The Phylogenetic Relationships Of Suborder Serpentes Based On The Complete Mitochondrial Genomes

Mitochondrial genome serves as an independent genetic material outside of cellnucleus, with small molecular weight, conservative gene organization, maternalinheritance and other characteristics. Therefore, it is used as an important molecularmarker and widely applied to the studies of molecular phylogeny and molecular evolution.In this paper, the complete mitochondrial sequences of five colubrids were sequenced bynormal PCR and long-and-accurate PCR (LA-PCR) methods. We combined the alreadypublished mitochondrial genome sequences of Serpentes in GenBank to analyse the snakemitochondrial genome organizations and discuss the phylogenetic relationships anddivergence time of Serpentes. The main results and conclusions as follows:1. Five mitochondrial genomes of Cyclophiops major (17217bp), Dinodonrufozonatum (17189bp), Oocatochus rufodorsatus (17159bp), Elaphe taeniurus (17183bp) and Zaocys dhumnades (17164bp) were sequenced in this study. The structures offive genomes were consistent with other alethinophidian snakes, which contained13protein-coding genes,22transfer RNA genes,2ribosomal RNA genes,2control regions(CRI and CRII), and an origin of light-strand replication (OL). Furthermore, an extratRNAPropesudogene was found in the genomes of D. rufozonatum, O. rufodorsatus and E.taeniurus.2. By comparison of base compositions of snake mitochondrial genomes, we foundthat the content of A and T was significantly higher than the content of G and C, and theAT skew was positive, the GC skew was negative. Some distinctive features are observedin all alethinophidian snakes: duplicated control regions that have nearly indenticalsequences at two different locations of mitogenome, translation of tRNALeu(UUR)genewhich giving rise to the LQM tRNA gene cluster, and truncations of TΨC arm for mosttRNA genes. In the tRNA secondary structure of Serpentes, the truncation of TΨC loopwas also found in some tRNA genes. Meanwhile, tRNACysgene in all five snakes missedthe TΨC loop, which was the first report in Serpentes.3. Sequences of twelve concatenated protein-coding genes were used to reconstructthe phylogenetic relationships among56snakes in suborder Serpentes employing themethods of maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI). All phylogenetic trees indicated that Serpentes was monophyletic withstrong support, and the Scolecophidia was basal to all other serpentes and divergedearliest among snakes. Within the Colubroidea, Achalinus meiguensis was a basal clade toall other colubroids, and paraphyletic to Viperidae, Elapidae and Colubridae respectively,and its divergence was also earlier than other colubroids, so the subfamilyXenodermatinae, which contains A. meiguensis, should be raised to a family rank.Thermophis zhaoermii always formed a sister-group relationship with subfamilyXenodontinae in all phylogenetic trees, so we suggested that T. zhaoermii should bepositioned under Xenodontinae in Coulubridae, not in Colubrinae based on morphologicalstudies. Enhydris plumbea showed a sister relationship with the Colubridae+Elapidaeclade in all phylogenetic methods, the familial rank of Homalopsidae was thereforeconsidered well-supported.4. The divergent time estimation indicated that the structure of snake mitochondrialgenome has undergone a significant and lasting change in66.57MYA (95%HPD,58.34to74.59MYA), with the symbol of appearance of duplicated control regions andtranslocation of tRNALeu(UUR)gene. Meanwhile, most species were split between10and40MYA in Colubroidea, which is closely related to the Cenozoic climate environmentthat was conducive to speciation and radiation evolution of snakes.