Phylogenetic Study Of Sciuridae Based On Complete Mitochondrial Genome And Evaluation Of Phylogenetic Performance Of Different Genes

Family Sciuridae is one of the largest families of Rodentia,species of this family show big diversity in morphology and habitations.They are good materials for study of speciation and evolution.Although phylogenies of some sciurid taxonomies within Sciuridae has been well studied,however,there have been few studies focused on the phylogeny of family Sciuridae,especially sciurid species distributed in China.This study used the complete mitochondrial genome as a molecular marker to explore the phylogeny of Sciuridae,and evaluate the phylogenetic performance of different genes in the genome.The complete mitochondrial genomes of six sciurid species including Spermophilus dauricus,Sciurotamias dividianus,Callosciurus erythraeus,Dremomys pernyi,D.pyrrhomerus,Tamiops maritimus were acquired by PCR.Based on the complete mitochondrial genome sequences of this six and other sciurid species downloaded from GenBank,we analyzed and compared the arrangement and composition of complete mitochondrial genomes the six species,searched for the best data partition scheme of the mitochondrial genome data,conducted phylogenetic analyses of the genome data according to the best data partition scheme and discussed the phylogeny of Sciuridae.Finally,we evaluated the phylogenetic performance of different genes of the mitochondrial genome.The main conclusions of this study are as follows:(1)The lengths of complete mitochondrial genomes of Spermophilus dauricus,Sciurotamias dividianus,Callosciurus erythraeus,Dremomys pernyi,D.pyrrhomerus,Tamiops maritimus were 16487bp,16570bp,16542bp,16549 bp,16573 bp and 16523 bp respectively,all of them contained 13 protein coding genes,22 tRNA genes and one non-coding control region.The arrangement,composition,codon usage,amino acid composition,secondary structure of tRNAs and the structure of control region were very similar among the six complete mitochondrial genomes.All these similarities indicated the conservatism of the sciurid mitochondrial genome.(2)The best prior data partition scheme was to divide the data into 12S rRNA,16S rRNA,H-tRNAs,L-tRNAs and each codon site of every protein coding genes.The best data partition scheme calculated by PartitionFinder divided the genome data into 11 subsets.(3)The ML and BI phylogenetic trees constructed by the best data partition scheme showed the same topology.The sciurid species included in this study formed four main lineages which corresponded to four subfamilies:Ratufinae,Callosciurinae,Xerinae and Sciurinae respectively.The phylogenetic relationship of the four main lineages is:(Ratufinae(Sciurinae(Xerinae,Callosciurinae)))which was coincident with the result of Steppan et al.(2004),It also rejected the result of Mercer and Roth(2003)who treated Xerinae and Sciurinae as sister group.All flying squirrels clustered with S.vulgaris which rejected the traditional division of Sciuridae into subfamily Pteromyinae and Sciurinae.Based on the phylogenetic result we speculated that the ancestor of the extant squirrels is arboreal,a reversal to a terrestrial habit may then have evolved once,leading to the "ground squirrel" clade.The close relationship of flying squirrel to S.valrigus indicated that flying squirrels evolved from tree squirrels.(4)Different genes of mitochondrial genome showed different pylogenetic resolution on different taxonomic level:ND1,ND2,ATP6,ND4,ND5,12S rRNA,16S rRNA and tRNAs genes were suitable to resolve phylogenetic relationships among species,16S rRNA,ND5 and ND1 were suitable to resolve phylogenetic relationships among genera,ND4 and12S rRNA were suitable to resolve phylogenetic relationships among subfamilies.ND1,ND5,ND4,12S rRNA and 16S rRNA genes showed relative good phylogenetic performance.The length of genes was an important factor to phylogentic performance.It is noteworthy that although with long sequence,COX1 and cyt b showed relatively poor performance,this may be resulted from the selection pressure of the protein they encoded or their relatively slow substitution rates.Phylonetic analysis of concentrated ND4 and ND5 gene showed the almost same topology compared with that of complete mitochondrial genome data We suggest using these two genes preferentially for sciurid phylogenetic study in the future.