Pairwise FST Estimates Research Articles

Genomic characterization of the Brazilian Crioulo Lageano: Insights for conservation of a Brazilian local bovine breed

Crioulo Lageano (CLAG) is a Brazilian taurine breed traditionally raised in the native fields of mountainous regions in the states of Santa Catarina and Paraná, located in the southern region from Brazil. The present study aimed to analyze the genetic diversity and structure of the breed to provide the basis for the development of strategies for its conservation. Samples from semen and DNA previously stored in the Brazilian Animal Gene Bank (BAGB), and samples collected from eight different farms registered in the Brazilian Association of Crioulo Lageano Cattle Breeders (ABCCL), were genotyped with different panels of SNP markers containing between 50 K and 777 K markers. Obtained estimates of average expected (HE = 0.373) and observed (HO = 0.382) heterozygosities suggest the presence of high levels of genetic variability in the breed. Molecular analysis of variance (AMOVA) revealed that only 2.11 % of the observed genetic variation could be attributed to differences between analyzed populations. Obtained pairwise FST estimates varied between 0.002 and 0.056, corroborating that the degree of differentiation between populations is low. Population structure analyses showed substructures between the studied populations, which could be related to the presence/absence of horns in the animals, in addition to other factors. The estimates obtained for the effective population size (Ne) considering bulls with semen stored in BGAB and the set of samples from the eight studied farms were 6 and 22, respectively, revealing that the Ne of the breed is far below that recommended by FAO for conservation of domestic animal populations. Population structure and admixture analyses comparing CLAG with six other taurine and zebu cattle breeds routinely raised in the region revealed evidence of possible unknown introgressions from animals of indicine origin. Obtained results provide solid insights into the diversity and genetic structure of the Brazilian CLGA breed and offer strategic information for the establishment of effective genetic management strategies for production herds, for the enrichment of the BAGB by collecting germoplasm and for the long-term conservation of this breed.

Population structure and genetic diversity of rainbow trout (Oncorhynchus mykiss) broodstocks from Brazil using SNP markers

Rainbow trout (Oncorhynchus mykiss) are native to the Pacific Ocean coast of North America and the Kamchatka Peninsula of Russia. Brazilian populations of rainbow trout derive from various imports from European countries, the United States of America (U.S.A.) and Canada, from the 1950 s onwards. A total of 347 samples from nine commercial broodstock groups sampled from five farms in Brazil were genotyped with a panel of 96 SNPs to analyze the genetic diversity and structure of commercial rainbow trout farmed in Brazil. Pairwise coefficients of relatedness of individual animals and coefficients of genetic differentiation and inbreeding of broodstock groups were obtained, in addition to tests of genetic allocation of animals to their respective group. The mean observed and expected heterozygosities were 0.405 and 0.398, respectively. The total Fst was 0.172 and the pairwise Fst estimates considering all strains ranged from 0.036 to 0.338. The UPGMA genetic distance tree shows that broodstocks declared to be originally from Canada (Kamloops region) and from Northern California (Mount Shasta) are the most genetically distant from each other and from the remaining studied groups. Genetic structure analyses suggest a best value of K= 2, separating broodstock groups originally from the U.S.A. and Canada. Structure and Principal Component Analyses (PCA) indicate that the management practices of one of the farms was efficient in properly maintaining different broodstocks separated, while in another farm unwanted admixture has been occurring. Reclassification of these animals using Structure analysis results were corroborated with PCA and GeneClass2 analyses, providing evidence that advanced analyzes with low-density SNP data can be used to improve farm management practices and even correct past errors. The present study represents the first analysis of diversity and genetic structure of commercial rainbow trout farmed in Brazil using SNP markers.

Cryptic Lineage and Genetic Structure of Acanthopagrus pacificus Populations in a Natural World Heritage Site Revealed by Population Genetic Analysis

Recent studies have revealed extensive genetic differentiation among some populations of marine taxa that were previously believed to be essentially homogeneous because larvae are widely dispersed in ocean currents. Acanthopagrus pacificus is a commercially and ecologically important teleost fish that is endemic to shallow coastal waters and estuaries of some tropical and sub-tropical areas in the West Pacific Ocean. Here, we examined genetic structure and the inferred demographic history of A. pacificus populations from mtDNA control region sequence data. A 677–678 base-pair fragment was sequenced from 159 individuals sampled at three localities across the West Pacific Ocean. Haplotype diversity was high, ranging from 0.915 to 0.989, while nucleotide diversity was low to medium, ranging from 0.8% to 2.60%. Analysis of molecular variance (AMOVA) showed significant genetic subdivision (FST = 0.155, p < 0.05) among sampled populations while pairwise FST estimates also revealed strong genetic differentiation among populations indicating that gene flow was restricted. Two distinct cryptic lineages were identified that were estimated to have diverged during the Pleistocene. In summary, contemporary factors including regional oceanic currents and self-recruitment are considered to have played significant roles in producing the population structure in this fish. In particular, the genetic information generated in the current study will allow appropriate fisheries management and conservation strategies to be developed for this important local fish in the waters around Iriomotejima Island, a World Heritage site.

Population genomics reveals a single semi-continuous population of a commercially exploited marine gastropod

Buccinum undatum is a commercially important marine gastropod with limited dispersal capabilities. Previous genetic studies utilising microsatellites and Double-digest Restriction-site Associated DNA sequencing (ddRADseq) provided evidence that B. undatum exhibits fine-scale genetic structure. Using ddRADseq, 128 individuals from the southern North Sea, English Channel, and the Irish Sea were genotyped using 7015 filtered single nucleotide polymorphisms (SNPs), 19 of which were identified as being under putative selection. Multiple genetic clustering methods – Discriminant analysis of principal components, Principal component analysis, and Sparse non-negative matrix factorisation,– were used to investigate population structure. Spatially explicit genetic structure was investigated using an Estimated Effective Migration Surface analysis and a Mantel correlogram. A single genetic population was found using neutral SNPs, with weak within-population structuring. Global FST was low (0.0046, p < 0.001), and pairwise FST estimates between sampling locations were between 0.0004 and 0.0224. There was a significant trend of isolation-by-distance across all sampling locations (r = 0.743, p < 0.001). Positive spatial autocorrelation indicated whelks located ≤ 50 km of one another were significantly more related than by chance (r = 0.12, p = 0.003), further emphasising the low dispersal capabilities of B. undatum. Finally, two barriers of lower-than-average dispersal were discovered; the Thames estuary and across the English Channel. Management implications are discussed for the sustainability of whelks from inshore fisheries.

Population genomic evidence for genetic divergence in the Northwest Pacific Ark shell (Scapharca broughtonii)

Combining population genetics with genomic data has transformed scientist’s ability and resolution of making ecological inferences, thus making it possible to detect previously unidentified structures and obtain more accurate estimates of demographic parameters in wild populations. Ark shell is an economically and ecologically important marine species for fisheries industry in China, but its habitats have been severely damaged due to overexploitation of natural resources. Recently, protection of the ark shell as a natural resource has attracted extensive attention. Here, we identified 10,108 single-nucleotide polymorphisms using Restriction-site Associated DNA Sequencing (2b-RAD) to explore the structure of seven populations of S. broughtonii from the Asian Pacific Northwest region (four sites in China, two in Korea, and one in North Korea). A high level of genetic diversity was detected in all seven S. broughtonii populations. Pairwise FST estimates and neighbor-joining (NJ) tree topologies showed a clear division between the populations from China and Korea, and Chinese populations exhibited low levels of divergence from one another. This significant genetic divergence of the Chinese population implies that translocation of individuals for aquaculture should be properly managed for the preservation of genetic diversity and eventual local adaptation in natural populations.

Genetic Divergence and Diversity Reflect a Predominant Freshwater Resident Life History in Rainbow Trout from Southwestern Alaska

AbstractRainbow Trout Oncorhynchus mykiss in southwestern Alaska occupy coastal watersheds near the northern boundary of the species’ native range and support a world‐class wild trout sport fishery. Although low freshwater temperatures and a short growing season in this region may favor anadromy, these populations appear to exhibit a freshwater resident life history strategy. We used genetic data to evaluate two hypotheses regarding the influence of the presumed migratory behavior of these Rainbow Trout on reproductive isolation among and within watersheds. The results were largely consistent with the predictions, but there were exceptions. The data supported the hypothesis that the freshwater resident behavior precludes marine‐mediated gene flow, resulting in large genetic divergence and low admixture among watersheds. The estimate of among‐watershed differentiation (FCT = 0.350) was large and reflected over 96% of the variation among all sampled aggregations (FST = 0.363). However, evidence of admixed individuals in two adjacent watersheds and five first‐generation migrants among five watersheds suggests that the potential for coastal migration with gene flow exists in these populations. The data also supported the hypothesis that aggregations formed within watersheds during the spawning period (May–June) represent reproductively isolated populations. Pairwise estimates of FST and the G‐test results revealed population structure in four of the six watersheds tested. However, not all aggregation pairs were found to be genetically distinct and there was notable variation in the pairwise FST estimates (0.000–0.067). In summary, the data reflected the predicted results for each hypothesis but also revealed exceptions that, consistent with tagging studies, demonstrate the complexity of migratory behavior in southwestern Alaska Rainbow Trout. We discuss the implications of these results for fishery management and conservation.

Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing

BackgroundThe Yarkand hare (Lepus yarkandensis Günther, 1875) is endemic to oasis and desert areas around the Tarim Basin in the Xinjiang Uyghur Autonomous Region of northwest China; however, genome-wide information for this species remains limited. Moreover, the genetic variation, genetic structure, and phylogenetic relationships of Yarkand hare from the plateau mountain regions have not been reported. Thus, we used specific-length amplified fragment sequencing (SLAF-seq) technology to evaluate the genetic diversity of 76 Yarkand hares from seven geographic populations in the northern and southwestern parts of the Tarim Basin to investigate single-nucleotide polymorphism (SNP) marker-based population differentiation and evolutionary processes. Selective sweep analysis was conducted to identify genetic differences between populations.ResultsUsing SLAF-seq, a total of 1,835,504 SNPs were initially obtained, of which 308,942 high-confidence SNPs were selected for further analysis. Yarkand hares exhibited a relatively high degree of genetic diversity at the SNP level. Based on pairwise FST estimates, the north and southwest groups showed a moderate level of genetic differentiation. Phylogenetic tree and population structure analyses demonstrated evident systematic phylogeographical structure patterns consistent with the geographical distribution of the hares. Hierarchical analysis of molecular variation further indicated that genetic variation was mainly observed within populations. Low to moderate genetic differentiation also occurred among populations despite a common genomic background, likely due to geographical barriers, genetic drift, and differential selection pressure of distinct environments. Nevertheless, the observed lineage-mixing pattern, as indicated by the evolutionary tree, principal component analysis, population structure, and TreeMix analyses, suggests a certain degree of gene flow between the north and southwest groups. This may be related to the migration of hares to high-altitude water sources southwest of the basin during glacial climatic oscillations, as well as river re-diffusion and oasis restoration in the basin following the glacial period. We also identified candidate genes, and their associated gene ontology terms and pathways, related to the adaptation of Yarkand hares to different environmental habitats.ConclusionsThe identified genome-wide SNPs, genetic diversity, and population structure of Yarkand hares expand our understanding of the genetic background of this endemic species and provide valuable insights into its environmental adaptation, allowing for further exploration of the underlying mechanisms.

Exploring genetic diversity and population structure of Punjab goat breeds using Illumina 50K SNP bead chip.

Pakistan has 35 goat breeds. Moreover, the province of Punjab has highest goat population constituting 37% of country's total population with seven goat breeds including Beetal, Daira Deen Panah, Nachi, Barbari, Teddi, Pahari, and Pothwari. The diversity study of breeds warrants the documentation of breeds particularly using genome wide panel of markers, i.e., SNP chip. The objective of the current study was to fill this gap of information. Therefore, in current study we collected total of 879 unrelated goat blood samples along with data on body weight measurements; genomic DNA was extracted, and genotyping was carried out using 50K SNP bead chip. Quality control measures were performed in Plink 1.07. Genetic diversity was observed among studied populations using heterozygosity and pairwise FST estimates, principal component analysis, admixture analysis in Plink software with visualization in Clumpak, and constructing phylogenetic tree in Mega 7 software. Moderate to high level of heterozygosity was observed among the studied populations. Coefficient of inbreeding varied from 0.0186 ± 0.0327 in Pahari to 0.183 ± 0.0715 in Barbari. Barbari and Daira Deen Panah had quite higher level of inbreeding coefficient as compared to all other breeds with value of 0.183 ± 0.0715 and 0.1378 ± 0.0741, respectively. PCA identified three steps of subdividing the seven goat breeds at various levels of K. All the seven breeds made independent clusters at various levels of PCA. Admixture analysis revealed the distinctness of Teddi and Barbari breeds. Genetic sub-structuring was observed in the admixture patterns of Beetal breed. Moreover, high level of genetic admixture was observed in Nachi, Pahari, Pothwari, and Daira Deen Panah breeds. Admixture results were further interpreted by calculating pairwise FST values. Our results provided first insights about genetic diversity of Pakistani goat breeds based on genomic data. To conclude, the enriched goat breed diversity in Pakistan could provide valuable genetic reservoir for national breeding schemes.

Come together: calibration of tiger shark (Galeocerdo cuvier) microsatellite databases for investigating global population structure and assignment of historical specimens

This study provides the first standardized global microsatellite database for a shark species, the tiger shark (Galeocerdo cuvier). Genotyping of reference individuals was used to develop and apply a calibration key for data from eight microsatellite loci data produced by three different laboratories, thereby allowing merging of genotypes into a single dataset. The unified data helped to elucidate the global population structure of the species and provided improved statistical power, through allowing a higher number of samples per location compared to the original studies from which the samples were obtained. Pairwise FST estimates and PCA plots showed significant genetic differentiation between Atlantic and Indo-Pacific samples, confirming previous findings by identifying the presence of a strong genetic break between tiger sharks inhabiting the two ocean basins. In turn, the standardized database (n = 799) also allowed archived historical samples to be genotyped and assigned back to their population (ocean basin) of origin. We demonstrate how calibration tests in population structure studies using microsatellite data is important as it simply provides more data to single studies. Importance factors for successful assignment analysis is discussed, as well as how the possibility of assigning historical samples of unknown origin back to the population, increases sample value. Our results demonstrate that global calibration of microsatellite and other genetic datasets can improve the statistical power and resolution of population structure analysis; an approach applicable not only when working with highly mobile globally distributed species such as the tiger shark, but with any species for which multiple genetic datasets exist.

Matrilineal evidence for genetic structure and Late Pleistocene demographic expansion of the Ornate goby Istigobiusornatus (Teleostei: Gobiidae) in the Persian Gulf and Oman Sea

AbstractThe Persian Gulf and Oman Sea are characterized by an interesting paleoclimatic history and different ecological settings, and offer a unique study area to investigate the genetic structure of marine organisms including fishes. The Ornate goby Istigobius ornatus is widely distributed throughout the tropical Indo‐West Pacific including the Persian Gulf and Oman Sea. Here, we present the population structure, genetic diversity, and demographic history of four populations of I. ornatus from the latter two regions using the D‐loop marker of mitochondrial DNA. The results reveal a shallow genealogy, a star‐like haplotype network, significance of neutrality tests, and unimodal mismatch distribution. This is concordant with a recent demographic expansion of I. ornatus in the Persian Gulf and Oman Sea at about 63,000–14,000 years ago, which appears to be related to Late Pleistocene sea level fall and rise. The results of the pairwise Fst estimates imply high gene flow along the coast of the Persian Gulf, which is probably due to larval dispersion, whereas the Oman Sea population clearly differs from all Persian Gulf populations. The AMOVA result indicates that 7.74% of the variation is related to differences among ecoregions, while inter‐ and intra‐population differences explained −3.20% and 95.47% of the variation, respectively. The haplotype network depicts two groups of haplotypes, most of them were specific to the Persian Gulf. No further evidence for geographic lineage substructuring was evident. The Mantel test result indicates that isolation by distance is not the main mechanism that promoted the genetic differentiation among the studied populations of I. ornatus. We suggest that cumulative effects of ecological and geographic barriers such as salinity, oceanographic conditions, and the presence of the Strait of Hormuz have shaped the genetic structure of I. ornatus in the Persian Gulf and Oman Sea.

Genetic structure of the Capoeta aculeata populations inferred from microsatellite DNA loci

Abstract. Gandomkar H, Shekarabi SPH, Abdolhay HA, Nazari S, Mehrjan MS. 2020. Genetic structure of the Capoeta aculeata populations inferred from microsatellite DNA loci. Biodiversitas 21: 4565-4570. The present study aimed to investigate the genetic variation of Capoeta aculeata on the basis of DNA microsatellite loci from three rivers (Beshar, Khersan, Maroun) in Kohgiluyeh and Boyer-Ahmad Province in Iran. DNA from fin clips of 120 specimens extracted and was examined with eight microsatellite markers. Genetic differences between the populations were discerned by pairwise comparison based on allelic distribution. The average number of alleles per locus ranged from 4 to 14, while the average observed heterozygosity (Ho) at various loci varied between 0.212 to 0.579, implying that a moderate level of genetic variation. Among three populations, Maroun River population displayed the highest level of variability in terms of heterozygosity. Tests of Hardy-Weinberg showed that the microsatellite loci deviated significantly in the populations. The results indicate that some of the populations were significantly differentiated from one another based on pairwise FST estimates. Genetic distance-based measures supported the clustering of Maroun, Beshar, and Khersan rivers. The neighbor-joining dendrogram topology constructed on the basis of genetic distances among populations supported observed division between the populations. The non-significant differentiation between C. aculeata samples from Beshar and Khersan can be explained by a relative disconnection of these two populations and/or small amounts of gene flow.

Gene conservation of six Hungarian local chicken breeds maintained in small populations over time.

Investigation into the genetic diversity of certain endangered native breeds of domestic animals has been in common practice for several decades. The primary objective of these investigations has been to reveal the exceptional genetic value of such breeds, both for their conservation and also to gain insight into their current genetic status, as they have been undergoing a progressive decrease in population size and general diversity; this has been compounded by the general lack of an optimal breeding scheme. In this study, we have investigated changes in the genetic diversity of six Hungarian local chicken breeds based on 29 microsatellite loci over a period of 15 years. In terms of the basic diversity measures, populations sampled in 2017 generally exhibited a lower heterozygosity and mean number of alleles and thus, experienced a higher degree of inbreeding. Although the effective population size increased, the estimates of populations sampled over different periods indicated comparatively low values, suggesting overall lower genetic variance. Pairwise FST estimates were higher in the populations sampled in 2017, showing a larger genetic distance between them. Considerable differences exist between the populations of the same breeds, which can most likely be attributed to genetic drift. STRUCTURE results have shown a clear separation between the Hungarian populations, which is in agreement with the principal coordinate analysis. The most likely clustering was found at K = 6, classifying the populations of the same breed as one group. No considerable allele loss was found in the Hungarian indigenous chicken breeds after 15 years of conservation. In general terms, after 15 years, the level of inbreeding within the populations was, in fact, higher, although this could be effectively reduced through the use of an improved mating system. Consequently, the breed management applied in the case of Hungarian local chicken breeds was found to be effective at adequately conserving their genetic variability.

Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region.

The domestication of a wild-caught aquatic animal is an evolutionary process, which results in genetic discrimination at the genomic level in response to strong artificial selection. Although black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, a systematic assessment of genetic divergence and structure of wild-caught and domesticated broodstock populations of the species is yet to be documented. Therefore, we used skim sequencing (SkimSeq) based genotyping approach to investigate the genetic structure of 50 broodstock individuals of P. monodon species, collected from five sampling sites (n = 10 in each site) across their distribution in Indo-Pacific regions. The wild-caught P. monodon broodstock population were collected from Malaysia (MS) and Japan (MJ), while domesticated broodstock populations were collected from Madagascar (MMD), Hawaii, HI, USA (MMO), and Thailand (MT). After various filtering process, a total of 194,259 single nucleotide polymorphism (SNP) loci were identified, in which 4983 SNP loci were identified as putatively adaptive by the pcadapt approach. In both datasets, pairwise FST estimates high genetic divergence between wild and domesticated broodstock populations. Consistently, different spatial clustering analyses in both datasets categorized divergent genetic structure into two clusters: (1) wild-caught populations (MS and MJ), and (2) domesticated populations (MMD, MMO and MT). Among 4983 putatively adaptive SNP loci, only 50 loci were observed to be in the coding region. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that non-synonymous mutated genes might be associated with the energy production, metabolic functions, respiration regulation and developmental rates, which likely act to promote adaptation to the strong artificial selection during the domestication process. This study has demonstrated the applicability of SkimSeq in a highly duplicated genome of P. monodon specifically, across a range of genetic backgrounds and geographical distributions, and would be useful for future genetic improvement program of this species in aquaculture.

Genetic Differentiation and Origin of Naturalized Rainbow Trout Populations From Southern Chile, Revealed by the mtDNA Control Region Marker.

Numerous self-sustaining naturalized or introduced populations of rainbow trout (Oncorhynchus mykiss) are widely distributed throughout the freshwaters of southern Chile. In this study, analysis of the mitochondrial DNA control region (CR) marker was conducted to investigate the level of genetic divergence among populations and their phylogenetic relationships with respect to native lineages. This information provided a framework to interpret the genetic structure and origin that was shaped during historical trout introduction efforts. To this end, we analyzed eleven naturalized populations of lakes and rivers from five basins. The CR marker revealed five haplotypes. The overall haplotype (H) and nucleotide (Π) diversities were 0.684 ± 0.030 and 0.00460 ± 0.00012, respectively. Global F ST was 0.169, with several pairwise F ST estimates showing significant differences (P < 0.05). The exact test of population differentiation corroborated this result (P < 0.001). Significant geographic structure was found (P < 0.05), with variations explained primarily by differences within populations (61.65%) and among group basins (20.82%). Maximum likelihood phylogenetic analysis resolved two distinct clades with medium bootstrap support when naturalized populations were aligned in conjunction with reference native lineages. The haplotype network revealed a close association between naturalized populations and four main haplotypes representative of three native ecotypes or lineages from western North America (rainbow trout, steelhead trout and redband trout). These results indicate a genetic population structuring for naturalized rainbow trout from southern Chile and an origin probably represented by multiple lineages sources. Thus, mitochondrial DNA data strongly suggest that stocking of rainbow trout from different origins may have occurred during or after the initial introduction efforts.

Single Nucleotide Polymorphisms (SNPs) Reveal Sibship Among Founders of a Bangladeshi Rohu (Labeo rohita) Breeding Population.

Rohu (Labeo rohita) is a significant freshwater aquaculture species with approximately 1.8 Mt produced annually. Fin clips obtained from the founders of a newly established Bangladesh-based breeding population (∼140 fish from each of the Halda, Jamuna, and Padma rivers) were used to identify 9157 SNPs and 14 411 silicoDArT markers using the Diversity Arrays Technology (DArT) genotyping-by-sequencing platform known as DArTseq. After quality control, 1985 SNPs were retained and used to examine population structure within and among river systems. Examination of genomic relationships revealed evidence of full- and half-sibling relationships among founders. Accordingly, sibship and dummy parents were assigned within each river population using a maximum likelihood approach with COLONY software. Founders that had no dummy parents in common were then identified for population genetic analyses. Only 40 unique dummy parents and 17 founders with no common dummy parents were identified from the Halda river, compared with 206 (96) from the Jamuna and 184 (83) from the Padma. Overall pairwise FST estimates among rivers were low (<0.005) and the optimum number of clusters using unsupervised K-means clustering was one, indicating little genetic divergence among the river populations in our SNPs. These results suggest that observed sibship among founders should be accounted for in future pedigree-based analyses and it cannot be assumed that fertilized spawn collections are representative samples of river populations.

Development of microsatellite markers and analysis of genetic diversity of Barbatia virescens in the southern coasts of China.

The blood clam Barbatia virescens is an ecologically and economically important species in the southern coast of China. Understanding of the genetic structure of B. virescens populations is vital to breeding strategies and conservation programs. To develop and characterize a set of microsatellites loci primers for B. virescens, and provide helpful information for reasonable utilization and protection of B. virescens natural resources. The microsatellites of B. virescens were detected using a RAD-seq approach based on an Illumina sequencing platform. For the test of microsatellite development, we calculated the number of alleles (Na), observed heterozygosities (Ho), expected heterozygosities (He) and exact tests for deviations from Hardy-Weinberg equilibrium (HWE). Twelve polymorphic loci were used to access the genetic diversity and population structure of four B. virescens populations. In this study, 50,729 microsatellites of B. virescens were detected. Twenty-two polymorphic microsatellite loci were developed for B. virescens. The number of alleles per locus ranged from 6 to 15, and expected heterozygosities varied from 0. 567 to 0.911. All the PIC values of the 22 loci were greater than 0.5, indicating that these markers were highly informative for further genetic analysis. Twelve loci were selected to analyze genetic diversity and population structure of four B. virescens populations collected from different geographical regions along the southern coast of China. The results showed moderate to high levels of genetic diversity in the four populations (mean Ar = 7.756-8.133; mean Ho = 0.575-0.639; mean He = 0.754-0.775). Pairwise FST estimates indicated that there was significant divergence among the four populations. This study not only provides a large scale of sequence information of microsatellites which are valuable for future genetic mapping, trait association and kinship among B. virescens, but also offers useful information for the sustainable management of natural stocks and the development of breeding industry of B. virescens.

Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

BackgroundThe scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species.ResultsAfter stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = − 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288–0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus.ConclusionsFindings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.

AFLP analysis revealed a north to south genetic break in the brown alga Sargassum thunbergii along the coast of China

Sargassum thunbergii, a common brown macroalga that occurs in the Asian Northwest Pacific, has important ecological services and economic values. In recent years, the distribution range and biomass of wild S. thunbergii resources have declined rapidly due to severe anthropogenic impacts and habitat loss. To slow the decline of this natural resource by taking appropriate measures, it is very important to evaluate the population genetic structure and diversity of S. thunbergii. In this study, we used amplified fragment length polymorphism (AFLP) markers to investigate population genetic differentiation and diversity of S. thunbergii along the coast of China at a genome-scanning scale. Five primer combinations that yielded high polymorphisms were identified in ten populations of S. thunbergii. Genetic analyses revealed low genetic diversity within populations and high levels of genetic differentiation among populations. Moreover, apparent gene flow occurred between S. thunbergii populations in the Yellow-Bohai Sea, whereas no such exchange was detected in the populations of the East China Sea. Genetic clustering, principal coordinates analysis (PCoA), and pairwise FST estimates consistently indicated that S. thunbergii populations divided into two genetic groups, coinciding with their geographical distribution (Yellow-Bohai Sea vs. East China Sea). The detected genetic diversity of S. thunbergii along the coast of China provides important insights not only for selecting high-yielding varieties for commercial cultivation, but also for proposing strategic management plans to protect and restore declining natural resources under anthropogenic climate change.

Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System.

Using a combination of population- and individual-based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population genetic structure and then assessed interannual variability in our estimates by sampling again in 2014. Genetic diversity showed little variation among sites or across years. In 2012, we observed weak genetic differentiation among sites (FST range=-0.005-0.014) following a pattern of isolation by distance (IBD) and significantly high relatedness among individuals within nine sampling sites. In 2014, pairwise FST estimates were lower (FST range=-0.014-0.007), there was no spatial autocorrelation, and fewer sites had significant evidence of relatedness. Based on these findings, we propose that interannual variation in the physical oceanographic conditions of the CCS influences larval recruitment and thus gene flow, contributing to interannual variation in population genetic structure. Estimates of effective population size (Ne ) were large in both 2012 and 2014. Together, our results suggest that Dungeness crab in the CCS may constitute a single evolutionary population, although geographically limited dispersal results in an ephemeral signal of IBD. Furthermore, our findings demonstrate that populations of marine organisms may be susceptible to temporal changes in population genetic structure over short time periods; thus, interannual variability in population genetic measures should be considered.

Mountains as barriers to gene flow in amphibians: Quantifying the differential effect of a major mountain ridge on the genetic structure of four sympatric species with different life history traits

AbstractAimTo test the role of mountains as barriers to gene flow in co‐distributed taxa with different life history traits.LocationSierra de Guadarrama, Central Spain.MethodsWe used larval genotypes of four amphibian species (Epidalea calamita, Hyla molleri, Pelophylax perezi and Pelobates cultripes) sampled on northern and southern slopes of Sierra de Guadarrama to describe genetic structure with FST, migration rates per generation, clustering algorithms and resistance by elevation surfaces. We also recorded individual displacement events as a proxy of dispersal potential during a seven‐year monitoring project based on capture–mark–recapture (CMR).ResultsAll species travelled longer cumulative distances than those reported in the study area for P. cultripes (0.71 km). Individuals of E. calamita travelled up to 3.55 km, followed by H. molleri (2.84 km) and P. perezi (1.51 km). Pairwise FST estimates showed lower overall connectivity in P. cultripes. Average migration rates per generation were low in all species, with exceptions in same‐slope populations of H. molleri and P. cultripes. Clustering algorithms consistently recovered well‐differentiated population groups of P. cultripes in northern versus southern slopes, but widely admixed areas were observed in the other species, especially near mountain passes. Resistance by elevation surfaces showed a strong barrier effect of Sierra de Guadarrama in P. cultripes and suggested a potential role of topography in the genetic structure of E. calamita and H. molleri.Main conclusionsSierra de Guadarrama currently acts as a strong barrier to gene flow for P. cultripes and, to a lesser extent, for E. calamita, H. molleri and P. perezi. This differential effect can be partly explained by differences in life history traits, including dispersal potential. Our findings support the general role of the Central System as a key feature shaping population connectivity and genetic variation in amphibian communities.