Population Genetic Structure And Phylogentic Analysis For Morone Americana In Delaware Bay Of United States

White perch(Morone americana,Gmelin,1789)is an abundant semi-anadromous species found along the east coast of United States.During late spring to early summer,M.americana moves upstream from brackish water or estuary into fresh waters to spawn.It is also considered as a good indicator species of contaminant.Given its abundance and widespread distribution,M.americana may serve as a good model for investigating the population genomics of a partially migrating estuarine species.Moreover.It plays important roles on monitoring pollutions.To date,available genetic markers for M.americana are limited to mitochondrial DNA RFLP polymorphisms.In order to obtain a high-resolution profile of population structure,larger numbers of nuclear as well as mitochondrial genetic markers are needed.In this study,the complete mitochondrial genome of M.americana was first amplified,then three mitochondrial genes(16S?COI?ND2)and double digest restriction site-associated DNA sequencing(ddRAD)technique were applied to analyze the population structure of four populations for M.americana in US eastern coast.Our study provided valuable tools for investigation into population resource of this species.In addition,our results are also promising to assist the decision making from department of environment protection.(1)Primer-walking PCR strategy was used to obtain the complete mitochondrial genome of M.americana.The total length of M.americana mitogenome is 17966 bp,consisting of 13 protein coding genes,22 transfer RNAs,two ribosomal RNA genes,and a non-coding control region.As with several other species in Moronidae,the ND6 gene in M.americana is found within the control region rather than at the canonical position between the ND5 and Cytb genes.In control region,we identified one termination-associated sequence(TAS),one central conserved sequence block(CSB-D)and two conserved sequence blocks(CSB-1,CSB-2).We also found a 121 bp tandem repeat sequence with eight complete repeats and one truncated repeat.Phylogenetic analysis based on mitochondrial gene places M.americana within Moronidae and confirms its close relationship with yellow perch(M.mississippiensis).(2)In total,96 samples were collected from US eastern coast.Three sampling sites were in Delaware Bay(Sta92?Bro_R?Mur_R)and one sampling site(Bro_Cr)was in Chesapeake Bay.We applied three mitochondrial genes(16S,COI,ND2)to evaluate the genetic structure of four populations.The preliminary results showed that single mitochondrial gene is not polymorphic enough to resolve the population structure.Then we concatenated three partial genes to obtain a new sequence.This sequence was used to calculate the corresponding genetic parameters.The haplotype diversity for four populations ranged from 0.507 to 0.902,the nucleotide diversity ranged from 0.00034 to 0.00085.A high haplotype diversity(h)and a low nucleotide diversity(?)were shown.The pair-wise Fst among populations were all significant except the Fst between Mur_R and Bro_R.The pair-wise Kimura-2p genetic distances among populations were low.Analysis of molecular variance(AMOVA)showed that the majority variance is within populations.In general,the mitochondrial data indicated that there are significant genetic differentiations among populations.However,the differentiations were not high enough to resolve the genetic structure of four populations.Salinity is a possible reason to cause the differentiation,but the short period after glaciations was not long enough to attain a clear population structure.(3)ddRAD technique was utilized to analyze the genetic structure for the four populations.We chose EcoRI and Nla? as the restriction enzymes to construct the ddRAD library.In total,438683 loci were identified from 96 individuals.After a stringent SNP filter,696 loci were left.Subsequent Hardy-weiberg test and Linkage Disequilibrium test exclude another 22 loci.Then a selection detection test divided the remaining loci into three categories:neutral loci(579),loci under natural selection(32),loci under banlancing selection(63).We used these three categories of loci to evaluate population structure,separately.The results showed that except the loci under banlancing selection,both the other two categories of loci can obtain a similar genetic structure for four populations.Moreover,the genetic differentiations calculated from loci under positive selection were the highest.The results based on neutral loci indicated that four populations can be identified as three groups,Mur_R and Bro_R clustered into one group,the other two populations formed another two groups,respectively.The genetic distance results revealed that Sta92 was closer to Bro_Cr than to the other two populations.This population structure was probably caused by salinity and anthropic activities.The demography for four populations was evaluated based on Bayesian method.The results showed that a hypothetical origin was first divided into two clades,then two clades divided into the four populations.Sta92 and Bro_Cr formed one clade,Mur_R and Bro_R formed another clade.This hypothetical origin was probably a southern shelter during glacial period.