Hardy-Weinberg Expectations Research Articles

Species composition and genetic diversity of farmed mussels in British Columbia, Canada

The common blue mussel (Mytilus edulis) was introduced to British Columbia, Canada, in the 1980s as an aquaculture alternative to native mussel species. Since then, the mussel industry in Pacific Canada has expanded and includes operations utilizing traditional methods of broodstock selection based on visual qualitative and quantitative traits. The impacts of hatchery propagation on genetic diversity and implications for animal fitness have been previously studied for other aquatic species, and this study further examines the effect of hatchery production on three M. edulis aquaculture populations in relation to a wild originator population. Prior to microsatellite genetic analysis, animals were identified to species using nuclear markers and were found to contain varying proportions of pure M. edulis as well as other pure species and hybrids from the ‘Mytilus edulis complex’. Subsequently seven microsatellite markers were used to genotype 166 pure adult M. edulis individuals, all of which exhibited high levels of polymorphism. Allele frequencies at multiple loci did not conform to Hardy–Weinberg expectations and substantially less genetic diversity and very low effective population size estimates (Ne, calculated from linkage disequilibrium) were observed in farmed populations compared to the wild reference population. All populations were found to be genetically distinct based on FST estimates. Mean allelic richness was approximately three times higher in the wild reference population than the three farmed populations (21 compared to 7.51, 7.91 in the two populations selecting for size and 8.24 in the population selecting for a colour morph). Observed heterozygosity was not significantly decreased in the cultured colour morph population, but was significantly different in the two other culture populations in comparison to the wild group. Reduced genetic diversity of the aquaculture populations is likely at least partially due to small effective breeding groups during hatchery propagation, creating genetic drift over successive generations. Speculations about the influence of broodstock selection practices are tentative and should be addressed in further temporal studies. These results indicate the need for the effective management of hatchery operations, the importance of rigorous site inventory, genetic broodstock characterization, and that ideally pedigree programs should be developed to help maintain healthy and productive shellfish culture populations with adaptive fitness capacity. Statement of relevanceHatchery methods impact species purity and genetic diversity.

Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

Ecological genetics of Italian peach‐potato aphid (Myzus persicae) populations in relation to geography, dispersal and insecticide resistance as studied using microsatellite and resistance markers

Abstract Eight polymorphic microsatellites and two insecticide resistance markers (kdr and R81T) were used to investigate the population genetics and demography of resistance mechanisms in field populations of the peach‐potato aphid, Myzus persicae (Sulzer), a global crop pest, in several areas of Italy, notably the north‐east, aiming to determine whether these parameters are linked to population structuring resulting from insecticide selective sweeps. Individuals collected directly from peach orchards (main primary host) in the spring, especially after control failure, revealed 90 microsatellite alleles, of which approximately one‐third were rare. Many populations deviated from Hardy–Weinberg expectations, in a few instances as a result of null alleles. FIS values were on average negative (indicating heterozygote excess), whereas FST values (mean = 0.137) reflected moderate interpopulation gene flow, with nonstructured populations having an estimated higher level than insecticide‐treated ones. Population assignment and Mantel testing showed a non‐homogenous pattern, with some populations isolated genetically. Linkage disequilibrium was detected in four of the microsatellites and both resistance markers. Contrasting FST patterns with resistance status supported the view that some populations were indeed structured. Neighbour‐joining trees revealed some populations to have similar insecticide resistance profiles, independent of geographical origin. Overall, the findings reveal that the natural M. persicae populations investigated in the present study, living within an intensively cultivated agro‐ecosystem, bear the signature of such management in terms of population structuring, as well as possibly also dynamics.

Rare sex or out of reach equilibrium? The dynamics of F IS in partially clonal organisms.

BackgroundPartially clonal organisms are very common in nature, yet the influence of partial asexuality on the temporal dynamics of genetic diversity remains poorly understood. Mathematical models accounting for clonality predict deviations only for extremely rare sex and only towards mean inbreeding coefficient overline{F_{IS}}<0 . Yet in partially clonal species, both FIS < 0 and FIS > 0 are frequently observed also in populations where there is evidence for a significant amount of sexual reproduction. Here, we studied the joint effects of partial clonality, mutation and genetic drift with a state-and-time discrete Markov chain model to describe the dynamics of FIS over time under increasing rates of clonality.ResultsResults of the mathematical model and simulations show that partial clonality slows down the asymptotic convergence to FIS = 0. Thus, although clonality alone does not lead to departures from Hardy-Weinberg expectations once reached the final equilibrium state, both negative and positive FIS values can arise transiently even at intermediate rates of clonality. More importantly, such “transient” departures from Hardy Weinberg proportions may last long as clonality tunes up the temporal variation of FIS and reduces its rate of change over time, leading to a hyperbolic increase of the maximal time needed to reach the final mean overline{F_{IS,infty }} value expected at equilibrium.ConclusionOur results argue for a dynamical interpretation of FIS in clonal populations. Negative values cannot be interpreted as unequivocal evidence for extremely scarce sex but also as intermediate rates of clonality in finite populations. Complementary observations (e.g. frequency distribution of multiloci genotypes, population history) or time series data may help to discriminate between different possible conclusions on the extent of clonality when mean overline{F_{IS}} values deviating from zero and/or a large variation of FIS over loci are observed.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0388-z) contains supplementary material, which is available to authorized users.

Frequencies of HID-ion ampliseq ancestry panel markers among greenlanders

The HID-Ion AmpliSeq Ancestry Panel from Life Techologies includes 123 SNPs from the Seldin panel and 55 SNPs from Kidd panel in a single multiplex assay that helps to determine the continental biogeographic ancestry of individuals. We tested the panel on 104 Greenlanders, divided into a training set of 89 individuals and a test set of 15 individuals. All loci showed genotype distributions consistent with Hardy-Weinberg expectations. Linkage disequilibrium tests indicated that 14 pairs of loci were in association in Greenlanders. Population assignment of the training set to populations included in the HID SNP genotyper plugin placed most individuals in American, Asian, and in a few cases European populations. By including the genotype frequencies of this training set as a possible population of origin, all 15 individuals from the test set were correctly predicted to be Greenlanders using the Seldin SNPs, and nine were classified as Greenlanders using the Kidd SNPs. Population structure analysis indicated that Greenlanders have a genetic profile that is distinguishable from those of populations from America or Asia.

Development and characterization of 29 microsatellite markers for Ligumia nasuta (Bivalvia: Unionidae) using an Illumina sequencing approach

Ligumia nasuta (Say, 1817; Eastern Pondmussel) is an imperiled freshwater mussel (Unionidae) in eastern North America. Population declines in the Laurentian Great Lakes resulting from the introduction of dreissenid mussels and habitat destruction in the 20th Century have greatly reduced and limited its distribution. To properly inform restoration and management efforts for L. nasuta, fine-scale genetic analyses must be performed on the remnant populations. This study used Illumina paired-end shotgun sequencing to identify potential microsatellite loci for L. nasuta, utilizing two samples to develop the Illumina paired-end shotgun library. Forty-eight primer pairs were tested on the remaining 24 samples. Twenty-nine of the 48 microsatellite primer sets screened were successfully amplified using 24 L. nasuta samples collected from the Great Lakes watershed. The estimated fragment size ranged from 167 to 445 base-pairs (bp) and the number of alleles per locus varied between 5 and 16 (mean = 9.7). Only five of the loci deviated significantly from Hardy–Weinberg expectations after Bonferroni corrections. The development of these new microsatellite loci will greatly facilitate future genetic studies on L. nasuta.

Polymorphism analysis of 20 autosomal short-tandem repeat loci in southern Chinese Han population

To evaluate the value of PowerPlex®21 System (Promega) and study the genetic polymorphism of its 20 short-tandem repeat (STR) loci in southern Chinese Han population. We conducted genotyping experiments using PowerPlex®21 System on 20 autosomal STR loci (D3S1358, D1S1656, D6S1043, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433 and FGA) in 2367 unrelated Chinese Han individuals living in South China. The allele frequencies and parameters commonly used in forensic science were statistically analyzed in these individuals and compared with the reported data of other populations. The PowerPlex®21 System had a power of discrimination (PD) ranging from 0.7839 to 0.9852 and a power of exclusion (PE) ranging from 0.2974 to 0.8099 for the 20 loci. No significant deviation from Hardy-Weinberg expectations was found for all the loci except for D5S818. This southern Chinese Han population had significant differences in the allele frequencies from 8 ethnic groups reported in China, and showed significant differences at 8 to 20 STR foci from 5 foreign populations. The allele frequency at the locus D1S1656 in this southern Chinese Han population differed significantly from those in the 5 foreign populations and from 3 reported Han populations in Beijing, Zhejiang Province and Fujian Province of China. The neighbor-joining phylogenetictree showed clustering of all the Asian populations in one branch, while the northern Italian and Argentina populations clustered in a separate branch. This southern Chinese Han population had the nearest affinity with the Yi ethnic population in Yunnan Province of China. The 20 STR loci are highly polymorphic in this southern Chinese Han population, suggesting the value of this set of STR loci in forensic personal identification, paternity testing and anthropological study.

Evidence for Inbreeding and Genetic Differentiation among Geographic Populations of the Saprophytic Mushroom Trogia venenata from Southwestern China.

During the past 40 years, more than 400 Sudden Unexplained Deaths (SUDs) have occurred in Yunnan, southwestern China. Epidemiological and toxicological analyses suggested that a newly discovered mushroom called Trogia venenata was the leading culprit for SUDs. At present, relatively little is known about the genetics and natural history of this mushroom. In this study, we analyzed the sequence variation at four DNA fragments among 232 fruiting bodies of T. venenata collected from seven locations. Our ITS sequence analyses confirmed that all the isolates belonged to the same species. The widespread presence of sequence heterozygosity within many strains at each of three protein-coding genes suggested that the fruiting bodies were diploid, dikaryotic or heterokaryotic. Within individual geographic populations, we found significant deviations of genotype frequencies from Hardy-Weinberg expectations, with the overall observed heterozygosity lower than that expected under random mating, consistent with prevalent inbreeding within local populations. The geographic populations were overall genetically differentiated. Interestingly, while a positive correlation was found between population genetic distance and geographic distance, there was little correlation between genetic distance and barium concentration difference for the geographic populations. Our results suggest frequent inbreeding, geographic structuring, and limited gene flow among geographic populations of T. venenata from southwestern China.

When two oceans meet: regional population genetics of an exploited coastal shark, Mustelus mustelus

Table S1 Summary of genetic diversity estimates at 12 microsatellite loci in eight Mustelus mustelus sampling sites in southern Africa. Number of alleles per locus (AN); allelic richness (AR); observed heterozygosity (HO); expected heterozygosity (HE); polymorphic information content (PIC); inbreeding coefficient (FIS) with statistically significant deviations from Hardy-Weinberg expectations indicated by * (P < 0.01) and ** (P < 0.001); null allele frequency (FrNULL) with b indicating the presence of null alleles at statistical significance at the 5% nominal level.

Low Major Histocompatibility Complex Class II Variation in the Endangered Indo-Pacific Humpback Dolphin (Sousa chinensis): Inferences About the Role of Balancing Selection.

It has been widely reported that the major histocompatibility complex (MHC) is under balancing selection due to its immune function across terrestrial and aquatic mammals. The comprehensive studies at MHC and other neutral loci could give us a synthetic evaluation about the major force determining genetic diversity of species. Previously, a low level of genetic diversity has been reported among the Indo-Pacific humpback dolphin (Sousa chinensis) in the Pearl River Estuary (PRE) using both mitochondrial marker and microsatellite loci. Here, the expression and sequence polymorphism of 2 MHC class II genes (DQB and DRB) in 32 S. chinensis from PRE collected between 2003 and 2011 were investigated. High ratios of non-synonymous to synonymous substitution rates, codon-based selection analysis, and trans-species polymorphism (TSP) support the hypothesis that balancing selection acted on S. chinensis MHC sequences. However, only 2 haplotypes were detected at either DQB or DRB loci. Moreover, the lack of deviation from the Hardy-Weinberg expectation at DRB locus combined with the relatively low heterozygosity at both DQB locus and microsatellite loci suggested that balancing selection might not be sufficient, which further suggested that genetic drift associated with historical bottlenecks was not mitigated by balancing selection in terms of the loss of MHC and neutral variation in S. chinensis. The combined results highlighted the importance of maintaining the genetic diversity of the endangered S. chinensis.

Characterization of novel polymorphic genomic microsatellite markers of Boehmeria tricuspis (Hance) Makino.

In the present study, 59 polymorphic microsatellite loci of Boehmeria tricuspis (Hance) Makino were developed from the specific length amplified fragment sequencing data library of genome. The number of alleles per locus ranged from two to five, and the observed and expected heterozygosities ranged from 0.0000 to 1.0000 and from 0.0769 to 0.6751, respectively. Among the 59 loci, 25 displayed significant deviations from Hardy-Weinberg expectations (P < 0.05). The developed simple sequence repeat markers should be useful for studying population genetics in B. tricuspis (Hance) Makino, for providing further knowledge on its population differentiation, breeding system, and dispersal ability, as well as quantitative trait locus mapping. These markers could also be valuable genetic resources for closely related species.

Forensic parameters of the Powerplex® 21 system (Promega Corp.) in mestizo populations from the West of Mexico

IntroductionMicrosatellites or short tandem repeats (STR) are the markers of choice in human identification. For this purpose, they must be analyzed in populations. This task has been scarcely performed for new generation human identification systems, which is critical in Mexican mestizo populations, because a significant genetic structure has been demonstrated due to admixture differences. ObjectiveTo validate the system in mestizo populations from the west region of Mexico. MethodsA total of 374 unrelated Mexican-mestizos from the west region were analyzed with the Powerplex® 21 system. Genetic data were analyzed using different softwares and including additional related populations for comparison purposes. Results and conclusionsWe estimated allele frequencies, and genotype distribution of all markers was in agreement with Hardy-Weinberg expectations; the linkage disequilibrium test discarded association between all pair of loci. The following forensic parameters were estimated: power of discrimination (PD), power of exclusion (PE), heterozygosity (Het), polymorphism information content (PIC), and typical paternity index (PI); its combined power of discrimination and exclusion was –100% and 99.999999473%, respectively. This constitutes an important increment with respect to typical 15 STR systems for the same population/region. This report validates the Powerplex® 21 system in western Mexican-mestizos for confident interpretation of DNA profiles in forensic cases and paternity testing. Sistema Powerplex® 21; México; Identificación humana; Poblaciones.

Forensic performance of Investigator DIPplex indels genotyping kit in native, immigrant, and admixed populations in South Africa.

The utilization of binary markers in human individual identification is gaining ground in forensic genetics. We analyzed the polymorphisms from the first commercial indel kit Investigator DIPplex (Qiagen) in 512 individuals from Afrikaner, Indian, admixed Cape Colored, and the native Bantu Xhosa and Zulu origin in South Africa and evaluated forensic and population genetics parameters for their forensic application in South Africa. The levels of genetic diversity in population and forensic parameters in South Africa are similar to other published data, with lower diversity values for the native Bantu. Departures from Hardy-Weinberg expectations were observed in HLD97 in Indians, Admixed and Bantus, along with 6.83% null homozygotes in the Bantu populations. Sequencing of the flanking regions showed a previously reported transition G>A in rs17245568. Strong population structure was detected with Fst, AMOVA, and the Bayesian unsupervised clustering method in STRUCTURE. Therefore we evaluated the efficiency of individual assignments to population groups using the ancestral membership proportions from STRUCTURE and the Bayesian classification algorithm in Snipper App Suite. Both methods showed low cross-assignment error (0-4%) between Bantus and either Afrikaners or Indians. The differentiation between populations seems to be driven by four loci under positive selection pressure. Based on these results, we draw recommendations for the application of this kit in SA.

Fcγ receptor polymorphisms in patients with transient hypogammaglobulinemia of infancy presenting with mild and severe infections.

Patients with transient hypogammaglobulinaemia of infancy (THI) may have mild infections or be asymptomatic. About 20% of THI patients have very severe and recurrent infections and receive intravenous immunoglobulins (IVIg) for replacement therapy and infection prophylaxis. It is still not clear why some THI patients are severely symptomatic; it has been suggested that there might be additional immunologic or environmental factors or other co-morbidities. As an immunological factor, Fcγ receptor polymorphisms (H/H-131, H/R-131 and R/R-131 for FcγIIa; V/V-158, V/F-158 and F/F-158 for FcγRIIIa; NA1/NA1, NA1/NA2 and NA2/NA2 for FcγRIIIb) were analysed in THI patients who had very severe infections and need hospitalisation (treated with IVIg) (n:18) and in THI patients who were asymptomatic or had mild infections (treated with antibiotics or received no medication) (n:25). Genotypic distributions between two groups did not deviate significantly from the Hardy-Weinberg equilibrium expectations (p > 0.05) and odds ratios for "disease risk estimate" did not show any dominance for any genotype. Allele frequencies did not show any significant difference between the two groups (p >0.05). The number of infections per year for each Fcγ receptor genotype was not significantly different between both groups. There is no association between the heterogeneous clinical picture of THI patients and Fcγ receptor gene polymorphisms.

Analysis of 30 insertion-deletion polymorphisms in the Japanese population using the Investigator DIPplex® kit.

Allele frequencies and forensic parameters for 30 insertion-deletion polymorphisms (INDELs) were investigated in a sample of 251 unrelated Japanese individuals using the Investigator DIPplex® kit (QIAGEN). The frequency distributions showed no deviations from Hardy-Weinberg equilibrium expectations. The combined powers of discrimination and match probability for the 30 INDELs were 0.9999999998 and 2.67×10(-11), respectively. To assess the effectiveness of the kit in typing degraded DNA, an ancient bone sample of a Jomon skeleton was analyzed; most of 30 INDELs and amelogenin were typed successfully. We concluded that the kit offers considerable potential for personal identification from degraded DNA samples due to the small amplicon length and high degree of polymorphisms.

Highly efficient identification of thousands of microsatellite loci in the pearl oyster (Pinctada martensii) from RNA-Seq

High-throughput RNA-Seq affords a cost and time effective means of obtaining large numbers of genetic markers for aquatic genomics. Here, we present thousands of novel microsatellite loci developed for the pearl oyster, Pinctada martensii from the Illumina HiSeq™ 2000 library of the pearl sac. Free user-friendly bioinformatics tools were employed to screen for microsatellite loci and design appropriate primers in 102,762 unigenes with 7216 microsatellite loci identified in total, 4862 of which had flanking sequences suitable for polymerase chain reaction primer design. The 50 randomly chosen primer pairs were tested in two populations of pearl oyster (base population (POP1) and selected population (POP2), with 30 individuals of each population). All the primer pairs were amplified successfully in two populations. All loci were polymorphic in POP1, while there were 3 loci showing monomorphism in POP2. In POP1 and POP2, observed heterozygosity from 0.033 to 1.000 and 0.000 to 1.000, 19 and 16 microsatellite loci deviated significantly from Hardy–Weinberg expectations including a Bonferroni correction (P < 0.001). Thirteen loci were highly informative content (PIC ≥ 0.5) in both populations. These identified loci will be useful for potential application for evolutionary, population genetic and chromosome linkage mapping research on pearl oyster.

Multiple Paternity and Preliminary Population Genetics of Giant Pacific Octopuses, Enteroctopus dofleini, in Oregon, Washington and the Southeast Coast of Vancouver Island, BC

A total of 77 giant Pacific octopus, Enteroctopus dofleini, tissue samples were collected from the Oregon Coast (OR), Neah Bay Washington (NB), Puget Sound Washington (PS) and the southeast coast of Vancouver Island, British Columbia, Canada (BC) for genetic analyses. A suite of eight variable microsatellite markers developed from giant Pacific octopuses were amplified in these samples to determine population diversity, structure, relatedness and paternity. The majority of loci met Hardy-Weinberg equilibrium expectations within each population. We found moderate genetic diversity (average observed heterozygosity = 0.445, range = 0.307–0.515 and average expected heterozygosity = 0.567, range = 0.506–0.696) and moderate population structuring with distinct separation of groups (FST values ranged from 0.101 between BC and PS to 0.237 between BC and NB). Several egg strings from the BC population were collected from three female octopus dens for relatedness and paternity analyses. Results suggest strong support for multiple paternity within one egg clutch with progeny sired by between two to four males.

Fine-scale genetic structure of Triatoma infestans in the Argentine Chaco

The patterns of genetic structure in natural populations provide essential information for the improvement of pest management strategies including those targeting arthropod vectors of human diseases. We analyzed the patterns of fine-scale genetic structure in Triatoma infestans in a well-defined rural area close to Pampa del Indio, in the Argentine Arid-Humid Chaco transition, where a longitudinal study on house infestation and wing geometric morphometry is being conducted since 2007. A total of 228 insects collected in 16 domestic and peridomestic sites from two rural communities was genotyped for 10 microsatellite loci and analyzed. We did not find departures from Hardy–Weinberg expectations in collection sites, with three exceptions probably due to null alleles and substructuring. Domestic sites were more variable than peridomestic sites suggesting the presence of older bug populations in domestic sites or higher effective population sizes. Significant genetic structure was detected using F-statistics, a discriminant analysis of principal components and Bayesian clustering algorithms in an area of only 6.32km2. Microsatellite markers detected population structuring at a finer geographic scale (180–6300m) than a previous study based on wing geometric morphometry (>4000m). The spatial distribution of genetic variability was more properly explained by a hierarchical island than by an isolation-by-distance model. This study illustrates that, despite more than a decade without vector control interventions enhancing differentiation, genetic structure can be detected in T. infestans populations, particularly applying spatial information. This supports the potential of genetic studies to provide key information for hypothesis testing of the origins of house reinfestation.

Gene dynamics of toll-like receptor 4 through a population bottleneck in an insular population of water voles (Arvicola amphibius)

Understanding the extent to which diversity at immunologically important genes is reduced by demographic perturbations such as population bottlenecks, and the resulting consequences this has on individual fitness, is of fundamental importance for the effective management of genetic resources in natural populations. Toll-like receptors are key immunological genes with well-established links to fitness. Here, levels of allelic diversity and heterozygosity at the toll-like receptor 4 locus (Tlr4) were characterised across 280 water voles (Arvicola amphibius) from an isolated, island population in north west Scotland that went through a severe population bottleneck between 2004 and 2006 that eroded neutral microsatellite variation. Two functional Tlr4 alleles were resolved prior to the population crash at frequencies close to parity and an excess of heterozygote genotypes relative to Hardy–Weinberg expectations. Through the population bottleneck both alleles were retained with genotype frequencies conforming to Hardy–Weinberg expectations. Tlr4 genotype was significantly associated with gamasid mite, flea (Megabothris walkeri) and sheep tick larva (Ixodes ricinus) burdens among individuals, suggesting a mechanism through which parasite mediated selection could affect Tlr4 diversity. The results are examined with recourse to the extent that they are consistent with the effects of genetic drift and balancing selection, and their significance is discussed in relation to identifying target genes that assay ecological and adaptively meaningful genetic variation in a conservation context.

Genetic and fitness consequences of interpopulation mating in Dianthus guliae Janka: conservation implications for severely depleted and isolated plant populations

Genetic constraints may increase the extinction risk in small and isolated plant populations. Introducing foreign genes may restore their genetic variability and fitness, but it could also be harmful, especially when recipient and donor populations have diverged. In such cases, data on genetic relationships and the possible consequences of different patterns of gene flow are essential for effective conservation. We examined five microsatellite loci to study the genetic relationships among three core populations and an isolated peripheral one of the threatened endemic Dianthus guliae Janka. This provided a base for further genetic analyses and experimental pollinations illustrating links between genetic richness and fitness, and the effects of inter-population mating in two contrasting populations (a large core vs. a small peripheral). Microsatellite loci did not show significant deviations from Hardy–Weinberg expectations. However, the peripheral population had lower heterozygosity, a higher inbreeding coefficient, and significant divergence from core units. Fitness and genetic data indicated an enhanced fitness, along with an improved capacity to rebound heterozygosity deficit after occasional selfing, in the core-population compared to the peripheral one. Crossing within-population did not enhance genetic diversity and fitness in the small peripheral unit, while between-population crossing improved its heterozygosity and fitness. Finally, in the study system, current genetic divergence did not preclude heterosis in the small and isolated population after mating with a larger donor unit.