Phylogeography Analysis Of Sarcocheilichthys Nigripinnis (Teleostei:Cyprinidae) Based On Mitochondrial And Nuclear DNA As Molecular

Sarcocheilichthys nigripinnis belonging to the family Cyprinidae,is a widely distributed freshwater fish in eastern China.In this study,mitochondrial gene（Cyt b and D-loop）and nuclear gene（RAG1 and S7）were used to examine the phylogeography of 13 S.nigripinnis geographical populations in the eastern water system of China.The genetic diversity and genetic structure,geographical pattern of the S.nigripinnis were analyzed,and the historical dynamics and the geographical events that form the existing distribution pattern we discussed.The main results and conclusions were shown as follows:1、Phylogeography of S.nigripinnis by mitochondrial DNA makersThe complete mt DNA cytochrome b gene（Cyt b）and control region（D-loop）sequences of 177 individuals of 13 populations were studied.Then studied the population genetic variation and phylogeographic patterns.（1）Genetic diversity.There are a total of 75 haplotypes defined by the 177 individuals,and the mt DNA combined sequence length is 2149 bp.the haplotype diversity（h）and nucleotide diversity（π）,ranged from 0.118 to 1.000 and from 0.00005 to 0.01119,average were 0.974 and0.02703.In general,the genetic diversity was lower for all sampled populations.（2）Genetic structure.The pairwise F_ST between populations of S.nigripinnis was from-0.10847 to 0.99166,and F_ST of all populations was 0.850,which showed the populations have a high genetic differentiation.The results of AMOVA analysis support that Qinling Mountains is a geographical barrier for S.nigripinnis form a north-south differentiation pattern,and Qinling Mountains is more effective than Nanling-Wuyishan.At the same time,it proves that Qinling,Wuyi,Nanling,Lianhua and Yunwu Mountains are important geographical barriers in the migration process of S.nigripinnis.（3）Demographic history.Neutrality test and nucleotide mismatch distribution analysis among all 13 populations showed that S.nigripinnis had experienced the population expansion.BSP analysis showed that the effective population of S.nigripinnis increased rapidly about 0.015 Ma,and lineage I and II began to expand about 0.02 Ma and 0.01Ma,We speculate that after the LGM period,the temperature rebounded,and the warm climate caused the population of S.nigripinnis to grow rapidly.（4）Phylogenetic Analysis.BI/NJ tree of haplotypes for S.nigripinnis revealed that 13 geographic populations form a north-south differentiation pattern bordered by Qinling Mountains,Most of the populations form independent clades and correspond to the water system.All evolution lineages are obviously distributed in different regions.And we infer that S.nigripinnis may have two north-south differentiation centers.The southern population manifested as migration from the lower reaches of the Yangtze River and Qiantang River to southern China.2、Phylogeography of S.nigripinnis by nuclear DNA makersWe invested the genetic structure and demographic history of 146 individuals of S.nigripinnis using RAG1 gene and S7 gene sequences as the genetic marker.（1）Genetic diversity.There are a total of 85 haplotypes defined by the 146 individuals,and the nu DNA combined sequence length is 2400 bp.the haplotype diversity（h）and nucleotide diversity（π）,ranged from 0.432 to 1.000 and from 0.00026 to 0.00335,average were 0.975 and 0.00651.In general,the genetic diversity was lower for all sampled populations.（2）genetic structure.The pairwise F_ST between populations of S.nigripinnis was from-0.24366 to 0.97574,and F_ST of all populations was 0.797,which showed the populations have a high genetic differentiation.The results of AMOVA analysis support that Nanling-Wuyi Mountains is a geographical barrier for S.nigripinnis form a north-south differentiation pattern,and Nanling-Wuyi Mountains is more effective than Qinling Mountains.At the same time,it proves that Qinling,Wuyi,Nanling,Lianhua and Yunwu Mountains are important geographical barriers in the migration process of S.nigripinnis.（3）Demographic history.Neutrality test and nucleotide mismatch distribution analysis showed that the population of S.nigripinnis had experienced the population expansion.（4）Genetic relationship.The genetic differentiation fixed index Nst>Gst indicates that there is a significant relationship between phylogeny and geographical events.Using haplotype data to reconstruct the phylogenetic tree of S.nigripinnis,The results show that the north-south differentiation pattern bounded by Nanling-Wuyi Mountain is formed.and most of the populations formed independent evolutionary branches.Comprehensively comparing the analysis results of the two molecular markers,we draw the following conclusions:（1）Genetic diversity:the genetic diversity of mt DNA and nu DNA is low,but the nucleotide diversity of mt DNA is much higher than that of nu DNA,because the evolution rate of mt DNA is faster than that of nu DNA,which is 5-10 times that of nu DNA.（2）Phylogenetic Analysis.The results based on nuclear gene markers show inconsistent patterns with the results based on mitochondrial gene markers.Compared with nu DNA,the ancestral polymorphism in mt DNA disappeared faster,therefore,the lineage sorting process can be completed earlier than nu DNA.（3）Genetic structure.Both mt DNA and nu DNA markers show a high level of genetic differentiation.In AMOVA analysis,mt DNA and nu DNA markers are inconsistent in evaluating the geographical barrier effect of Qinling and Nanling-Wuyi Mountain.We speculate that this inconsistency may be due to incomplete lineage sorting.However,the results all support Qinling,Wuyi,Nanling,Lianhua and Yunwu Mountain as the geographical barriers for the migration and differentiation of S.nigripinnis.（4）Historical dynamics:Neutral test and mismatch distribution results of mt DNA and nu DNA both indicate that S.nigripinnis has been highly differentiated and has recently undergone population expansion.In summary,although mt DNA and nu DNA present inconsistent genetic structures and phylogenetic patterns,they reveal significant genetic differentiation,phylogenetic relationships and geographic barriers between the populations of black-finned loach,and the Pleistocene ice age Strong influence of population size.In addition,we believe that mt DNA markers are more suitable than nu DNA in explaining population genetic structure,genetic patterns of phylogenetic,and population expansion.3、Genetic diversity and structure of the Chinese lake gudgeon（Sarcocheilichthys sinensis）based on mitochondrial and nuclear datasetsThe complete mt DNA cytochrome b gene（Cyt b）and control region（D-loop）sequences of 65 individuals of 5 populations were studied.Then studied the population genetic variation and phylogeographic patterns.the haplotype diversity（h）and nucleotide diversity（π）,average were 0.949 and 0.0106.In general,the genetic diversity was lower for all sampled populations.The pairwise F_ST of all populations was0.503,which showed the populations have a high genetic differentiation.The results of AMOVA and F_ST analysis showed that there was a highly significant genetic differentiation between the Yangtze river and other sampling areas.At the same time,ML and BI methods were used to construct molecular phylogenetic trees,and the results showed that the populations of the Yangtze river（DTH and GJ）were closely related to the populations of the minjiang river（WYS）,indicating that wuyi mountain did not play a role as a geographical barrier between the Yangtze river and the minjiang river.Neutrality test and nucleotide mismatch distribution analysis show that China did not experience the population expansion,BSP analysis found that s.sinensis grew rapidly about 15,000 years ago.S-DIVA analysis showed that there were two colonization routes among these populations:before Wuyi Mountain lifted and hindered colonization routes from the Yangtze River to the Zhejiang-Fujian subregion.the populations of S.sinensis in Yangtze River and Minjiang diverged;during glaciations,the continental shelves were exposed,and the populations migrated from the Yangtze River to Qiantang and Minjiang Rivers.