to identify morphologically. We evaluated lineage diversification using a number of statistical phylogenetic methods (general mixed Yule-coalescent model; SpeciesIdentifier; net p-distances) to objectively delimit lineages that we here consider as operational taxonomic units (OTUs), and for which the taxonomic status remains largely unknown. In addition, we compared molecular and morphological differentiation in detail for one particularly diverse clade (the C. boettgeri complex) from northern Madagascar. To assess the species boundaries within this group we used an integrative taxonomic approach, combining evidence from two independent molecular markers (ND2 and CMOS), together with genital and other external morphological characters, and conclude that some of the newly discovered OTUs are separate species (confirmed candidate species, CCS), while others should best be considered as deep conspecific lineages (DCLs). Our analysis supports a total of 33 OTUs, of which seven correspond to described species, suggesting that the taxonomy of the C. nasutum group is in need of revision.     

Multiple Lineages of the Mitochondrial Gene NADH Dehydrogenase Subunit 1 (ND1) in Parasitic Helminths: Implications for Molecular Evolutionary Studies of Facultatively Anaerobic Eukaryotes

The task of using partial ND1 sequences to infer a phylogeny for species of the genus Paragonimus (Trematoda: Digenea) was complicated by the discovery of at least two ND1 lineages within individual worms. The divergence of the ND1 lineages is shown by phylogenetic analysis not only to predate the divergence of the three Paragonimus species or species groups investigated but also the divergence of some trematode families. Some sequences are clearly pseudogenes as they contain single base deletions and/or premature termination codons. The presence of both pseudogenes and/or mitochondrial heteroplasmy are invoked to explain the presence of multiple and divergent ND1 lineages in these trematodes, which have two distinct cytochemical types of mitochondria. The implications for phylogenetic studies generally and of parasitic helminths specifically, using ND1 sequence data, are discussed. The ability of these organisms to adapt their metabolic processes to the variable availability of oxygen as an electron acceptor are proposed to explain some of the molecular diversity observed in parasitic helminths and possibly also in other anaerobically adapted eukaryotes. Received: 18 October 1999 / Accepted: 23 June 2000     

基于Cytb和ND1基因序列的弄蝶亚科(鳞翅目:弄蝶科)族级系统发育关系分析

【目的】探讨中国弄蝶亚科各族之间的系统发育关系。【方法】对22属32种弄蝶亚科蝶类的Cytb和ND1基因部分序列进行了联合分析,分别采用最大似然法(maximum likelihood,ML)和贝叶斯法(Bayesian inference,BI)构建了系统发育树。【结果】测得的Cytb和ND1基因联合后,获得的序列总长为836 bp,包含保守位点450个,变异位点386个,简约信息位点304个;A+T的平均含量为76.9%,明显高于C+G的平均含量(23.1%)。基于Cytb和ND1基因联合序列的系统发育分析显示,钩弄蝶族(Ancistroidini)、刺胫弄蝶族(Baorini)、弄蝶族(Hesperiini)为单系群,且亲缘关系较近,其亲缘关系为:(弄蝶族Hesperiini+(刺胫弄蝶族Baorini+钩弄蝶族Ancistroidini));而锷弄蝶族Aeromachini(=酣弄蝶族Halpini)是一个复系群。【结论】本文支持钩弄蝶族(Ancistroidini)、刺胫弄蝶族(Baorini)、弄蝶族(Hesperiini)的族级地位,锷弄蝶族(Aeromachini)与Warren等研究结果矛盾,其他族有待补充样本后做进一步研究。     

Molecular differentiation and phylogeny of entomopathogenic nematodes (rhabditida: heterorhabditidae) based on ND4 gene sequences of Mitochondrial DNA.

We determined partial ND4 gene sequences of mitochondrial DNA from 15 heterorhabditid nematode isolates, representing 5 species collected from different regions of the world, by using polymerase chain reaction (PCR) and direct-sequencing of PCR products. Aligned nucleotide as well as amino acid sequences were used to differentiate nematode species by comparing sequence divergence and to infer phylogeny of the nematodes by using maximum parsimony and likelihood methods. Robustness of our phylogenetic trees was checked by bootstrap tests. The 15 nematode isolates can be divided into 7 haplotypes based on DNA sequences. On a larger scale, the sequence divergence revealed 4 distinct groups corresponding to 4 described species. No sequence divergence was detected from 5 isolates of Heterorhabditis bacteriophora or between Heterorhabditis marelatus to Heterorhabditis hepialius. Our sequence data yielded phylogenetic trees with identical topologies when different tree-building methods were used. Most relationships were also confirmed by using amino acid sequences in maximum parsimony analysis. Our molecular phylogeny of Heterorhabditis species support an existing taxonomy that is based largely on morphology and the sequence divergence of the ND4 gene permits species identification.     

Phylogeny of Limia (Teleostei: Poeciliidae) based on NADH dehydrogenase subunit 2 sequences

Complete sequences for the mitochondrial gene NADH Dehydrogenase 2 (ND2) and partial sequences for the tRNA-Met and tRNA-Trp genes were obtained for 11 populations of the poeciliid fish genus (or subgenus) Limia, including species from Hispaniola, Cuba, Jamaica, and Grand Cayman Islands. Additional sequences for Limia (2 species), Pamphorichthys (3), Poecilia (16), and Xiphophorus (1), all from the tribe Poeciliini, were extracted from GenBank, as was a sequence for Heterandria formosa, from the tribe Heterandriini. Phylogenetic analyses included parsimony, distance methods, and maximum-likelihood. Several Limia species groups that had been proposed based on morphological data were evaluated. The versicolor species group was strongly supported, as was the close relationship between the Cuban Limia vittata and the Grand Cayman Limia caymanensis. However, the proposed vittata species group was not upheld by the ND2 data. The phylogenetic position of Limia melanogaster, from Jamaica, was either sister to the versicolor species group or basal to all other included Limia species. Limia was found to be monophyletic; however, Limia species from the island of Hispaniola were not monophyletic. There was little support for any proposed sister group to Limia. The phylogeny was used to reconsider a previous comparative study of poeciliid courtship behavior and sexual dimorphism. The data indicated that there may have been two independent appearances of courtship display behavior in Limia; considering the tribe Poeciliini as a whole, there is evidence for as many as five appearances of display (including two within Limia), or a complex pattern of gains and losses of such behavior. The application of phylogenetic information to the comparative study did not refute the previously hypothesized correlation between the presence of a courtship display and the presence of sexual dimorphism in poeciliid fish.     

Molecular phylogeny of the lemur family cheirogaleidae (primates) based on mitochondrial DNA sequences

Cheirogaleidae currently comprises five genera whose relationships remain contentious. The taxonomic status and phylogenetic position of both Mirza coquereli and Allocebus trichotis are still unclear. The taxonomic status of the recently discovered Microcebus ravelobensis (a sympatric sibling species of Microcebus murinus) and its phylogenetic position also require further examination. A approximately 2.4-kb mitochondrial DNA sequence including part of the COIII gene, complete ND3, ND4L, and ND4 genes, and 5 tRNAs was used to clarify relationships among cheirogaleids. Mirza and Microcebus form a clade representing the sister group of Allocebus, with a clade containing Cheirogaleus major and Cheirogaleus medius diverging first. M. ravelobensis and Microcebus rufus form a subclade within Microcebus, with M. murinus as its sister group. The molecular data support the generic status of Mirza coquereli and species-level divergence of M. ravelobensis. Furthermore, "M. rufus" may well represent more than one species.     

Molecular phylogeny and phylogeography of the Australian Diplodactylus stenodactylus (Gekkota; Reptilia) species-group based on mitochondrial and nuclear genes reveals an ancient split between Pilbara and non-Pilbara D. stenodactylus

There is a paucity of research on intra-specific morphological and genetic diversity in Australian arid-zone reptiles, and a number of Australian reptile species have for many years been regarded as "species complexes" that classical morphological analyses could not resolve. We conducted a phylogenetic and phylogeographic study of a widespread species group of Australian geckonid lizards to address two main aims. First, based on a large mitochondrial and nuclear gene data set, we have generated the first molecular phylogeny for the Diplodactylus stenodactylus species group (D. alboguttatus, D. damaeus, D. maini, and D. squarrosus, D. stenodactylus) and multiple outgroups to examine the evolutionary relationships among these arid-zone species and phylogenetic patterns within some species. The edited alignment of 41 individuals comprises 2485 characters (1163 ND2+tRNAs; 490 16s; 832 RAG-1), and of these 717 (29%) were variable and parsimony informative (568 ND2+tRNAs; 89 16s; 60 RAG-1). This broad-scale, multi-gene phylogeny has supported previous conjectures on the higher-level phylogenetic relationships among members of the D. stenodactylus species-group based on morphology, but also has uncovered hidden diversity within the group with two new species identified. Analysis at this broad level has identified patterns associated with the distribution of the D. stenodactylus species group that appear to be influenced by environmental processes operating at large geographic scales. Two major clades within the species group were associated with broad differences in habitat types, with one group largely restricted to the temperate zone of the Southwest Province and another largely restricted to central and northern Western Australia north of Kalgoorlie, in line with the Eremaean Province of the Eremaean Zone and the Northern Province of the Tropical Zone. Second, we have assembled phylogeographic data based on a mitochondrial gene (ND2+tRNAs) for five species (Rhynchoedura ornata, Diplodactylus maini, D. pulcher, D. squarrosus, D. stenodactylus) where larger sampling is available, with particular focus on D. stenodactylus, which is distributed both in the iconic but little-known Pilbara area of endemism in north-western Australia as well as in other parts of the Australian arid zone. The edited alignment of 95 individuals comprises 1142 characters and of these 601 (53%) are variable and parsimony informative. We found significant intra-specific genetic variation in all five species, highlighting the need for large-scale screening of cryptic species, with sampling specifically targeted at determining the geographic limits of such taxa. In particular, within D. stenodactylus, a deep and ancient phylogenetic split distinguishes populations in the Pilbara region from non-Pilbara populations. This split may be the result of broad differences in underlying geological substrate, with the Pilbara clade generally preferring harder soils and the non-Pilbara clade adapted to sand.     

Molecular phylogeny of the Australian frog genera Crinia, Geocrinia, and allied taxa (Anura: Myobatrachidae).

We present a mitochondrial gene tree for representative species of all the genera in the subfamily Myobatrachinae, with special emphasis on Crinia and Geocrinia. This group has been the subject of a number of long-standing taxonomic and phylogenetic debates. Our phylogeny is based on data from approximately 780 bp of 12S rRNA and 676 bp of ND2, and resolves a number of these problems. We confirm that the morphologically highly derived monotypic genera Metacrinia, Myobatrachus, and Arenophryne are closely related, and that Pseudophryne forms the sister group to these genera. Uperoleia and the recently described genus Spicospina are also part of this clade. Our data show that Assa and Geocrinia are reciprocally monophyletic and together they form a well-supported clade. Geocrinia is monophyletic and the phylogenetic relationships with the genus are fully resolved with two major species groups identified: G. leai, G. victoriana, and G. laevis; and G. rosea, G. alba, and G. vitellina (we were unable to sample G. lutea). We confirm that Taudactylus forms the sister group to the other myobatrachine genera, but our data are equivocal on the phylogenetic position of Paracrinia. The phylogenetic relationships among Crinia species are well resolved with strong support for a number of distinct monophyletic clades, but more data are required to resolve relationships among these major Crinia clades. Crinia tasmaniensis and Bryobatrachus nimbus form the sister clade to the rest of Crinia. Due to the lack of generic level synapomorphies for a Bryobatrachus that includes C. tasmaniensis, we synonymize Bryobatrachus with Crinia. Crinia georgiana does not form a clade distinct from other Crinia species and so our data do not support recognition of the genus Ranidella for other Crinia species. Crinia subinsignifera, C. pseudinsignifera, and C. insignifera are extremely closely related despite differences in male advertisement call. A preliminary investigation of phylogeographic substructure within C. signifera revealed significant divergence between samples from across the range of this species.     

Phylogenetic relationships in the Sceloporus variabilis (Squamata: Phrynosomatidae) complex based on three molecular markers,continuous characters and geometric morphometric data

The monophyly of the Sceloporus variabilis group is well established with five species and two species complexes, but phylogenetic relationships within species complexes are still uncertain. We studied 278 specimens in 20 terminals to sample all taxa in the “variabilis group,” including three subspecies in the “variabilis complex,” and two outgroups (Sceloporus grammicus and Sceloporus megalepidurus). We assembled an extensive morphological data set with discrete and continuous characters (distances and scale counts), including geometric morphometric data (landmark coordinates of three shapes), and a three‐marker molecular data set as well (ND4, 12S and RAG1). We conducted parsimony and Bayesian phylogenetic inferences on these data, including several partitioning and weighting schemes. We suggest elevating three subspecies to full species status. Therefore, we recommend recognition of nine species in the “variabilis group.” First, S. variabilis is sister to Sceloporus teapensis. In turn, Sceloporus cozumelae is sister to Sceloporus olloporus. These four species are a monophyletic group, which is sister to Sceloporus smithi. Finally, Sceloporus marmoratus is sister of the clade of five species. The other species in the “variabilis group” (Sceloporus chrysostictus, Sceloporus couchii and Sceloporus parvus) are a paraphyletic grade at the base of the tree. Our analyses reject the existence of the “variabilis complex.” We conducted a parsimony‐based ancestral reconstruction on body size (snout–vent length), femoral pores and dorsal scales and related morphological changes to geographic distribution of the species. Our phylogenetic hypothesis will allow best designs of comparative studies with species in the “variabilis group,” one of the earliest divergent lineages in the genus.     

Molecular phylogenetic systematics of twelve species of Acipenseriformes based on mtDNA ND4L -ND4 gene sequence analysis

Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.