| The order Squamata is the most thriving group of reptiles, including approximate7200living species. Because of the great diversity in morphology, ecology, behavior, and life history between its members, it became an ideal model for evolutionary biology and systematic biology studies. Clarifying the phylogenetic relationships between squamates is important to our understanding that how the organisms change their shapes, behaviors and living strategies to adapt the environment during evolution and is of great guidance value for people studying the evolutionary progress of organisms using their phenotypes and molecular informations.To explore the phylogenetic relationships of squamates, the present study used complete mitogenome sequence as molecular marker and constructed phylogenetic trees with several data sets and tree reconstruction methods. The main contents and conclusions of this work are:1) The complete mitochondrial genome sequence of Gekko swinhonis was obtained through PCR and sequencing, the full length of which was16818bp. Thirty-seven genes were identified in the genome, including13protein coding genes (PCGs),2rRNA genes and22tRNA genes, as well as a non-coding control region. The gene arrangements and transcribing directions were identical to most of the reported squamates mitogenomes. The base composition of the whole genome and genes or regions were similar to the general vertebrates’, showing high AT content, positive GC bias and negative AT bias. The secondary structures of tRNAs were predicted by tRNAscan-SE on-line server; all the tRNAs form typical cloverleaf structure except for tRNA-Ser(AGY), whose T-arm was lacking.2) The nearly full length sequence of mitogenome of Takydromus sexlineatus was determined. From the15583bp sequence obtained,13PCGs,2rRNA genes and20tRNA genes were identified, lacking tRNA-Thr, tRNA-Pro and the Control Region comparing to the normal complete mitogenome of vertebrate. The base composition, gene location and arrangement and some other featrues of the determined sequence were similar to most of other vertebrates.3) Thirty-one mitogenome sequence of other squamatas were downloaded from GenBank, to analysis the phylogenetic relationships of squamates, together with the two genomes we determined newly. Five data sets derived from the sequence then involved in the analyses, were aminoacid sequences of13PCGs (AA13), AA13data set excluding ND6sequences (AA12), DNA sequences of13PCGs (DNA13), DNA13data set excluding ND6sequences (DNA12) and DNA12data set excluding the3rd codon positions (DNA12-3rd). Phylogenetic analyses were conducted using maximum parsimony (MP) and Bayesian inferring (BI) methods for each data set. The ten phylogenetic trees obtained were similar but not all the same in topology and supported the monophyly of all sampled families except for Amphisbaenidae. The higher level relationships of this study did not agree the division of Squamata into Iguania and Scleroglossa and the monophyly of Scincomorpha. The limb-reduced taxa (Dibamidae, Amphisbaenia and Serpentes) did not clustered in a clade, and their phylogenetic positions in squamates were not certain. Furthermore, Serpents was placed as sister group to Acordonta, which was probably caused by long-branch attraction.4) Comparing the results of different data sets and tree reconstructing methods, some deep effect they had on the phylogenetic analysis could be found. Firstly, the ND6gene may had some useful phylogenetic information at the aminoacid level, but may be noise at the DNA level. Secondly, base of the third codon positions could also reduced the accuracy of phylogenetic analysis. And finally, MP method may be less reliable in tree reconstruction than BI method. |
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