Study On The Phylogeographic Pattern Of Two Specialized Grades Schizothoracine Fishes

D.maculates is a kind of specialized Schizothoracinae fish has been locally listed as a protected animal in Xinjiang Province,China.Ili River located in north of Tianshan Mountain and Tarim River located in north of Qinghai-Tibetan Plateau were two main distribution areas of this fi sh.To investigate the genetic diversity and genetic structure of D.maculates,four populations from Tarim River system and two populations from Ili River system were collected in this study.A 570-bp equence of the control region was obtained for 105 specimens.Twenty-four haplotypes were detected from six populations,only Kunes River population and Kashi River population shared haplotypes with each other.For all the populations examined,the haplotype diversity(h)was 0.904 8±0.012 6,nucleotide diversity(?)was 0.027 9±0.013 9,and the average number of pairwise nucleotide differences(k)was 15.878 3±7.139 1.The analysis of molecular variance(AMOVA)showed that 6.31% of the total genetic variation was apportioned among populations,and the variation within sampled populations was 13.69%.Genetic differences among sampled populations were highly signifi cant.Fst statistical test indicated that all populations were signifi cantly divergent from each other(P<0.01).The largest Fst value was between Yurungkash River population and Muzat River population,while the smallest Fst value was between Kunes River population and Kashi River population.NJ phylogenetic tree of D-loop haplotypes revealed two main clades.The neutrality test and mismatch distribution analysis suggested that the fi sh had went through a recent population expansion.The uplift of Tianshan Mountain and movement of Qinghai-Tibetan Plateau might contribute to the wide genetic divergence of D.maculates in northwest China.Gymnodiptychus dybowskii is endemic to Xinjiang,China and has been locally listed as protected animals.To investigate its genetic diversity and structure,specimens were collected from six localities in Yili River system and Kaidu River.Fragments of 1092 bp Cyt b gene were sequenced for 116 individuals.A total of 21 haplotypes were found in all samples,and no haplotype was shared between Yili River system and Kaidu River population.Sequence comparisons revealed 123 variable sites,with eight singleton sites and 115 parsimony informative sites.For all the populations examined,the haplotype diversity(h)was 0.8298 ± 0.0226,nucleotide diversity(p)was 0.2521 ± 0.1202,and average number of pairwise nucleotide differences(k)was 275.3369 ± 118.5660.AMOVA analysis showed that the differences were significant for total populations except for Yili River system populations.The pairwise Fst values revealed same conclusion with AMOVA analysis: Kaidu River population was divergent from Yili River system populations.The genetic distance between two groups was 0.108 and the divergence time was estimated at 5.4-6.6 Ma,the uplift of Tianshan Mountain might have separated them and resulted in the genetic differentiation.The neutrality test and mismatch analysis indicated that both two groups of G.dybowskii had went through population expansion,the expansion time of Yili River system and Kaidu River population was estimated at 0.5859-0.7146 Ma and 0.5151-0.6282 Ma,respectively.The climate changes of Qinghai-Tibetan Plateau might have influenced the demographic history of G.dybowskii.Gymnodiptychus dybowskii belonging to subfamily Schizothoracinae is a rare and endangered aboriginal fish in Xinjiang.In this study,the complete mitochondrial genomes of G.dybowskii from Tarim River system(16,677bp)and Ili River system(16,667bp)were sequenced.Besides,their genetic characteristics were also identified and compared simultaneously.Genetic distance and sequence differentiation suggested that great genetic variation existed within species and the sample from Kaidu River in South Xinjiang might be a cryptic species or subspecies of G.dybowskii.The phylogenetic analyses from 12 concatenated H-strand-encoding protein genes were conducted by Neighbor-Joining method to reveal the evolutionary relationships within subfamily Schizothoracinae.Three different grades of schizothoracine fishes were well recognized from each other in branching diagram.The primitive group and the specialized group + the highly specialized group constituted a sister relationship with strong supports.Scizothoracins are a group of cyprinid fish distributed around the Qinghai Tibet Plateau.According to different degrees of adaptation to plateau environment,it can be classified to three grades: primitive,specialized and highly specialized grade.The Diptychus maculates and Gymnodiptychus dybowskii are the only two Specialized Schizothoracins in Xinjiang,China,and they are good materials for studying the adaptive evolution of Schizothoracine fishes.The population genetic structures of two species were analyzed by SLAF technology.Based on the SNP loci,the genetic diversity level of them at the whole genome level was evaluated and calculated.In general,their genetic diversities tended to the same tendency: BM and LKG were the lowest,while BK and LK were the highest of all.Cluster and PCA analysis demonstrated the genetic affinity among BS,BG,BM and BK,but were quite distantly related to BT.Specimens of LKG clustered one clade and the rest aggregated another one.Outlier SNP loci were discovered both in D.maculates and G.dybowskii,showing Schizothoracinae were still under selection pressure of plateau environments.A total of 14041 SNPs in D.maculates and 10 SNPs in G.dybowskii associated with altitude adaptation were found by Bayenv method,respectively.In the aspect of the temperature factor,14357 SNPs were revealed in D.maculates versus 12 SNPs in G.dybowskii.In this study,numerous SNP loci associated with altitude and temperature were detected in D.maculates,while fewer loci were found in G.dybowskii.It indicated that D.maculates was under much greater selection pressure.A significant signal of IBD was detected across D.maculates(Mantel test,rs = 0.65,P = 0.05)populations using Mantel correlations.The pairwise Fst value genetic and environmental distances were only significantly positive correlated by Mantel test in D.maculates.The results indicated a higher gene exchange in Yili River.The IBD test of D.maculates is significant,showing the more obvious geographical isolation of the Tarim River.The IBE analysis indicated that the temperature and altitude selection was more intensively in D.maculates,the greater environment variation resulted in its weak gene flow.