Small Genetic Differentiation Research Articles

Quantifying genetic differentiation and population assignment between two contingents of Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic

In the Northwest Atlantic (NWA), the Atlantic mackerel ( Scomber scombrus) has a northern and a southern contingent, which spawn in Canada and the United States (U.S.), respectively. Both contingents mix mostly along the U.S. shelf during overwintering. The discrimination of individuals from each contingent in fisheries could improve the management of this depleted species in both countries. Here, we used genome-wide markers (>10 000 single nucleotide polymorphisms (SNPs)) to assess genomic differences between mackerel of both contingents, and possibly infer the proportions of each contingent in NWA management units. Small but significant genetic differentiation was observed between the northern and southern contingents ( FST = 0.0010). Genetic assignments to reference samples from the two contingents were performed with predictive accuracy > 85%. Fish from both contingents were present along the U.S. shelf during late winter and early spring but also, without prior evidence of this, likely in Canadian waters from late spring to fall. Genetic assignments could be used as a stock discrimination tool so that fishery removals can be effectively determined and managed on a contingent level.

Diversity and enrichment of breeding material for resilience in European forests

Delivering material selected for breeding purposes into the wild in the context of sustainable forest management might reduce the levels of genetic diversity of future forests in comparison to that of natural populations. Another consequence might be a reduction of their resilience under uncertain future climatic and socio-economic conditions if these new populations lack adaptability. Despite the long tradition of breeding activities in Europe, there is still a need to assess the impact of genetically enriched material on forests’ resilience. In this study, we address (1) the genetic diversity of selected material compared to its wild ancestors, and (2) how to enrich breeding material to support forests’ resilience under changing socio-environmental conditions. We analysed 16 study cases of selected material delivered from breeding activities in four European forest tree species (Pinus halepensis Mill., Pinus nigra J.F. Arnold, Pinus pinaster Ait. and Populus nigra L.) with different levels of breeding. To answer these two questions, we first assessed and compared the genetic diversity of selected material versus natural populations using both putatively neutral and adaptive (based on diverging selection) Single Nucleotide Polymorphisms (SNPs). We then suggest how to enrich these populations for resilience under future climatic conditions by defining a core collection for each species including material from populations that will likely disappear under future conditions. Thanks to the large SNP datasets available for our focal species, we were able to detect some trends in our data. Expected and observed heterozygosity values for selected populations were almost always identical. The selected material showed small but significant genetic differentiation from their original population and their inbreeding coefficient was generally lower. However, the level of genetic improvement (i.e. low vs high) was not correlated with the observed genetic differences between selected material and natural populations.The genetic characterization of natural populations distributed across the species range, and the future projection of their range stability, made it possible to identify core-collections that would significantly enrich breeding populations under uncertain future environmental conditions.

Inconsistency Between Socio-Spatial and Genetic Structure in a Coastal Dolphin Population

Identifying population structure and boundaries among communities of wildlife exposed to anthropogenic threats is key to successful conservation management. Previous studies on the demography, social and spatial structure of Indo-Pacific bottlenose dolphins (Tursiops aduncus) suggested four nearly discrete behavioral communities in Perth metropolitan waters, Western Australia. We investigated the genetic structure of these four communities using highly polymorphic microsatellite markers and part of the hypervariable segment of the mitochondrial control region. Overall, there was no evidence of spatial genetic structure. We found significant, yet very small genetic differentiation between some communities, most likely due to the presence of highly related individuals within these communities. Our findings of high levels of contemporary migration and highly related individuals among communities point toward a panmictic genetic population with continuous gene flow among each of the communities. In species with slow life histories and fission-fusion dynamics, such asTursiopsspp., genetic and socio-spatial structures may reflect different timescales. Thus, despite genetic similarity, each social community should be considered as a distinct ecological unit to be conserved because they are exposed to different anthropogenic threats and occur in different ecological habitats, social structure being as important as genetic information for immediate conservation management. The estuarine community, in particular, is highly vulnerable and appropriate conservation measures are needed in order to maintain its connectivity with the adjacent, semi-enclosed coastal communities.

Sequence analyses of insulin-like growth factor 1 gene in Nigerian indigenous and arbor acre chickens

Alpha % Indigenous chicken % Gene % Sequence KR nema The chicken Insulin-like growth factor 1 (IGF1) is a candidate gene for growth, body composition and metabolism, skeletal characteristics and growth of adipose tissue and fat deposition in chickens. It is mapped to 165.95 cM on chromosome 1 and composed of four exons and three introns, spanning more than 50 kb. Genomic DNA was extracted from blood samples collected from the experimental birds using Qiagen DNA extraction kits. Polymersae chain reaction (PCR) was carried out using established primers. The PCR amplicon involving 5?untranslated region were sequenced. The sequences were analysed to identify polymorphisms, their genetic diversities and evolutionary relationships among three strains of Nigerian indigenous chickens [Frizzle Feathered (7), Normal Feathered (19) and Naked Neck (19), and the Arbor Acre broiler chicken (17)]. Nucleotide sequences generated were edited and aligned using Codon Code Aligner. Diversity analysis was done using DnaSp while MEGA6 software was used to plot phylogenetic tree using maximum likelihood method. A total of nineteen single nucleotide polymorphisms (SNPs) were detected from 560 bp portions of the 5?UTR among the four chicken populations studied with none detected in the Frizzle feathered chicken. The Naked neck chicken had the highest number of SNP?s (13), haplotypes (6), haplotype diversity (0.778), nucleotide diversity (0.00487), average number of nucleotide differences (2.725), highest number of polymorphic (segregating) sites (13), parsimony informative site (5) and singleton variable site (8). The Naked neck chicken therefore had the highest rate of mutation and degree of allelic variation compared to other chicken strains used in this study. The phylogenetic tree showed that small genetic differentiation exists among the chicken populations studied. Some of the SNPs are newly discovered; hence, association between these alleles and productive traits in Nigerian native chickens is desirable in future studies.

DNA Analysis of Juvenile Scalloped Hammerhead Sharks Sphyrna lewini (Griffith, 1834) Reveals Multiple Breeding Populations and Signs of Adaptive Divergence in the South Pacific

Shark species have undergone drastic population declines in recent decades due to overfishing and habitat destruction; thus, establishing connectivity among the populations of various shark species is important to determine the appropriate units and spatial scale for conservation and management, particularly as this group is long-lived with late age of maturation. Consequently, we used DNA variation at 1,317 putatively neutral and 25 potentially adaptive single nucleotide polymorphisms (SNPs) to analyze population genetic structure among 174 unrelated individuals of scalloped hammerhead sharks (Sphyrna lewini) from the Rewa Delta and the Ba Estuary, where documented aggregations of neonates and young-of-the-year occur in the island of Viti Levu, Republic of Fiji. Results of the pairwise FST analysis for the neutral loci revealed a small but significant genetic differentiation (FST: 0.004; P-value = 0.0009). Furthermore, the 25 potentially adaptive loci (i.e., under putative selection) revealed a magnitude of differentiation four times bigger than the estimate obtained using neutral genetic diversity (FST: 0.017; P-value = 0.0009). Interestingly, population assignment tests, using the neutral SNP data set and two different software packages, Admixture and assignPOP, provided evidence for the existence of up to four genetically differentiated populations among our samples. Assignment probabilities ranged from 0.98 ± 0.01 to 0.81 ± 0.03. Admixture and assignPOP assigned the same individuals to the same putative populations for all sampled neonates. Thus, our results provide unequivocal evidence that adult females from multiple genetically differentiated breeding populations contribute to these juvenile aggregation sites.

Phylogeography of the bitterling Tanakia lanceolata (Teleostei: Cyprinidae) in Japan inferred from mitochondrial cytochrome b gene sequences

The bitterling Tanakia lanceolata is a primary freshwater fish with wide distribution range in Japan; therefore, analysis of this species will yield much information on the formation of Japanese freshwater fish fauna. However, populations of this species are threatened by several human activities. To reveal the genetic population structure of T. lanceolata and the process of its formation, as well as its genetic status, we conducted phylogenetic analyses and estimated divergence times based on partial sequences of the mitochondrial DNA cytochrome b gene, using specimens collected across the distribution range. The results of the analysis showed that Japanese T. lanceolata is monophyletic and consists of seven local population groups that diverged from the Late Pliocene to the Middle Pleistocene. The population structure in western Japan was similar to that of other freshwater fishes (e.g., separation by the Suzuka Mountains), although there were several differences in population boundaries and the presence/absence of a secondary contact zone. The Central Highlands in central Honshu are the primary, or at least the most effective, geological barrier responsible for population divergence in Japanese freshwater fish species. However, the small genetic differentiation of the T. lanceolata population between the western and eastern sides of the Central Highlands suggested recent dispersal and gene flow across the region after uplift of the highlands. The genetic population structure indicated extensive genetic disturbance in the Kanto Region. Our results provide information on the formation process of the Japanese freshwater fish fauna, which could aid conservation efforts toward T. lanceolata.

GENETIC DIVERSITY STUDIES OF LATVIAN VACCINIUM MYRTILLUS L. POPULATIONS FOR IN SITU CONSERVATION

Plants and berries of bilberries (Vaccinium myrtillus L.) are traditionally used in many nations as a local medicine as well as edible plants. They are an important feed source for wild animals and birds. In situ conservation is an important component for the conservation of crop wild relatives (CWR) and wild harvested plants (WHP). Research on population structure and genetic diversity is important and is required for the development and implementation of in situ conservation strategies as well as being useful for ecosystem services management. The aim of this study was to test EST-SSR markers for bilberry genotyping and determine genetic diversity in different forest types – Vacciniosa, Myrtillosa, Hylocomiosa as well as compare populations from various regions of Latvia. Our results indicated that there was a small genetic differentiation between bilberries grown in different forest types (0-2%); most of the variation was found within individuals. Analysing populations in different regions of Latvia, 5% of the genetic variation was found among populations. Analysis using the STRUCTURE software package showed that there were no isolated populations or distinct groups. There was a positive correlation between geographic and genetic distances, indicating that the analysed populations differentiation can be explained by isolation-by-distance, without additional dispersal barriers.

Spatial genetic diversity in the Cape mole-rat, Georychus capensis: Extreme isolation of populations in a subterranean environment.

The subterranean niche harbours animals with extreme adaptations. These adaptations decrease the vagility of taxa and, along with other behavioural adaptations, often result in isolated populations characterized by small effective population sizes, high inbreeding, population bottlenecks, genetic drift and consequently, high spatial genetic structure. Although information is available for some species, estimates of genetic diversity and whether this variation is spatially structured, is lacking for the Cape mole-rat (Georychus capensis). By adopting a range-wide sampling regime and employing two variable mitochondrial markers (cytochrome b and control region), we report on the effects that life-history, population demography and geographic barriers had in shaping genetic variation and population genetic patterns in G. capensis. We also compare our results to information available for the sister taxon of the study species, Bathyergus suillus. Our results show that Georychus capensis exhibits low genetic diversity relative to the concomitantly distributed B. suillus, most likely due to differences in habitat specificity, habitat fragmentation and historical population declines. In addition, the isolated nature of G. capensis populations and low levels of population connectivity has led to small effective population sizes and genetic differentiation, possibly aided by genetic drift. Not surprisingly therefore, G. capensis exhibits pronounced spatial structure across its range in South Africa. Along with geographic distance and demography, other factors shaping the genetic structure of G. capensis include the historical and contemporary impacts of mountains, rivers, sea-level fluctuations and elevation. Given the isolation and differentiation among G. capensis populations, the monotypic genus Georychus may represent a species complex.

Higher immunocompetence is associated with higher genetic diversity in feral honey bee colonies (Apis mellifera)

Honey bees are the most important managed pollinators as they provide key ecosystem services for crop production worldwide. Recent losses of honey bee colonies in North America and Europe have demonstrated a need to develop strategies to improve their health and conserve their populations. Previously, we showed that feral honey bees—colonies that live in the wild without human assistance—exhibit higher levels of immunocompetence than managed colonies in North Carolina (USA). In a first attempt to investigate the underlying mechanisms of this difference in immune response, here we characterize the genetic composition of feral and managed honey bees using microsatellite markers. Our results reveal significant but small genetic differentiation between feral and managed honey bee colonies (ϕCT = 0.047, P = 0.03) indicating admixture between these two groups. Higher genetic diversity was correlated with higher immune response in feral (P MANOVA = 0.011) but not managed bees, despite the fact that the latter group showed significantly higher average genetic diversity (P ANCOVA < 0.001). These findings suggest that genetic diversity is positively associated with immunocompetence in feral honey bee colonies, and that the benefits of genetic diversity are obscured in managed bees, perhaps as a result of artificial selection. We hypothesize that high genetic variability provides the raw material upon which natural selection acts and generates adaptive genotypes in unmanaged populations. Feral populations could be useful sources of genetic variation to use in breeding programs that aim to improve honey bee health.

Distinct matrilines in the panmictic population of the European eelAnguilla anguilla?

Determining the genetic population structure and intraspecific evolution of species is important for efficient management. Here we investigated 394 sequences of the mtDNA cyt b of the critically endangered European eel, Anguilla anguilla . We found 62 different haplotypes, among which 32 novel ones. All those sequences were grouped into 9 haplogroups on the basis of their frequency and links in the haplotype network. Two pairwise comparisons revealed significant genetic differentiation between regions. One comparison indicated small (ΦST = 0.02768; P = 0.0071) genetic differentiation between the Atlantic Ocean and the North Sea. Another comparison indicated small (ΦST = 0.01144; P = 0.0440) genetic differentiation between eel samples caught in the Baltic Sea, the Curonian Lagoon and the Gulf of Riga and those captured in the North Sea. The results of the study are in agreement with the recent findings obtained using the mtDNA D-loop region as a molecular marker, indicating that although A. anguilla is considered a panmictic species the genetic structure of its population indicated by mtDNA markers could be characterized as a genetic mosaic.

Blastocystis Isolates from Patients with Irritable Bowel Syndrome and from Asymptomatic Carriers Exhibit Similar Parasitological Loads, but Significantly Different Generation Times and Genetic Variability across Multiple Subtypes.

Blastocystis spp is a common intestinal parasite of humans and animals that has been associated to the etiology of irritable bowel syndrome (IBS); however, some studies have not found this association. Furthermore, many biological features of Blastocystis are little known. The objective of present study was to assess the generation times of Blastocystis cultures, from IBS patients and from asymptomatic carriers. A total of 100 isolates were obtained from 50 IBS patients and from 50 asymptomatic carriers. Up to 50 mg of feces from each participant were cultured in Barret’s and in Pavlova’s media during 48 h. Initial and final parasitological load were measured by microscopy and by quantitative PCR. Amplicons were purified, sequenced and submitted to GenBank; sequences were analysed for genetic diversity and a Bayesian inference allowed identifying genetic subtypes (ST). Generation times for Blastocystis isolates in both media, based on microscopic measures and molecular assays, were calculated. The clinical symptoms of IBS patients and distribution of Blastocystis ST 1, 2 and 3 in both groups was comparable to previous reports. Interestingly, the group of cases showed scarce mean nucleotide diversity (π) as compared to the control group (0.011±0.016 and 0.118±0.177, respectively), whilst high gene flow and small genetic differentiation indexes between different ST were found. Besides, Tajima’s D test showed negative values for ST1-ST3. No statistical differences regarding parasitological load between cases and controls in both media, as searched by microscopy and by qPCR, were detected except that parasites grew faster in Barret’s than in Pavlova’s medium. Interestingly, slow growth of isolates recovered from cases in comparison to those of controls was observed (p<0.05). We propose that generation times of Blastocystis might be easily affected by intestinal environmental changes due to IBS probably because virulent strains with slow growth may be selected, reducing their genetic variability.

Genetic similarity and differences between the Orobanche cumana Wallr. Populations from Russia, Kazakhstan, and Romania revealed using the markers of simple sequence repeat

The molecular genetic diversity of the broomrape (O. cumana) populations, parasitizing on sunflower in Russia, Romania and Kazakhstan, was studied with codominant microsatellite markers. By means of cluster analysis, the populations of broomrape were divided into two clusters, regardless of their racial composition. In the first cluster, 19 samples from Russia and Kazakhstan, representing one gene pool are grouped; the second cluster consisted of five populations from Romania, united in another pool. According to Nei, the genetic distance between the clusters was 0.137. The analysis of molecular variance revealed that 22% of total variance were caused by differences between the genetic pools and 78% appeared due to differences between the samples within the each gene pool. The pairwise comparisons performed by Wright’s statistics showed that the differences between these two gene pools are sufficient (Fst = 21.9%) in order to make the conclusion about the existence of small genetic differentiation between the pools. The descriptive population genetic statistics for each pool indicate that the broomrape populations from Russia and Kazakhstan are characterized by a higher level of intrapopulation diversity than the populations from Romania.

Genetic diversity and insecticide resistance during the growing season in the green peach aphid (Hemiptera: Aphididae) on primary and secondary hosts: a farm-scale study in Central Chile

The seasonal dynamics of neutral genetic diversity and the insecticide resistance mechanisms of insect pests at the farm scale are still poorly documented. Here this was addressed in the green peach aphid Myzus persicae (Sulzer) (Hemiptera: Aphididae) in Central Chile. Samples were collected from an insecticide sprayed peach (Prunus persica L.) orchard (primary host), and a sweet-pepper (Capsicum annum var. grossum L.) field (secondary host). In addition, aphids from weeds (secondary hosts) growing among these crops were also sampled. Many unique multilocus genotypes were found on peach trees, while secondary hosts were colonized mostly by the six most common genotypes, which were predominantly sensitive to insecticides. In both fields, a small but significant genetic differentiation was found between aphids on the crops vs. their weeds. Within-season comparisons showed genetic differentiation between early and late season samples from peach, as well as for weeds in the peach orchard. The knock-down resistance (kdr) mutation was detected mostly in the heterozygote state, often associated with modified acetylcholinesterase throughout the season for both crops. This mutation was found in high frequency, mainly in the peach orchard. The super-kdr mutation was found in very low frequencies in both crops. This study provides farm-scale evidence that the aphid M. persicae can be composed of slightly different genetic groups between contiguous populations of primary and secondary hosts exhibiting different dynamics of insecticide resistance through the growing season.

Interpopulation Genetic Differentiation Orobanche cumana Wallr. from Russia, Kazakhstan and Romania Using Molecular Genetic Markers

AbstractBroomrape (

AFLP analysis reveals high genetic diversity but low population structure in Coccidioides posadasiiisolates from Mexico and Argentina

BackgroundCoccidioides immitis and C. posadasii cause coccidioidomycosis, a disease that is endemic to North and South America, but for Central America, the incidence of coccidioidomycosis has not been clearly established. Several studies suggest genetic variability in these fungi; however, little definitive information has been discovered about the variability of Coccidioides fungi in Mexico (MX) and Argentina (AR). Thus, the goals for this work were to study 32 Coccidioides spp. isolates from MX and AR, identify the species of these Coccidioides spp. isolates, analyse their phenotypic variability, examine their genetic variability and investigate the Coccidioides reproductive system and its level of genetic differentiation.MethodsCoccidioides spp. isolates from MX and AR were taxonomically identified by phylogenetic inference analysis using partial sequences of the Ag2/PRA gene and their phenotypic characteristics analysed. The genetic variability, reproductive system and level of differentiation were estimated using AFLP markers. The level of genetic variability was assessed measuring the percentage of polymorphic loci, number of effective allele, expected heterocygosity and Index of Association (IA). The degree of genetic differentiation was determined by AMOVA. Genetic similarities among isolates were estimated using Jaccard index. The UPGMA was used to contsruct the corresponding dendrogram. Finally, a network of haplotypes was built to evaluate the genealogical relationships among AFLP haplotypes.ResultsAll isolates of Coccidioides spp. from MX and AR were identified as C. posadasii. No phenotypic variability was observed among the C. posadasii isolates from MX and AR. Analyses of genetic diversity and population structure were conducted using AFLP markers. Different estimators of genetic variability indicated that the C. posadasii isolates from MX and AR had high genetic variability. Furthermore, AMOVA, dendrogram and haplotype network showed a small genetic differentiation among the C. posadasii populations analysed from MX and AR. Additionally, the IA calculated for the isolates suggested that the species has a recombinant reproductive system.ConclusionsNo phenotypic variability was observed among the C. posadasii isolates from MX and AR. The high genetic variability observed in the isolates from MX and AR and the small genetic differentiation observed among the C. posadasii isolates analysed, suggest that this species could be distributed as a single genetic population in Latin America.

Regional genetic differentiation among northern high-latitude island populations of a broadcast-spawning coral

Knowledge of genetic connectivity is useful for understanding of the recovery potential of coral populations after various disturbances, such as coral mass bleaching. Population genetic studies in corals are mostly restricted to Australian and Caribbean species; studies in the northern Pacific are relatively limited. Using microsatellite markers, the population genetics of Acropora sp. 1 was examined between two regions in Japan, the Okinawa-Aka and Bonin Islands, which are separated by approximately 1,500 km of open water in a high-latitude area. Statistically significant but small genetic differentiation in Acropora sp. 1 was detected between and within these regions. Genetic diversity was not obviously reduced in populations of the Bonin Islands, which are relatively isolated. Thus, some level of connectivity appears to be maintained between the two regions, likely because of the high dispersal ability of this broadcast spawner.

Genetic diversity analysis of Arius manillensis (Siluriformes: Ariidae) using the mitochondrial control region

Arius manillensis is a Philippine endemic species and is an economically important fishery resource in Laguna de Bay, the largest lake in the country. Drastic reduction in population sizes of A. manillensis has been recorded in the past, which may have resulted in genetic bottleneck. In this study, the genetic diversity and population structure of A. manillensis in Laguna de Bay were assessed using the mitochondrial DNA control region. Specimens were obtained from three localities along Laguna de Bay, namely Binangonan (n = 27), Tanay (n = 29), and Calamba (n = 30). Of the 86 DNA sequences generated, 22 distinct haplotypes were observed. There were four unique haplotypes for Binangonan, six for Calamba, and five for Tanay. There were two haplotypes common to the three sites. The maximum likelihood tree and median-joining network showed little geographic separation among the haplotypes. Chi-square test showed no significant differentiation in A. manillensis from the three sites. The overall computed FST was 0.0144, indicating small genetic differentiation in A. manillensis from the three localities sampled. Likewise, analysis of molecular variance showed a greater percentage of variation within population (98.62%) than variation among populations (1.38%; P = 0.21). Total haplotype diversity and nucleotide diversity among the specimens from the three sites were 0.775 and 0.013, respectively. The high haplotype diversity coupled with low nucleotide diversity observed in this study confirms that genetic bottleneck occurred in A. manillensis which was followed by population expansion. This is also supported by the non-significant values for both Tajima's D and Fu's F. Furthermore, multimodal mismatch distribution plots were generated, which is consistent with the model of spatial range expansion followed by demographic expansion.

Genetic structure of indigenous and migratory populations in the area of Tuzla region considering some static and dynamic-morphological properties

Genetic structure of two human populations, indigenous and migratory population in the area of the Tuzla region, was analyzed with respect to some static and dynamic-morphological properties. The analyzed genetic data were collected by direct observation and survey of 472 pupils of school age. The investigated parameters of genetic heterogeneity were estimated by: analysis of the frequency of recessive phenotypes for every observed property, t-test analysis, and assessment of intragroup variation by analysis of Wahlund variance. Based on the obtained results it was observed that the frequency of the recessive homozygote for most of the analyzed properties was slightly higher in migratory populations. All values obtained by Wahlund variance analysis indicated a small genetic differentiation.

Genetic differentiation of Japanese sardinella (Sardinella zunasi) populations in the Northwest Pacific revealed by ISSR analysis

Knowledge of population genetic structure plays an important role in fisheries management. In this research, Inter-Simple-Sequence-Repeat (ISSR) markers were employed to evaluate the genetic structure of Japanese sardinella (Sardinella zunasi) populations in the Northwest Pacific. Eighty seven individuals from 5 locations were screened using 4 highly polymorphic primers. A total of 173 polymorphic loci were detected out of 191 loci amplified. Small but significant genetic differentiation was detected between the Chinese and Japanese populations by both AMOVA and pairwise FST analyses, which was further supported by cluster analysis. We consider that climate change during glaciations should be responsible for the genetic differentiation. Isolation by geographic distance among populations was observed, indicating that the distance might also lead to the genetic differentiation. However, no genetic structure was found within the populations off both the Chinese and Japanese coasts, indicating a high-level along-coast gene flow, which might result from ocean current transport and common ground for over-wintering.

Microsatellites reveal fine-scale genetic structure of the Chinese surf clam Mactra chinensis (Mollusca, Bivalvia, Mactridae) in Northern China

As a commercially important fisheries resource in East Asia, the Chinese surf clam Mactra chinensis has experienced severe population declines in the past decades, probably due to over-exploitation. To provide scientific bases for fisheries management and artificial breeding, we investigated genetic variation and population structure of Mactra chinensis in Northern China using microsatellites. Samples collected from eight localities throughout natural habitats of the species in Northern China were genotyped. Nine microsatellites revealed high allelic diversity with 14–36 alleles per locus. Observed and expected heterozygosity varied from 0.593 to 0.945 and from 0.638 to 0.958, respectively. Pairwise FST values indicated that all population pairs had small but significant genetic differentiation. A Mantel test showed statistically significant correlations between genetic distance and geographical distance, indicating that genetic differentiation of the Chinese surf clam conformed to a pattern of isolation-by-distance. Cluster analysis using neighbor-joining separated the eight populations into three groups. The three areas of low gene flow identified by barrier analysis corresponded with local oceanographic features, suggesting that marine currents and peninsulas play an important role in population structuring of this species.