Population Genetic Structure And Local Adaptation Of The Small Yellow Croaker(Larimichthys Polyactis) And Japanese Eel(Anguilla Japonica)

The small yellow croaker(Larimichthys polyactis)and the Japanese eel(Anguilla japonica)are two of the most economically important marine fishery species in China and East Asian countries,however,the abundance of these species had severely decreased due to overfishing as well as other anthropogenic factors.Especially for the Japanese eel,the abundance of Japanese eel had sharply decreased more than 90% since 1970 s,and in March 2014,the Japanese eel was included in the IUCN(International Union for the Conservation of Nature)Red List of Threatened Species,with a current status as ‘endangered'(http://www.iucnredlist.org/details/166184/0).Population genetics can be used to detect the genetic structure of marine fish,thereby providing important insights into the sustainable management and utilization of fisheries resources.Limited source of markers has somehow constrained genetic studies of L.polyactis and A.japonica,and previous studies based on various types of genetic markers have obtained discrepant or even conflicting results.Hence,it is urgently needed to assess population genetic structure,genetic diversity,and possible regions of genome under selection for L.polyactis and A.japonica,in order to better manage and conserve these two species.The main results are as follows:1.Seventeen polymorphic microsatellite loci were developed and characterized for L.polyactis using magnetic beads enrichment procedure.The number of alleles per locus ranged from 4 to 21,and the observed and expected heterozygosities varied from 0.4583-0.9167 and 0.7154-0.9566,respectively.Two loci showed significant deviations from Hardy–Weinberg equilibrium,most likely because of null alleles.These highly polymorphic nuclear markers would be useful for studies of genetic diversity and population genetic structure of the highly exploited L.polyactis2.Using fifteen microsatellites markers,we noted a non-significant decrease in genetic diversity between different time periods,and no obvious change in allelic richness was observed.Measures of population structure indicated substantial temporal genetic changes according to population differentiation tests(FST),the PCo A,STRUCTURE and the AMOVA analysis.To our knowledge,this is the first study that showed the temporal genetic variation of the L.polyactis.The temporal genetic variation of L.polyactis populations might be attributed to genetic drift,fishing-induced or ecological changes for this species.3.Fifteen microsatellite loci were used to estimate genetic diversity and population structure of fifteen samples along China coast.High genetic diversity and low genetic differentiation among populations were detected with all microsatellites.No evidence of isolation by distance and recent genetic bottleneck events was detected.However,outlier analyses indicated that the locus Lpol03 might be under directional selection,which showed a strong homology with Grid2 gene encoding the glutamate receptor ?2 protein(Glu R?2).Based on Lpol03,two distinct clusters were identified by both STRUCTURE and PCo A analyses,suggesting that there were two overwintering aggregations of L.polyactis,and these results provided new perspectives on the population genetic structure and migratory routine of L.polyactis.4.Based on restriction site-assosciated DNA(RAD)sequencing technology,we analyzed 264 Japanese eel(Angullia japonica)individuals from eleven geographic locations.A total of 4,149,717,848 Raw Reads were generated after sequencing,and 45,552,012 SNPs were called using SAMTOOLS.After the quality filtering,a total of 37,700 SNPs were retained,the identified 37,700 SNPs were widely distributed across the draft genome of the Japanese eel.The overall low genetic differentiation found(FST=0.002012,P > 0.05)indicated that most of the genome is homogenized by gene flow.Results of ADMIXTURE revealed that all individuals were grouped into a single cluster when using all the SNPs.While the results of DAPC and NETVIEW suggested that there might some substructure for the 11 populations,which might be attributed to genetic drift for this species.5.We tested for local selection by searching for increased population differentiation using FST-based outlier tests and by testing for significant associations between allele frequencies and environmental variables,and a total of 355 outlier SNPs were detected.Functional categorization of the annotated sequences involved in signaling,response to stimulus,metabolic process,biological regulation,catalytic activity and development process,etc..The KEGG pathway analysis showed some of putative targets of local selection,including genes in several important pathways such as Wnt signaling pathway,Oocyte meiosis,calcium signaling pathway and MAPK signaling pathway.These results will be useful to inform conservation and management decisions for these two species.