Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045–0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.
The complete sequences of the mitochondrial DNA genome from Paradoxornis webbianus was determined using the polymerase chain reaction method. The genome (16,960 bp in length) contained 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes), a control region (D-loop) and a non-coding region at two different locations of mitogenome, which is similar to the typical mtDNA of vertebrates. All the protein-coding genes in P. webbianus were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.
We determined the complete nucleotide sequence of the mitochondrial genome of Odorrana schmackeri (family Ranidae). The O. schmackeri mitogenome (18 302 bp) contained 13 protein-coding genes, 2 rRNA genes, 21 tRNA genes and a single control region (CR). In the new mitogenome, the distinctive feature is the loss of tRNA-His, which could be explained by a hypothesis of gene substitution. The new sequence data was used to assess the phylogenetic relationships among 23 ranid species mostly from China using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses support two families (Ranidae, Dicroglossidae) for Chinese ranids. In Ranidae, we support the genus Amolops should be retained in the subfamily Raninae rather than in a distinct subfamily Amolopinae of its own. Meanwhile, the monophyly of the genus Odorrana was supported. Within Dicroglossidae, four tribes were well supported including Occidozygini, Dicroglossini, Limnonectini and Paini. More mitochondrial genomes and nuclear genes are required to decisively evaluate phylogenetic relationships of ranids.
The complete mitochondrial genome of Microhyl pulchra was determined in this work. This mitogenome was 16,744 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region (CR). The following four distinctive features were observed: a protein-coding gene (ND1) began with GTG as start codon; eight protein-coding genes (ND1, COII, ATP6, COIII, ND3, ND4, ND5 and Cytb) ended with incomplete stop codon T; four tRNA genes positions (tRNA-Leu (CUN)/tRNA-Thr/Trna-Pro/tRNA-Phe) located between CR and 12S rRNA genes, which was a novel mtDNA gene rearrangement in amphibians; there was no significant repeat regions in the CR.
The complete sequence of the mitochondrial DNA genome from Garrulax cineraceus was determined using the polymerase chain reaction method. The genome (17,800 bp in length) contained 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and 2 control regions (D-loop) at two different locations of mitogenome, which is similar to the typical mtDNA of vertebrates. All the protein-coding genes in G. cineraceus were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.
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