A Preliminary Study Of The Genetic Population Structure And Local Adaptation In The Japanese Eel (Anguilla Japonica)

Figuring out the genetic population structure within species can help understand the importance of biodiversity,and is also the basis on which we can accomplish scientific management of biological resources.Previous studies on the genetic population structure of the Japanese eel（Anguilla japonica）were based on neutral markers;our study aimed to dig this issue from a new perspective,using geneassociated microsatellite markers and outlier SNP markers resulted from whole-genome scan instead.Local adaptation of the genus Anguilla is another hot scientific issue.Populations can evolve traits that confer a Darwinian fitness advantage in their local habitat,due to the interaction between genotype and their local conditions.The process and the resulting pattern are termed “local adaptation”.It has long been accepted that adaptive evolution requires the accumulation of signature of natural selection for many generations,and it is too slow to influence contemporary ecological dynamics,which we now know is not always true.Evolution can happen within a few generations.Freshwater eels,of the genus Anguilla,are ideal materials for the study of contemporary local adaptation owing to their panmixic features.The case studies on the American eel（Anguilla rostrata）and European eel（Anguilla anguilla）detected signatures of local adaptation happening within single-generation time scale,which lighted the road for other Anguilla eels.We extended the study to the Japanese eel,the results would advance our understanding on local adaptation that happens within single-generation time scale and provide some clues on how to deal with the globally changing environment.The resource of the Japanese eel has been declining since 1980 s.The wild population of glass eel,yellow eel and silver eel has decreased dramatically.The Japanese eel was ranked as “Endangered” by the IUCN red list published in 2016.Figuring out the population structure of the Japanese eel is the basis of scientific management and protection,and a good understanding of the local adaptation can help understand the mechanism of the fluctuation of the Japanese eel resource.The main results of the study are as follows:1.Developing gene-associated microsatellite markersWe developed gene-associated microsatellite markers for the Japanese eel.A total of 24 loci were polymorphic.The 24 loci were polymorphic in all sampled localities.Among these loci,a total of 18 loci were developed based on the genes under selection in North Atlantic eels（European eel and American eel）,and the other 6 loci were developed from transcript sequence randomly selected from database.The average number of alleles per locus across populations ranged from 4.846 to 29.231.Observed and expected mean heterozygosities per sample across loci ranged from 0.675 and 0.746 to 0.716 and 0.769,respectively.Twenty-nine out of 312 cases showed significant departure from HWE after Bonferroni correction（α= 0.05,K = 13）.No linkage disequilibrium was detected after Bonferroni correction（α= 0.05,K = 276）.Eight loci showed evidence of null alleles in more than three samples（not in all samples）.2.Developing SNP markersTwelve glass eels from each of the two populations were chosen for RAD-Seq（Restriction site-associated DNA sequencing）.After quality filtering,the reads were sorted according to their unique index sequences and aligned to the draft genome of the Japanese eel using BWA version 0.5.9.SNP calling was conducted using a conservative Bayesian approach as implemented in the package SAMTOOLS.We identified 73,557 putative SNPs in total.ARLEQUIN version 3.5 were utilized to detect SNPs potentially affected by diversifying selection between the two geographic localities DD and SS.We detected 250 outlier SNPs with FST value located above the 99.5% quantile of simulated distribution,among which 85 loci could find annotation match using BLAST2 GO.We then performed KASPar（KBiosciences Competitive Allele-Specific PCR genotyping system）genotyping for 373 specimens from 12 populations in 96 loci（85 outlier loci with annotation match + 11 outlier SNPs without annotation match）.3.Genetic analysis based on the gene-associated microsatellite markersThe global insignificant FST value of-0.001（95% CI:-0.002 < FST < 0.000）indicated that there was no significant genetic differentiation among these samples.None of the pairwise FST values were significant after FDR correction（α= 0.05,K = 78）.In STRUCTURE analysis,the optimal value of ΔK occurred at K = 5.However,all samples showed similar patterns when K = 5,suggesting no genetic structure.Mantel test showed no significant pattern of IBD among 13 geographic samples（R2 = 4.634e-03,P = 0.6233）.All measures of differentiation were accordant with a panmixic scenario.4.Detecting signatures of local adaptation based on SNP markersThe appearance of several significant FST values indicated that adaptive genetic divergence should exist among different geographic populations of the Japanese eel.The STRUCTURE results showed that the 12 populations could be divided into 2 groups: Group I（MA,MY and MJ）and Group II（populations from Mainland China）.And the clustering results were confirmed by DAPC analysis.The locus AVPY01361442₁313 and locus AVPY01361442₁313 were found to be significantly associated with environmental parameters by both BAYENV2 software and SAMBADA software.The locus AVPY01361442₁313 was associated with SMC6 gene,and locus AVPY01361442₁313 was associated with taar13 c gene.The function of DNA repair played by SMC6 gene might be a way of dealing with the unstable external environment to keep the chromosome in a stable state.And taar13 c gene might play a role in the diamine sensing,which affects the response to diamine of glass eels of the Japanese eel;however,to further understand the function of taar13 c gene,more experiments on odor-driven behavior of glass eels are needed.The present study confirmed the hypothesis of panmixia and detected the signature of local adaptation in the Japanese eel.Based on outlier SNPs,we detected the adaptive divergence between island-source populations and continent-source populations.The results of the study could provide basic data needed by scientific management and protection on the Japanese eel resource.