Phylogeny Of Chinese Ranidae Inferred From The Complete Mitochondrial Genomes And Phylogeography Of Odorrana Schmackeri

The family Ranidae is one of the most species-rich amphibian families. Phylogenetic relationship of Ranidae is controversial. In this study, we sequenced the complete mitochondrial genomes of Odorrana schmackeri and Amolops ricketti. The 13 protein-coding genes of O. schmackeri and A. ricketti mitogenomes were aligned with homologous sequences of previously reported ranid mitogenomes and combined into a single sequence data set, which was used to assess the phylogenetic relationships in Ranidae. O. schmackeri is widely distributed and occurs in southern and south-central China. Its wide distribution and strict habitat requirements make it an excellent model to study the effects of the past geological events and climatic cycles on the genetic structure and demographic history in this region. The present study investigated the phylogeographic pattern of O. schmackeri species complex and its causes, using mtDNA. The main results were presented as following: 1. Phylogeny of Chinese ranidsThe length of the O. schmackeri mitogenome is 18,302 bp, containing 13 protein-coding genes, 2 rRNA genes, 21 tRNA genes(losing tRNA-His) and non-coding regions(including the D-loop region). The length of D-loop region is 2,531 bp. The D-loop region contains two sets of tandem repeats. The length of the A. ricketti mitogenome is 17,771 bp, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The D-loop region was 2,404 bp in length. The gene arrangements are similar to the typical neobatrachian-type arrangements. Based on the 13 protein-coding gene sequences, the phylogenetic relationship was reconstructed among the 23 ranid species. The 23 ranid species referred in this study formed two well supported major clades(A, B). It is sound that present representatives of Chinese ranids should be divided into two families, including Ranidae(Clade A) and Dicroglossidae(Clade B), as proposed by Frost et al.(2006; 2014). 2. Phylogeography of O. schmackeri species complexBased on mitochondrial sequences(1,151bp) of 511 individuals from 25 sites, we investigated the population genetic structure and Phylogeography of the O. schmackeri species complex. All analyses unambiguously showed that O. schmackeri species complex were genetically structured. First, BI and MP trees revealed that O. schmackeri species complex was composed of seven geographically structured clades. Second, about 86% of the haplotypes occured in one location only. No haplotype was shared among all the 25 populations of O. schmackeri species complex. Third, the AMOVA analysis also obtained a high level of geographic structuring. Finally, there was no unambiguous link among the six haplotype networks and the separate haplotype(SH-SNJ1). The results showed significant genetic differentiation among the species complex.The high levels of splits likely reflect long-term isolation, which is likely associated with the complex geological history of southern China. The first divergence between lineage A+B mainly occurring in the Pearl River, the Min River and the Qiantang River and other lineages(C-G) occupying midstream and downstream tributaries of the Yangtze River was approximately estimated during the late Miocene. The orogenesis of the mountains in southeastern China was thought to have begun in the Middle Jurassic, and during the Mio-Pliocene period the mountains were further uplifted to about 1000 m, thus forming a natural barrier separating the lineages between the southeast Coastal range and Yangtze River basin. The subsequent divergences(1.02-5.92Ma) between the lineages C-G occupying the midstream and downstream tributaries of the Yangtze River may have followed the formation of the Three Gorges and the strengthening of the East Asian summer monsoon. It is reasonable to assume that the Yangtze River and its major tributaries formed natural barriers separating the lineages occupying the Yangtze River basin.Molecular and morphological analyses suggest that these seven lineages represent seven different species, three described species and four cryptic species. Considering the limitation of using only the mitochondrial genes discriminate genotype, further studies including ecology, development, behaviour, etc. should be made for the species delineation.