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Lycodon liuchengchaoi is a new species discovered in recent years which is widely distribute in Anhui, Hubei and Sichuan Province. In this study, we determined the complete mitochondrial genome of L. liuchengchaoi. The result shows that the complete mitogenome of L. liuchengchaoi is 17,171bp. It is similar with the typical mtDNA of Serpentes, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, 2 control regions, and a stem-loop region. The phylogenetic tree, contains 17 Serpentiforms species, is divided into two clades which correspond to six genera in Colubridae. The L. liuchengchaoi which appeared into Clade A, clustered within Lycodon.

Background Climate oscillation may have a profound effect on species distributions, gene flow patterns and population demography. In response to environmental change, those species restricted to montane habitats experienced expansions and contractions along elevation gradients, which can drive differentiation among sky islands. Results The Shangcheng stout salamander (Pachyhynobius shangchengensis) is a cool stream amphibian restricted to high-elevation areas in the Dabie Mountains, East China. In the present study, we used mtDNA genes (Cyt b and ND2) of 193 individuals and 12 nuclear microsatellite loci genotyped on 370 individuals, representing 6 populations (JTX, KHJ, MW, TTZ, BYM and KJY) across the taxon’s distribution area, to investigate their genetic variation and evolutionary history of P. shangchengensis. Most populations showed unusually high levels of genetic diversity. Phylogenetic analyses revealed five monophyletic clades with divergence times ranging from 3.96 to 1.4 Mya. Accordingly, significant genetic differentiation was present between these populations. Bayesian skyline plot analyses provided that all populations underwent long-term population expansions since the last inter-glacial (0.13 Mya ~ 0.12 Mya). Msvar analyses found recent signals of population decline for two northern populations (JTX and KHJ) reflecting a strong bottleneck (approximately 15-fold decrease) during the mid-Holocene (about 6000 years ago). Ecological niche modelling has shown a discontinuity in suitable habitats for P. shangchengensis under different historical climatic conditions. Conclusions Our results suggest that the niche conservatism of P. shangchengensis and sky island effects may have led to long-term isolation between populations. In sky island refuges, the mid-latitude Dabie Mountains have provided a long-term stable environment for P. shangchengensis, which has led to the accumulation of genetic diversity and has promoted genetic divergence. Electronic supplementary material The online version of this article (10.1186/s12862-018-1333-8) contains supplementary material, which is available to authorized users.

A new species Rana dabieshanensis sp. n. is described from the Dabie Mountains in Anhui Province, China, based on morphological character differences and molecular analyses. The new species can be distinguished from its congeners by a combination of diagnostic characters. The results of phylogenetic analyses (based on 12s rRNA, 16s rRNA, ND2, Cyt b, RAG1, BDNF and Tyr) and genetic distances (based on Cyt b) indicate that the new species belongs to the Rana longicrus group, and is placed as the sister taxon to R. hanluica.

Background Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake’s mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. Results In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. Conclusions The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity. Electronic supplementary material The online version of this article (10.1186/s12864-018-4717-7) contains supplementary material, which is available to authorized users.

Table S3. Primers sequences used in this study. (DOC 66 kb)

Figure S3. Homology analysis of OL. The sequences of OL of Alethinophidians and four saurians are aligned. (PDF 574 kb)

Figure S2. Bayesian phylogenetic inference tree based on the combined data set of RNA genes and Protein-coding genes. The numbers above the branches indicate the posterior probability. (PDF 256 kb)

Table S2. List of taxa used in this study. *: the species were used in Yan et al. [18]. #: the species were used in Chen and Zhao. [19]. (DOC 132 kb)

Table S1. Features of the mitogenomes of three Lycodon species. (DOCX 22 kb)

Table S4. Best-fit models and partitioning schemes selected by PartitionFinder for the dataset analyzed. (DOCX 22 kb)

Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genusRhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification withinRhacophoruswere related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures inRhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). TheRhacophoruslineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area ofRhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification inRhacophorus.

The complete sequence of the mitochondrial genome was determined for Asio flammeus, which is distributed widely in geography. The length of the complete mitochondrial genome was 18,966 bp, containing 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes (PCGs), and 1 non-coding region (D-loop). All the genes were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The D-loop of A. flammeus contained many tandem repeats of varying lengths and repeat numbers. The molecular-based phylogeny showed that our species acted as the sister group to A. capensis and the supported Asio was the monophyletic group.

Many bufonidae species distributed in Asia are inhabited in a variety of environments. However, there are few studies focusing on the speciation of Asia Bufonidae. In this study, we reconstruct the phylogeny tree of Asia Bufonidae with timescale in BEAST based on a multiple sequence alignment of 12S gene and 16S gene sequences from 13 Bufonidae species and whole mtDNA from five Bufonidae species. The results show that the bufonids split into two major clades. In general, there are two lineages mainly distributed on different sides of the Himalayas. According to the divergence time and distribution of the two lineages, we imply that the differentiation of Bufonidea may be closely linked to the uplift of QTP and consequent monsoon climate.

Protobothrops kaulbacki is a new record in China, and in this study, the complete mitochondrial genome sequence of P. kaulbacki had been determined. The length of mitogenome is 17,237 bp, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S and 16S rRNA), 1 origin of L-strand replication (OL), and 2 control regions (CRs). The maximum-likelihood (ML) tree based on the whole mitogenome shown that P. kaulbacki belongs to the genus Protobothrops.

Motacilla cinerea is a species of small- and medium-sized songbird in the Family Motacillidae, which is widely distributed. In this study, we determined the complete mitochondrial genome of M. cinerea. The result showed that the total length of the mitogenome was 16 825 bp and contained two ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and one control region. All the genes in M. cinerea were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which are encoded on the L-strand. The phylogenetic tree was reconstructed using Bayesian analysis methods, and containing two clades: Motacilla and Anthus. The first lineage is Motacilla including M. cinerea and other nine species. The genus Anthus makes up the second group, which containing 17 species.

Anthus hodgsoni is a species of small passerine bird in the family Motacillidae, which is widely distributed. In this study, we determined the complete mitochondrial genome of A. hodgsoni. The result showed that the total length of the mitochondrial genome was 16,886 bp and contained 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes and 1 control region. The phylogenetic tree was reconstructed using the Bayesian analysis method and divided into four genera, Anthus, Dendronanthus, Motacilla and Tmetothylacus. The A. hodgsoni which we determined was clustered into genus Anthus and received strong support.

The complete mitochondrial genome sequence of Hyla tsinlingensis was determined in this research. The length of mitogenome is 17850 bp, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, 1 OL and 1 control region. The phylogentic tree was reconstructed using the BI method based on concatenated nucleotide sequences of mtDNA genes (12S ribosomal small subunit gene/12S rRNA; NADH dehydrogenase subunit 1 gene/ND1, including adjacent transfer RNAs and the partial 16S ribosomal large subunit gene). The phylogenetic tree was split into two clades, Clade A and Clade B. The H. tsinlingensis which we determined clustered into Clade A.

Lycodon liuchengchaoi is a new species discovered in recent years which is widely distribute in Anhui, Hubei and Sichuan Province. In this study, we determined the complete mitochondrial genome of L. liuchengchaoi. The result shows that the complete mitogenome of L. liuchengchaoi is 17,171bp. It is similar with the typical mtDNA of Serpentes, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, 2 control regions, and a stem-loop region. The phylogenetic tree, contains 17 Serpentiforms species, is divided into two clades which correspond to six genera in Colubridae. The L. liuchengchaoi which appeared into Clade A, clustered within Lycodon.

In this paper, the complete mitochondrial genome of Pachytriton feii is sequenced and reported for the first time. In our result, the complete mitochondrial genome of P. feii is 16 293 bp in length. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and 1 non-coding region (D-loop). All the genes in P. feii 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 was reconstructed using the Bayesian analysis method and contained two major clades. Among Pachytriton (P. feii, Pachytriton labiatus, and Pachytriton brevipes), Paramesotriton laoensis make up the first lineage.

Motacilla alba is a species of small and passerine songbird in the Family Motacillidae, which is widely distributed. In this study, we determined the complete mitochondrial genome of M. alba. The result showed that the total length of the mitogenome was 16 826 bp and contained 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and one control region. All the genes in M. alba 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 was reconstructed using maximum-likelihood analysis and divided into three major clades. The species from genus Anthus were clustered into clade A. The clade B contained M. alba and other seven Motacilla species. Dendronanthus indicus as one species from Dendronanthus comprised the clade C, and received strong support.

Dinodon rufozonatum is a species of nocturnal snake in the family Colubridae, which is native to East Asia. In this study, we determined the complete mitochondrial genome of D. rufozonatum. The results showed that the total length of the mitogenome was 17,188 bp and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, 2 control regions and 1 stem-loop region. Overall base composition of the complete mitochondrial DNA was A (34.37%), G (12.61%), C (28.24%), and T (24.78%), so the percentage of A and T (59.15%) was slightly higher than G and C. All the genes in D. rufozonatum were distributed on the H-strand, except for the ND6 subunit gene and ten transfer RNA genes which were encoded on the L-strand.

Lycodon flavozonatum, a species of Colubcridae family, is mainly inhabited in hilly region of forest in South China, India, Myanmar, and Vietnam. In this study, the complete mtDNA of L. flavozonatum is 17 172 bp long, which contains 13 protein-coding genes, 22 tRNA genes, two rRNA (12S and 16S rRNA), and two control regions and a stem-loop region. Most of these genes are encoded in the H-strand; only ND6, stem-loop and other nine tRNA genes are on the L-strand. The phylogenetic tree among the 14 Serpentiformes species was divided into three major clade; Lycodon makes up the first clade, which showed a sister relationship to the second clade, Elaphe; Hypsiglena forms the third clade and is sister to Lycodon and Elaphe. And the species of L. flavozonatum which we studied belongs to the first clade.

In this paper, the complete mitochondrial genome of Glaucidium brodiei is sequenced and reported for the first time. The mitochondrial genome is a circular molecule of 17,318 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. Overall base composition of the complete mitochondrial DNA is A (29.9%), G (14.1%), C (32.1%) and T (23.9%), the percentage of A and T (53.8%) is slightly higher than G and C (46.2%). All the genes in G. brodiei are distributed on the H-strand, except for the ND6 subunit gene and nine tRNA genes, which are encoded on the L-strand.

Ixobrychus flavicollis is the largest bittern in Ixobrychus which has very wide geographical range. In our results, the complete mitochondrial genome of I. flavicollis is 17,016 bp in length. Thirteen protein-coding genes, two rRNA genes, twenty-two tRNA genes and one non-coding region (D-loop) are present in this mitochondrial genome. No special arrangement when compared with other typical mitochondrial of vertebrates. The percentage of A and T (56.7%) was slightly higher than G and C.