Estimates Of Population Differentiation Research Articles

English

Genetic integrity of commercially important fish species is being compromised due to ongoing anthropogenic interventions. Hitherto, there are limited number of studies addressing the questions related to population structure of dwindling fish populations. Studies were undertaken to assess the genetic status of Bagarius bagarius populations from Indus River System by using five microsatellite DNA markers. DNA was extracted by PCI method and genotypic data was generated by PCR amplification of targeted loci. Results showed low-to-moderate level of genetic diversity in terms of number of alleles (Na), allelic richness (Ar), effective number of alleles (Nae) and heterozygosity (Ho and He). The observed heterozygosity (Ho) declined in comparison to the expected heterozygosity (He) in the wild stocks, with mean values ranging from 0.667 to 0.718 and 0.786 to 0.853, respectively. Significant deviation from H-W test was observed in 6 out of 25 tests. The population differentiation (FST) estimates were low (0.0013 to 0.0367) and insignificant. AMOVA showed that 62.38% genetic variation existed within individuals while 4.93% between populations. All of the populations were divided into two clusters by the UPGMA dendrogram constructed for genetic relatedness analysis. The study will be helpful in understanding the impact of genetic integrity on fish populations and, for sustainable management of fish genetic resources

Revealing the Shamefaced Crab Calappa granulata (Crustacea: Brachyura) from the Adriatic Sea, Northern Basin of the Mediterranean

This study presents the first data on morphometry, length–weight relationship, diet, reproductive biology, epibionts and genetic identity of the shamefaced crab Calappa granulata from the central eastern Adriatic Sea. A total of 92 crabs were collected during 2011, 2014 and 2015, of which 64 were females and 28 were males. Overall, 11 morphometric characteristics were measured. Carapace length of sampled individuals ranged from 48.46 to 76.09 mm, and body weight from 47.06 to 221.39 g. The length–weight relationship showed negative allometry for males and isometric growth for females. Analysis of the stomach content revealed the crab’s preference for crustaceans (20.28%) and cephalopods (10.58%), less for fish (3.4%) and shellfish (0.28%). Size at first sexual maturity (CL50%) of 59.25 and 66.92 mm was estimated for males and females, respectively. Epibiotic serpulid polychaetes were recorded on the crab exoskeleton with an overall prevalence of 29.3%. Analyses of a partial sequence of mtCOI showed high haplotype (Hd = 0.964) and low nucleotide diversity (π = 0.00598). Phylogenetic inference and estimation of population differentiation (FST = 0.013, p = 0.271) with publicly available Mediterranean sequences currently imply one homogenous population unit. To the best of our knowledge, these are the first nucleotide sequences of C. granulata from the Adriatic Sea made publicly available.

Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms.

Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here, we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced substantial data sets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in molluscs, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.

Genetic characterization of wild, broodstock and seed samples of Polititapes rhomboides (Bivalvia: Veneridae): Implications for hatchery seed production

The banded carpet shell Polititapes rhomboides is a fishery resource and a suitable candidate for the development of native clam aquaculture in Europe. Here, we analyzed nine microsatellite loci in wild samples to provide estimates of genetic diversity and population differentiation for NW Spain, the main production area of this clam. We also analyzed wild-caught broodstock and hatchery-reared seed to investigate the genetic consequences of seed production for stock enhancement purposes by mass spawning. We examined the seed sample as a whole (total seed), but also subdivided it into three size classes to assess the genetic consequences of size grading. While wild samples, broodstock included, displayed minimal or no genetic differences, the total seed showed a reduction in allelic richness (12–24 %) and a significant level of differentiation (FST = 0.026−0.043) with respect to wild samples. After performing parentage assignment, we detected a drastic reduction in the effective number of breeders (Ne) compared to the census number (85 %), and an inbreeding rate of 0.036 per generation. The low Ne and high inbreeding rate were mainly due to high variance in reproductive success. The seed size classes also showed a decrease in allelic richness and significant genetic differentiation, but we did not find significant differences in parental contribution to each size class. Our results may help the genetic-assisted management of wild populations, give insight into the genetic composition of the seed produced by mass spawning and provide a basis for the development of more effective hatchery practices and sustainable stock enhancement programs in P. rhomboides.

Estimation of population differentiation using pedigree and molecular data in Black Slavonian pig

Estimation of population differentiation using pedigree and molecular data in Black Slavonian pig

Genetic structure of the Africanized Apis mellifera L. in a river valley in the semi-arid region of Brazil

The effect of the basin of the Gurgueia River (perennial river in the semiarid region of Brazil) on the dispersion and migration of Africanized bees (Apis mellifera) was evaluated using six microsatellite markers. Four municipalities located within (n = 53 colonies) and three outside the Gurgueia River Basin (n = 41 colonies) were sampled. Based on the number of alleles found (mean of 18.5 alleles per locus ±4.18), we concluded that there was high genetic diversity. Estimates of population differentiation (FST) were significant among different localities, except for the populations of Corrente, Cristino Castro, and Bertolínia, which are within the river basin. At a regional level, analysis of molecular variance (AMOVA) and Bayesian approaches corroborated this result, indicating greater connectivity among populations in the valley. For the remaining populations collected outside the valley, no defined pattern of population structure was observed.

Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike (Esox lucius) and a Synthesis of Previous Studies.

Population genetic studies reveal biodiversity patterns and inform about drivers of evolutionary differentiation and adaptation, including gene flow, drift and selection. This can advance our understanding and aid decision making regarding management and conservation efforts. Microsatellites have long been used in population genetic studies. Thanks to the development of newer techniques, sequencing approaches such as restriction site associated DNA sequencing (RADseq) are on their way to replace microsatellites for some applications. However, the performance of these two marker types in population genetics have rarely been systematically compared. We utilized three neutrally and adaptively differentiated populations of anadromous pike (Esox lucius) to assess the relative performance of microsatellites and RADseq with respect to resolution and conclusiveness of estimates of population differentiation and genetic structure. To this end, the same set of individuals (N = 64) were genotyped with both RADseq and microsatellite markers. To assess effects of sample size, the same subset of 10 randomly chosen individuals from each population (N = 30 in total) were also genotyped with both methods. Comparisons of estimated genetic diversity and structure showed that both markers were able to uncover genetic structuring. The full RADseq dataset provided the clearest detection of the finer scaled genetic structuring, and the other three datasets (full and subset microsatellite, and subset RADseq) provided comparable results. A search for outlier loci performed on the full SNP dataset pointed to signs of selection potentially associated with salinity and temperature, exemplifying the utility of RADseq to inform about the importance of different environmental factors. To evaluate whether performance differences between the markers are general or context specific, the results of previous studies that have investigated population structure using both marker types were synthesized. The synthesis revealed that RADseq performed as well as, or better than microsatellites in detecting genetic structuring in the included studies. The differences in the ability to detect population structure, both in the present and the previous studies, are likely explained by the higher number of loci typically utilized in RADseq compared to microsatellite analysis, as increasing the number of markers will (regardless of the marker type) increase power and allow for clearer detection and higher resolution of genetic structure.

Population history explains the performance of an annual herb – Within and beyond its European species range

Abstract The centre–periphery hypothesis (CPH) predicts a decrease in population performance from the centre of the species range towards the edge, hindering further species expansion. To overcome ecological limitation, local adaptation of peripheral populations is assumed necessary to extend niche space and thus to potentially facilitate species’ range expansion. However, adaptive changes do not necessarily correspond to current ecological marginality. Instead, population history may provide a fuller context for understanding patterns of local adaptation within the species range. Here, we test whether local adaptation to current conditions or population history explains current species distribution in an annual heterocarpic species, Atriplex tatarica, in Europe. The ecological marginality and population history were estimated using species distribution modelling (SDM) and 13 microsatellite markers. To test for local adaptation, we evaluated the population performance of both currently central and currently peripheral populations by examining germination and growth traits under three temperature regimes which correspond to climates within, and also beyond, the species’ current range. In addition, we compared Bayesian estimates of population differentiation in neutral genetic markers and quantitative traits to test whether phenotypic differentiation evolved by local adaptation and/or by genetic drift. We found population performances were not higher under temperature regimes corresponding to their own habitats, suggesting that patterns of local adaptation in A. tatarica do not correspond to current centre–periphery gradient. In contrast, population genetic structure indicated a strong influence of population history on variation in the germination phenotype. Species distribution modelling suggested a more cold–tolerant genetic lineage was located at the species' range periphery during the last glacial period. Meanwhile, a less cold‐tolerant lineage occurred in more suitable areas of the Balkan Peninsula and southeastern Europe. Thus, the strong adaptive divergence of evolutionary lineages may reflect a past spatial arrangement of populations, suggesting evolutionary processes were ongoing before the species expansion in the Holocene. Synthesis. There is continuing debate concerning the speed of trait evolution during range expansion with climate change. Our results indicate that even though organisms expand rapidly, the accompanying evolutionary changes in phenotype may be much slower.

Microsatellite Marker Discovery in the Stingless Bee Uruçu-Amarela (Melipona rufiventris Group, Hymenoptera, Meliponini) for Population Genetic Analysis.

The species Melipona rufiventris Lepeletier, 1836 is a Brazilian native stingless bee that is part of a species complex known as the ‘rufiventris group’, making it difficult to distinguish between the different species. Populations in this group are facing a severe decline, leading to the risk of local extinction, and therefore, their conservation should be treated as a major concern. This study describes the first set of tri- and tetranucleotide microsatellite markers, using next-generation sequencing technology for use in the identification of genetic diversity and population structure in the ‘rufiventris group’. A total of 16 microsatellite loci displayed polymorphism. Analysis of the whole data set (n = 50) detected 63 alleles in all loci, ranging from 2 to 7 with a mean of 3.9 alleles/locus. A genetic diversity analysis revealed high values for population differentiation estimates (FST = 0.252, RST = 0.317, and DEST = 0.284) between the Atlantic Forest, Cerrado, and Caatinga biomes. An additional evidence for genetic divergence among populations was also found in the ’rufiventris group’; these should be treated as separate conservation units or even as separate species. These microsatellite markers have demonstrated a strong potential for assessing population discrimination in this threatened stingless bee group.

Population structure and male-biased dispersal in the short-tail stingray Bathytoshia brevicaudata (Myliobatoidei: Dasyatidae)

Selective pressures driving dispersal in vagile species often differ between males and females, resulting in sex-biased dispersal. Male-biased dispersal is common in mammals, where there is greater reproductive investment by females, and there is emerging evidence for a similar pattern in elasmobranchs. We examine the population structure of the short-tail stingray (Bathytoshia brevicaudata), a large, viviparous coastal species common in southern hemisphere waters. Using 11 nuclear (nDNA) microsatellite markers from 202 individuals in comparison to mitochondrial (mtDNA) data reported by Le Port and Lavery (J Hered 103:174–185, 2012), we elucidate patterns of dispersal at both southern hemisphere and New Zealand scales. At a global scale, estimates of population differentiation were comparable across marker types (microsatellite FST = 0.148, p 0.05) than for mtDNA (ϕST = 0.054, p < 0.05). Female-only data displayed a greater degree of population differentiation from both nDNA and mtDNA compared to male-only data, and population assignment tests indicated that males were significantly more likely to be immigrants to the population from which they were sampled. We estimate that within New Zealand, male-mediated gene flow is at least fivefold greater than female-mediated gene flow. This molecular evidence for sex-biased dispersal in a batoid species adds further support to male-biased dispersal as a recurrent pattern in viviparous elasmobranchs. Many elasmobranch species are vulnerable to extinction, and understanding movement patterns is crucial to management of threatened populations.

Genome-wide discovery and characterization of microsatellite markers from Melipona fasciculata (Hymenoptera: Apidae), cross-amplification and a snapshot assessment of the genetic diversity in two stingless bee populations

Brazilian native meliponines are currently threatened by increased human impacts. The assessment of their genetic variation by microsatellite DNA markers can assist in the conservation of populations and help in the planning and establishment of efficient management strategies. The purpose of this study was to develop the first set of microsatellite markers for Melipona fasciculata, selected from partial genome assembly of Illumina paired-end reads. Primer pairs were designed for each detected locus at their flanking regions. Bee samples were genotyped from two different populations of Northeastern Brazil for marker characterization and validation. A total of 17 microsatellite loci displayed polymorphism. Mean HE and HO heterozygosities were 0.453 and 0.536, respectively. PIC across all loci ranged from 0.108 to 0.714. A genetic diversity analysis revealed high values for population differentiation estimates (FST = 0.194, RST = 0.230, and Dest = 0.162) within the investigated region. PCoA and Bayesian clustering showed a separation of the species into two distinct clusters. These microsatellite markers have demonstrated strong potential for population-level genetic studies. Moreover, the preliminary analysis of the genetic diversity in M. fasciculata provides provisional evidence of significant population differentiation between the two studied populations.

Sea surface currents and geographic isolation shape the genetic population structure of a coral reef fish in the Indian Ocean.

In this contribution, we determine the genetic population structure in the Skunk Clownfish (Amphiprion akallopsisos) across the Indian Ocean, and on a smaller geographic scale in the Western Indian Ocean (WIO). Highly restricted gene flow was discovered between populations on either side of the Indian Ocean using the control region as a mitochondrial marker (mtDNA). We verify this conclusion using 13 microsatellite markers and infer fine scale genetic structuring within the WIO. In total 387 samples from 21 sites were analysed using mtDNA and 13 microsatellite loci. Analysis included estimation of genetic diversity and population differentiation. A haplotype network was inferred using mtDNA. Nuclear markers were used in Bayesian clustering and a principal component analysis. Both markers confirmed strong genetic differentiation between WIO and Eastern Indian Ocean (EIO) populations, and a shallower population structure among Malagasy and East African mainland populations. Limited gene flow across the Mozambique Channel may be explained by its complex oceanography, which could cause local retention of larvae, limiting dispersal between Madagascar and the East African coast. Two other potential current-mediated barriers to larval dispersal suggested in the WIO, the split of the SEC at approximately 10° S and the convergence of the Somali Current with the East African Coast Current at approximately 3° S, were not found to form a barrier to gene flow in this species.

Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing.

Genotyping-by-sequencing (GBS) was conducted on 333 Cercospora isolates collected from Beta vulgaris (sugar beet, table beet and swiss chard) in the USA and Europe. Cercospora beticola was confirmed as the species predominantly isolated from leaves with Cercospora leaf spot (CLS) symptoms. However, C. cf. flagellaris also was detected at a frequency of 3% in two table beet fields in New York. Resolution of the spatial structure and identification of clonal lineages in C. beticola populations using genome-wide single nucleotide polymorphisms (SNPs) obtained from GBS was compared to genotyping using microsatellites. Varying distance thresholds (bitwise distance = 0, 1.854599 × 10−4, and 1.298 × 10−3) were used for delineation of clonal lineages in C. beticola populations. Results supported previous reports of long distance dispersal of C. beticola through genotype flow. The GBS-SNP data set provided higher resolution in discriminating clonal lineages; however, genotype identification was impacted by filtering parameters and the distance threshold at which the multi-locus genotypes (MLGs) were contracted to multi-locus lineages. The type of marker or different filtering strategies did not impact estimates of population differentiation and structure. Results emphasize the importance of robust filtering strategies and designation of distance thresholds for delineating clonal lineages in population genomics analyses that depend on individual assignment and identification of clonal lineages. Detection of recurrent clonal lineages shared between the USA and Europe, even in the relaxed-filtered SNP data set and with a conservative distance threshold for contraction of MLGs, provided strong evidence for global genotype flow in C. beticola populations. The implications of intercontinental migration in C. beticola populations for CLS management are discussed.

Diversity of mitochondrial DNA in three Arabian horse strains.

Arabian horse registries classify Arabian horses based on their dam lineages into five main strains. To test the maternal origin of Syrian Arabian horses, 192 horses representing the three major strains Saglawi, Kahlawi, and Hamdani were sequenced for 353bp of their mitochondrial displacement loop (D-loop) region. Sequencing revealed 28 haplotypes comprising 38 sequence variations. The haplotype diversity values were 0.95, 0.91, and 0.90 in Kahlawi, Hamdani, and Saglawi strains, respectively. The pair-wise population differentiation estimates (Fst) between strains were low, ranging between 0.098 and 0.205. The haplotype diversity and the pair-wise population differentiation estimates (Fst) between strains showed high diversity within individuals of each strain and low variation between the three strains. Mitochondrial haplotypes scattered all over the neighbor-joining tree without clear separation of the three strains. In the median-joining network, the Syrian horses were grouped into seven major haplogroups. These results suggest that more than five ancestors exist that share common maternal haplotypes with other horse breeds.

Repeated randomized selection of genotypes for reliable estimates of population differentiation in data containing siblings

In population genetic studies, a proper sampling design is crucial for reliable population differentiation estimates. For genetic studies on amphibians, fish or insects, larvae are often sampled instead of adults due to their higher accessibility and abundance. However, population genetic parameters derived from larval (sibling) sampling can be biased if adults are represented unevenly in the larval population. The removal of full-siblings from data may improve the quality of the results but entails in a low number of individuals per site, especially in small populations. Using simulated data of ten microsatellite loci for ten populations, we estimated pairwise FST and RST values as well as FIS and RIS values for the F0 generation (parental) and the F1 generation (descendant). We applied a repeated randomized selection of genotypes (RRSG) to investigate the impact of removing full-siblings from the data. We also investigated the impact of reduced sample size on the results generated by RRSG as well as the advantages of RRSG over a single estimate of genetic parameters after removal of full-siblings. The RRSG approach produced pairwise FST values that deviated on average only by 0.0050 (N = 45) from their respective estimates for F0. Estimates for HE deviated less the 5% over all data sets. We henceforth suggest applying the described method to interpretations of genetic differentiations in studies with (i) small effective population sizes and (ii) data containing siblings where (iii) offspring can be assigned to at least one parent due to reproduction practice.

An assessment of spatio-temporal genetic variation in the South African abalone (Haliotis midae), using SNPs: implications for conservation management

The South African abalone (Haliotis midae) is a gastropod mollusc of economic importance. In recent years natural populations have come under considerable pressure due to overharvesting and ecological shifts. The spatial genetic structure of H. midae has been determined; however there has not been a temporal assessment of abalone population dynamics around the South African coast. Using a population genomics approach this study aimed to assess fluctuations in genetic diversity among wild and cultured South African abalone populations through time and space. Various estimates of genetic diversity and population differentiation were calculated using EST-derived SNP markers. All populations had comparable levels of genetic diversity and the long-term effective population size appears to be sufficiently large for the wild populations, despite evidence of recent bottlenecks. Population differentiation was for the most part geographically correlated, with spatial genetic structure maintained across temporal samples. Significant genetic differentiation was, however, detected among temporal samples taken from the same locality. There was evidence for comparatively small short-term effective population sizes that could explain large changes in allele frequencies due to stochastic effects. Temporal heterogeneity could also be explained by changes in selection pressures over time. H. midae populations could, therefore, be more dynamic than previously estimated and this could have implications for effective conservation and fisheries management.

Population Genetic Structure of a Widespread Bat-Pollinated Columnar Cactus.

Bats are the main pollinators and seed dispersers of Stenocereus thurberi, a xenogamous columnar cactus of northwestern Mexico and a good model to illustrate spatial dynamics of gene flow in long-lived species. Previous studies in this cactus showed differences among populations in the type and abundance of pollinators, and in the timing of flowering and fruiting. In this study we analyzed genetic variability and population differentiation among populations. We used three primers of ISSR to analyze within and among populations genetic variation from eight widely separated populations of S. thurberi in Sonora, Mexico. Sixty-six out of 99 of the ISSR bands (P = 66.7%) were polymorphic. Total heterozygosity for all populations sampled revealed high genetic diversity (Hsp = 0.207, HBT = 0.224). The AMOVA showed that most of the genetic variation was within populations (80.5%). At the species level, estimates of population differentiation, θ = 0.175 and θB = 0.194, indicated moderate gene flow among populations. The absence of a significant correlation between genetic and geographic distances indicated little isolation by geographic distance. The large genetic variation and diversity found in S. thurberi is consistent with its open reproductive system and the high mobility of bats, a major pollinator. However, small changes in number or kind of pollinators and seed dispersal agents, in the directionality of migratory routes, and/or in the timing of flowering and fruiting among populations, can critically affect gene flow dynamics.

Characterization of novel microsatellite markers for Hyphantria cunea and implications for other Lepidoptera.

This is the first report of microsatellite markers (simple sequence repeats, SSR) for fall webworm, Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), an important quarantine pest in some European and Asian countries. Here, we developed 48 microsatellite markers for H. cunea from SSR enrichment libraries. Sequences isolated from libraries were sorted into four categories and analyzed. Our results suggest that sequences classified as Grouped should not be used for microsatellite primer design. The genetic diversity of microsatellite loci was assessed in 72 individuals from three populations. The number of alleles per locus ranged from 2 to 5 with an average of 3. The observed and expected heterozygosities of loci ranged from 0 to 0.958 and 0 to 0.773, respectively. A total of 18 out of 153 locus/population combinations deviated significantly from Hardy-Weinberg equilibrium. Moreover, significant linkage disequilibrium was detected in one pair of loci (1275 pairs in total). In the neutral test, two loci were grouped into the candidate category for positive selection and the remainder into the neutral category. In addition, a complex mutation pattern was observed for these loci, and F ST performed better than did R ST for the estimation of population differentiation in different mutation patterns. The results of the present study can be used for population genetic studies of H. cunea.

Mixed stock analysis of a resident green turtle, Chelonia mydas, population in New Caledonia links rookeries in the South Pacific

Context Migratory species are known to pose a challenge for conservation because it is essential to understand their complex life history in order to implement efficient conservation actions. Aims In New Caledonia, large seagrass habitats in the Grand Lagon Sud (GLS) are home to resident green turtles (Chelonia mydas) of unknown origins. To assess the stock composition in the GLS, 164 foraging turtles were sampled for genetic analysis of ~770 base pairs of the mitochondrial DNA (mtDNA) control region. Methods Foraging turtles ranging in size from 48.0 to 108.4 cm curved carapace length were captured at five different sites within the GLS between September 2012 and December 2013. To provide baseline data for mixed stock analysis, published data from rookeries were used in addition to 105 samples collected at rookeries in the d’Entrecasteaux Islands and Chesterfield Islands in New Caledonia and at Malekula Island in Vanuatu. Exact tests of population differentiation and pairwise FST estimates were used to test for differences in mtDNA haplotype frequencies. Key results These analyses indicated that rookeries in the d’Entrecasteaux Islands and Vanuatu form unique management units and that the Chesterfield Islands rookeries are linked to the Coral Sea management unit. Mixed stock analysis indicated the highest proportion (mean = 0.63) of foraging turtles originate from the d’Entrecasteaux stock. Conclusions The larger contribution is estimated to be from a large rookery from New Caledonia, but smaller contributions are suggested from other rookeries in the South Pacific. Implications Marine conservation policies in New Caledonia need to consider the links between the foraging and nesting populations of C. mydas in New Caledonia and other rookeries and foraging grounds in the Coral Sea.

Genetic Structure of and Evidence for Admixture between Western and Korean Native Pig Breeds Revealed by Single Nucleotide Polymorphisms.

Comprehensive information on genetic diversity and introgression is desirable for the design of rational breed improvement and conservation programs. Despite the concerns regarding the genetic introgression of Western pig breeds into the gene pool of the Korean native pig (KNP), the level of this admixture has not yet been quantified. In the present study, we genotyped 93 animals, representing four Western pig breeds and KNP, using the porcine SNP 60K BeadChip to assess their genetic diversity and to estimate the level of admixture among the breeds. Expected heterozygosity was the lowest in Berkshire (0.31) and highest in Landrace (0.42). Population differentiation (FST) estimates were significantly different (p<0.000), accounting for 27% of the variability among the breeds. The evidence of inbreeding observed in KNP (0.029) and Yorkshire (0.031) may result in deficient heterozygosity. Principal components one (PC1) and two (PC2) explained approximately 35.06% and 25.20% of the variation, respectively, and placed KNP somewhat proximal to the Western pig breeds (Berkshire and Landrace). When K = 2, KNP shared a substantial proportion of ancestry with Western breeds. Similarly, when K = 3, over 86% of the KNP individuals were in the same cluster with Berkshire and Landrace. The linkage disquilbrium (LD) values at r2 0.3, the physical distance at which LD decays below a threshold of 0.3, ranged from 72.40 kb in Landrace to 85.86 kb in Yorkshire. Based on our structure analysis, a substantial level of admixture between Western and Korean native pig breeds was observed.