Comparison, Evolution And Lineage Mitochondrial Genomics Studies Of Snowbirds

Qinghai-Tibet Plateau is listed as the world's most important biodiversity hotspots as its remarkable species diversity and high levels of endemism characteristic diversity of ecosystem types.The formation and uplift of this region have a great impact on the change of the local fauna.Snow bird genus(Montifringilla)and ground finch genus(Pyrgilauda)birds,due to their adaptation to the plateau habitats and alpine climate,are representative groups of alpine meadow fauna in Qinghai-Tibet Plateau.Snow finch birds as Palaearctic birds belong to Aves(Aves),passerines(Passeriformes),Finch(Passeridae).Currently there are eight species are known all over the world,in which seven species distributed in China,and one distributed in Afghanistan.They are mainly distributed in the Qinghai-Tibet Plateau and adjacent areas in china,including five species endemic to the Tibetan Plateau.There are three species of viewpoints for snow finch birds in taxonimy:One view is that seven species of snow finch exist as a genus;Another view is that the genus is divided into two genera,which are the Snow bird genus and ground finches genus;The third view classified finch species into three genera:that is Snow bird genus,plateau finches genus and ground finches bird genus(Onychostruthus).Mitochondrial genomes have been widely used in systematics and evolutionary studies with a good resolution to resolve the phylogenetic relationship at subfamily,genus and species levels.The animal mitochondrial genome is a circular DNA molecule encoding a key enzyme associated with energy metabolism,which is used to research high altitude adaptation of different animals(horse,chicken,Artemia,Tibetan antelope,etc.).The mitochondrial genome is a good molecular marker to study the characteristics of snow finch birds adapted to the plateau environment,and understanding their origin,evolution and phylogeny.These species of studies also have an important significance on the understanding of the formation and evolution of the Qinghai-Tibet Plateau avifauna.By using long-range PCR and conserved primer walking method,whole mitochondrial genome of six species of snow and ground finch birds were sequenced and the sequences were annotated and analyzed.Combined with 46 species of whole mitochondrial genome sequence of passerine birds downloaded from GenBank,we compared 13 protein-coding mitochondrial genes of passerine birds.Phylogenetic tree of passerine birds was reconstructed from different data sets by combinations of genes using different methods,and the evolutionary pressures and divergence time also analyzed.The main findings are as following:1.Mitochondrial genome of white-winged snow finch(Montifringilla nivalis)is 16923bp;brown-winged snow finch(Montifringilla adamsi)is 16912bp;Brown back snow finch(Pyrgilauda blanfordi)is 16913bp;brown-necked snow finch(Pyrgilauda ruficollis)is 16909bp;white-rumped snow finch(Onychostruthus taczanowskii)is 16917bp;black-throated snow finch(Pyrgilauda davidiana)is 16912bp.All mitochondrial genomes of six species include 37 genes(13 protein-coding genes,two ribosomal RNA genes(rRNAs)and 22 transfer RNA genes(tRNAs))and one non-coding control region(CR),of which 28 gene is encoded by heavy chain(H-chain),the remaining genes(ND6 and 8 tRNA genes tRNAGln?tRNAAla?tRNAAsn?tRNACys?tRNATry?tRNASer(UCN)?tRNAThr?tRNAGlu)are encoded by the light chain(L chain).The gene order of passerine mitochondrial genome is consistent with other bird species.2.The base composition of whole mitochondrial genome of 6 species is C>A>T>G,and nucleotide content of PCGs,rRNAs,tRNAs and control region is A + T greater than G+ C.The A + T content is highest at tRNA heavy chain(H chain)genes while A +T content is minimum at first point of protein-coding gene.The nucleotide A + T content of snow finch is lower than ground finch for every gene,especially the gap reached 10%between ATP6 and ATP8 genes.Except the second codon site and tRNA encoded by the light chain,the A are skewed in AT skew(AT/A + T);GC skew(GC/G+ C)in the light chain(L)coding tRNA bias G,the rest bias C.Protein-coding genes CO? of snow finch is skewed to T,ground finches belong to A skewed,and the rest is the same.The rate of change in nucleic acid variation(NVR)in protein-coding gene and control region between the two genus is higher.NVR value is relatively high in ATP8?ATP6?ND1?ND3 gene,while NVR has smaller value in CO??Cytb?CO?gene.The rate of change in amino acid variation(AAVR)is highest for ATP8 gene,the second is the ND3 gene,and CO??CO??Cytb genes has smaller value.3.The predicted second structures of mitochondrial control region for the six snow finches species is similar with other birds,including Domain ?,Domain ?,Domain ?(Figure 5).Domain ? includes two parts A and B,where A also includes two conserved regions(ETAS2 and ETAS1),and the poly(C)sequence separated by a 2-5 "T" in the middle,which is similar with snow goose(Anas caerulescens)of "goosehairpin"conservative box;District B has CSB1-like sequences.Domain ? belongs to the central conserved region,and has four conserved sequence region(similarity-boxB,C-box,D-box,E-box,F-box).Domain ? has translated bidirectional promoter(LSP and HSP),is not found similar poly(C)sequences of replication initiation sites found in mammalian heavy chain.4.The results showed that there are differences in A+T%content among the mitochondrial genomes and protein coding regions,which mainly caused by variation in the third codon of protein-coding genes;selection pressures are relatively large at first and second codons sites,and the third codon site sufferes less selection pressure;the purified selection of the second codons is much larger than the first and third codon sites;G has remained at relatively low levels(less than 10%)in 12 protein-coding genes;the content of base C is average above 40%at third codon site of 12 protein-coding genes in 51 passerine birds species,and the C content increases with the base T decreasing.5.dN/dS values of 13 protein-coding genes of 46 passerine species are less than 1,indicating that they are suffered a positive selection.But dN/dS value of ATP8 and ND6 gene exhibits relatively high value comparing to other genes,and dN/dS of COI gene is minimum.This phenomenon have found in other studies.we analyze evolutionary rate of 51 species of passerine birds based on altitude,diet,migratory birds and different distribution regions,the results revealled the birds experienced different evolutionary selection pressures and different evolutionary rate,the birds living in high altitude areas,with migratory birds,herbivorous birds and distributed in Africa have accumulated more nonsynonymous substitution.6.The results of phylogenetic analysis are consistent with Sibley&Ahlqulst and Howard and Moore's view,and support the two sub-order division,suborder songbird dividing into Corvida and Passerida,and Passerida including Musicicapoidea,Sylvioidea and Passemidea.For the Sylvioidea,long-tailed tits and swallow clade are closely related.The tree also support the view that the snow birds genus are divided into two monophyletic subgenus,namely,white-winged birds and brown-winged snow finch belong to snow finches subgenus,and brown-necked snow finch,white-rumped snow finch,brown back snow finch,black-throated finch snow finch belong to finch subgenus.7.The differences and evolution time of Passerine is consistent with the geological events,which reveals the original ancient ancestors of passerine birds evolved and multiplied on the same ancient land;in the late Mesozoic,with the split and drift of the original ancient land,primitive birds also will split and disperse and be brought to the everywhere;Passerine differentiated and formed the current distribution in Cenozoic;as the endemic species in Qinghai-Tibet Plateau,the occurrence of burst event,the radiation evolution and speciation of snow finch are consistent with the tectonic event and the climate transition of the Tibetan Plateau.