The complete mitochondrial genome of Pelodiscus axenaria (Testudines: Trionychidae).

The complete mitochondrial genome sequence of Pelodiscus axenaria was determined by shotgun sequencing. The total length of mitogenome is 16,593 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes, and 1 control region. Most of the genes of P. axenaria were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of P. axenaria and 11 other closely related species was reconstructed. The phylogenetic analyses based on these mitogenomes presented here will be useful for further insights on the evolutionary relationships of Trionychidae.

The complete mitochondrial genome of Lycodon ruhstrati (Serpentes: Colubridae).

The complete mitochondrial genome sequence of Lycodon ruhstrati was determined by shotgun sequencing. The total genome size is 17,168 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 2 control regions (D-loops). Most of the genes of L. ruhstrati were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of L. ruhstrati and 12 other closely related species was reconstructed. The mitogenome sequence presented here will be useful to study the evolutionary relationships and genetic diversity of L. ruhstrati.

The complete mitochondrial genome of Bufotes zamdaensis (Anura: Bufonidae).

The complete mitochondrial genome sequence of Bufotes zamdaensis was reported in the present research by shotgun sequencing. The total length of mitogenome is 17,189 bp, and contains 13 protein-coding genes, 22 tRNA genes, two ribosome RNA genes, and one D-loop region. All gene conformations were consistent with the gene arrangement in vertebrates. Most of the genes of B. zamdaensis were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. Phylogenetic analysis of B. zamdaensis and 12 other closely amphibian species was reconstructed using Maximum-likelihood methods. The sequences of B. zamdaensis were clustered in genus Bufotes. The phylogenetic analyses based on these mitogenomes presented here will be useful to further insights on the evolutionary relationships of Bufonidae.

The complete mitochondrial genome of Laudakia stoliczkana stoliczkana (Iguania; Agamidae).

The complete mitochondrial genome sequence of Laudakia stoliczkana stoliczkana was determined by shotgun sequencing. The total length of mitogenome is 16,133 bp and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes, and 2 control regions. The base composition was 38.0% for A, 24.0% for T, 25.6% for C, and 12.4% for G. Most of the genes of L. stoliczkana stoliczkana were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of L. stoliczkana stoliczkana and 16 other related species was built. The mitogenome sequence presented here will be useful to study the evolutionary relationships and genetic diversity of Laudakia.

The complete mitochondrial genomes of Laudakia Papenfussi (Iguania; Agamidae).

The Papenfuss' Rock Agama Laudakia papenfussi is an endemic species in the Tibet Autonomous Region of China. The complete mitochondrial genome sequence of this species was determined by shotgun sequencing. The total length of mitogenome is 17,005 bp and its base composition was 37.3% for A, 23.9% for T, 12.5% for G, and 26.3% for C, which contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes, and 2 control regions. The phylogenetic tree of L. papenfussi and 15 other related species was reconstructed using maximum likelihood (ML) methods. The mitogenome sequence presented here will be useful to understand the phylogenetic relationships of Laudakia.

Genealogy and Demographic History of a Widespread Amphibian throughout Indochina.

Relatively little is known about spatial patterns of cryptic diversity in tropical species and the processes that generate them. Few studies examine the geographic distribution of genetic lineages in Southeast Asia, an area hypothesized to harbor substantial cryptic diversity. We investigated the evolutionary history of Asian tree frogs of the Polypedates leucomystax complex (n = 172) based on 1800 bp of the mtDNA genes ND1 and cytochrome b and tested hypotheses pertaining to climate, geology, and dispersal patterns. Analyses revealed substantial genetic diversity and lineage divergence throughout the region with evidence for widespread sympatric lineages and a general north versus south clustering. Relaxed molecular clock analysis and tests for demographic expansion identified an initial cladogenesis during the Miocene with subsequent Plio-Pleistocene diversification, with the former corresponding to periods of increased aridity and the onset of monsoonal weather systems. Rates of diversification were relatively constant until the Early Pleistocene when rates increased exponentially. We found equivocal evidence for isolation-by-distance and a potential role of some landscape features as partial barriers to dispersal. Finally, our analyses showed that divergence between insular and mainland populations occurred before Homo sapiens colonized Southeast Asia, suggesting that historical human-mediated dispersal did not drive insular diversification. Our results suggested that demographic expansion in the Late Pleistocene resulted in widespread sympatric lineages in the P. leucomystax complex throughout southern China and Indochina and further clarified the evolutionary history of lineages within P. leucomystax.

A phylogeny of the Tylototriton asperrimus group (Caudata: Salamandridae) based on a mitochondrial study: suggestions for a taxonomic revision.

A phylogenetic hypothesis for the Asian newts of the Tylototriton asperrimus group was generated using data from two mitochondrial fragments including COI and the ND1-ND2 regions. Four distinct clades (A, B, C, D) were resolved with high nodal support within this monophyletic group. Clade A included T. asperrimus, T. hainanensis, T. notialis, "T. vietnamensis", and two unnamed salamander populations from Vietnam. Clade A, constituted the sister group of clades B + C. Newly identified clade C likely represents a new cryptic species. Clade C was the sister group of T. wenxianensis. The true T. vietnamensis exclusively constituted clade D. Our results bring into question some previous taxonomic decisions, and a revision is required. This study illustrates the necessity to include samples from type localities in taxonomic studies, and highlights the importance of fine-grained geographical sampling.

Bioinformatics analysis of the complete sequences of cytochrome b of Takydromus sylvaticus and modeling the tertiary structure of encoded protein.

Cytochrome b (cyt b) gene complete sequences (1143bp) of Takydromus sylvaticus were sequenced. In order to clarify the phylogenetic position of the Takydromus sylvaticus, we investigated the phylogeny of 15 Takydromus spp. distributed in East-Asia by Maximum Parsimony (MP), Bayesian Inference (BI), and Maximum Likelihood (ML) methods using DNA fragments of cyt b genes. The results supported that the Platyplacopus merged into Takydromus and negated the validity of Platyplacopus. Furthermore, the prediction of tertiary structures of cyt b exhibited the CD loop region contain two short helices forming a hairpin arrangement, namely cd1 and cd2. Thermostability analysis shows that the CD-loop region is unstable thermodynamically and may provide mobility to amino acids located at the heme, and might provide high flexibility to the top of ISP (iron-sulfur protein) and the cavity region of Qo binding site. It suggested that the two short helices of CD loop region of cyt b was a dominating portion for ISP binding site.