Evidence Of Inbreeding Research Articles

Local Heterozygosity Effects on Nestling Growth and Condition in the Great Cormorant.

Under inbreeding, heterozygosity at neutral genetic markers is likely to reflect genome-wide heterozygosity and, thus, is expected to correlate with fitness. There is, however, growing evidence that some of heterozygosity-fitness correlations (HFCs) can be explained by ‘local effects’, where noncoding loci are at linkage disequilibrium with functional genes. The aim of this study was to investigate correlations between heterozygosity at seven microsatellite loci and two fitness-related traits, nestling growth rate and nutritional condition, in a recently bottlenecked population of great cormorant Phalacrocorax carbo sinensis. We found that heterozygosity was positively associated with both nestling traits at the between-brood level, but the individual (within-brood) effects of heterozygosity were non-significant. We also found that only one locus per trait was primarily responsible for the significant multi-locus HFCs, suggesting a linkage disequilibrium with non-identified functional loci. The results give support for ‘local effect’ hypothesis, confirming that HFCs may not only be interpreted as evidence of inbreeding and that genetic associations between functional and selectively neutral markers could be much more common in natural populations than previously thought.

Population genetic structure at the northern range limit of the threatened eastern hog-nosed snake (Heterodon platirhinos)

Habitat loss and fragmentation have important consequences for population persistence by reducing dispersal, connectivity, and population size. Characterizing patterns of population genetic structure and gene flow, and testing for the genetic signature of population declines and inbreeding can provide key insights into conservation for at-risk species. We use 12 microsatellite DNA markers to quantify the spatial structuring across two regional populations of the threatened eastern hog-nosed snake (Heterodon platirhinos) in Ontario, Canada. We further test for inbreeding and recent, rapid population declines, for the latter using both a ‘heterozygosity excess’ approach and Approximate Bayesian computation. Spatial Bayesian assignment tests revealed four distinct genetic clusters that were not apparent from species occurrence data, suggesting that the current designation of a single management unit for this species is invalid. We found some evidence for inbreeding in all studied locales. However, heterozygosity excess tests provided only weak evidence for recent bottlenecks and varied according to mutational model specified. In contrast, ABC provided strong support for a recent and rapid reduction in population size within one sample locale (Wasaga Beach), where individuals are largely confined to a small area circumscribed by expanding urban areas. For three other locales investigated, we found equal support for either recent rapid or gradual population declines. Immediate action is required for Wasaga Beach if this population is to persist.

Environmental requirements trump genetic factors in explaining narrow endemism in two imperiled Florida sunflowers

The mechanisms generating narrow endemism have long been of interest to biologists, with a variety of underlying causes proposed. This study investigates the origins of narrow endemism of two imperiled Florida endemics, Helianthus carnosus and Phoebanthus tenuifolius, in relation to a widespread sympatric close relative, Helianthus radula, as well as other members of the genus Helianthus. Using a combination of population genetics and environmental niche modeling, this study compares evidence in support of potential mechanisms underlying the origin of narrow endemism, including environmental specialization versus inbreeding, loss of diversity, or other predominantly genetic factors. The two narrow endemics were found to be comparable in genetic diversity to H. radula as well as other widespread Helianthus species, with little to no evidence of inbreeding. Environmental niche modeling indicates that distributions of both narrow endemics are strongly related to temperature and precipitation patterns, and that both endemics are threatened with severe reductions in habitat suitability under projected climate change. Evidence indicates that genetic factors likely are not the cause of narrow endemism in these species, suggesting that these species are likely ecological specialists and thus historical narrow endemics. This makes both species vulnerable to climate change, and of immediate conservation concern.

High molecular diversity in the true service tree (Sorbus domestica) despite rareness: data from Europe with special reference to the Austrian occurrence.

Sorbus domestica (Rosaceae) is one of the rarest deciduous tree species in Europe and is characterized by a scattered distribution. To date, no large-scale geographic studies on population genetics have been carried out. Therefore, the aims of this study were to infer levels of molecular diversity across the major part of the European distribution of S. domestica and to determine its population differentiation and structure. In addition, spatial genetic structure was examined together with the patterns of historic and recent gene flow between two adjacent populations. Leaf or cambium samples were collected from 17 populations covering major parts of the European native range from north-west France to south-east Bulgaria. Seven nuclear microsatellites and one chloroplast minisatellite were examined and analysed using a variety of methods. Allelic richness was unexpectedly high for both markers within populations (mean per locus: 3·868 for nSSR and 1·647 for chloroplast minisatellite). Moreover, there was no evidence of inbreeding (mean Fis = -0·047). The Italian Peninsula was characterized as a geographic region with comparatively high genetic diversity for both genomes. Overall population differentiation was moderate (FST = 0·138) and it was clear that populations formed three groups in Europe, namely France, Mediterranean/Balkan and Austria. Historic gene flow between two local Austrian populations was high and asymmetric, while recent gene flow seemed to be disrupted. It is concluded that molecular mechanisms such as self-incompatibility and high gene flow distances are responsible for the observed level of allelic richness as well as for population differentiation. However, human influence could have contributed to the present genetic pattern, especially in the Mediterranean region. Comparison of historic and recent gene flow may mirror the progress of habitat fragmentation in eastern Austria.

Conservation genetics and genetic mating system of the yellow-shouldered blackbird (Agelaius xanthomus), an endangered island endemic

The yellow-shouldered blackbird (Agelaius xanthomus) is a managed endemic species in Puerto Rico that experienced a bottleneck in the 1970s and currently faces high levels of brood parasitism and habitat loss. Little is known about its overall genetic profile and genetic mating system, which potentially shapes effective population size by contributing to variation in reproductive success. Here I used nine microsatellite loci to characterize the population genetics and mating system of a southwestern Puerto Rican population. Although the population showed no evidence of inbreeding, it had significantly lower allelic diversity, effective population size, and expected heterozygosity than both island and continental populations of the related red-winged blackbird (A. phoeniceus). In particular, the low effective population size of the yellow-shouldered blackbird (~71, 18 % of the 2012 census size) raises concerns about its long-term viability. Paternity tests on 30 nests provided the first evidence of genetic polyandry in this species. Of all young, 23 % were extra-pair (sired by a male other than the social father), and 37 % of nests contained extra-pair young, which does not differ from proportions observed in red-winged blackbirds. Extra-pair paternity was not found to contribute significantly to variation in individual reproductive output, suggesting the bottleneck is more likely to have contributed to the current population genetic profile than the species’ mating system. Together, these data suggest that while genetic diversity on the individual level may be intact, the population as a whole remains vulnerable to adverse stochastic events and loss of evolutionary potential.

Genetic Diversity of White Sharks, Carcharodon carcharias, in the Northwest Atlantic and Southern Africa.

The white shark, Carcharodon carcharias, is both one of the largest apex predators in the world and among the most heavily protected marine fish. Population genetic diversity is in part shaped by recent demographic history and can thus provide information complementary to more traditional population assessments, which are difficult to obtain for white sharks and have at times been controversial. Here, we use the mitochondrial control region and 14 nuclear-encoded microsatellite loci to assess white shark genetic diversity in 2 regions: the Northwest Atlantic (NWA, N = 35) and southern Africa (SA, N = 131). We find that these 2 regions harbor genetically distinct white shark populations (Φ ST = 0.10, P < 0.00001; microsatellite F ST = 0.1057, P < 0.021). M-ratios were low and indicative of a genetic bottleneck in the NWA (M-ratio = 0.71, P < 0.004) but not SA (M-ratio = 0.85, P = 0.39). This is consistent with other evidence showing a steep population decline occurring in the mid to late 20th century in the NWA, whereas the SA population appears to have been relatively stable. Estimates of effective population size ranged from 22.6 to 66.3 (NWA) and 188 to 1998.3 (SA) and evidence of inbreeding was found (primarily in NWA). Overall, our findings indicate that white population dynamics within NWA and SA are determined more by intrinsic reproduction than immigration and there is genetic evidence of a population decline in the NWA, further justifying the strong domestic protective measures that have been taken for this species in this region. Our study also highlights how assessment of genetic diversity can complement other sources of information to better understand the status of threatened marine fish populations.

Harbor porpoise Phocoena phocoena strandings on the Dutch coast: No genetic structure, but evidence of inbreeding

Conservation management in the North Sea is often motivated by the population size of marine mammals, like harbor porpoises Phocoena phocoena. In the Dutch part of the North Sea, sighting and stranding data are used to estimate population sizes, but these data give little insight into genetic structuring of the population. In this study we investigated genetic structure among animals stranded at different locations and times of year. We also tested whether there is a link between stranding and necropsy data, and genetic diversity. We made use of both mitochondrial (mtDNA) and microsatellite DNA analysis of samples from dead stranded porpoises along the Dutch coast during 2007. mtDNA analysis showed 6 variable positions in the control region, defining 3 different haplotypes. mtDNA haplotypes were not randomly distributed along the Dutch coastline. However, microsatellite analysis showed that these mtDNA haplotypes did not represent separate groups on a nuclear level. Furthermore, microsatellite analysis revealed no genotypic differences between seasons, locations or genders. The results of this study indicate that the Dutch population is panmictic. In contrast, heterozygosity levels were low, indicating some level of inbreeding in this population. However, this was not corroborated by other indices of inbreeding. This research provided insight into genetic structuring of stranded porpoises in 2007, but data from multiple years should be included to be able to help estimate population sizes.

Towards a more holistic research approach to plant conservation: the case of rare plants on oceanic islands.

Research dedicated to rare endemic plants is usually focused on one given aspect. However, holistic studies, addressing several key issues, might be more useful, supporting management programmes while unravelling basic knowledge about ecological and population-level processes. A more comprehensive approach to research is proposed, encompassing: phylogenetics/systematics, pollination biology and seed dispersal, propagation, population genetics, species distribution models (SDMs), threats and monitoring. We present a holistic study dedicated to Veronica dabneyi Hochst. ex Seub., an endangered chamaephyte endemic to the Azores. Veronica dabneyi was mainly found associated with other endemic taxa; however, invasive plants were also present and together with introduced cattle, goats and rabbits are a major threat. Most populations grow at somewhat rocky and steep locations that appeared to work as refuges. Seed set in the wild was generally high and recruitment of young plants from seed seemed to be frequent. In the laboratory, it was possible to germinate and fully develop V. dabneyi seedlings, which were planted at their site of origin. No dormancy was detected and time for 50 % germination was affected by incubation temperature. Eight new microsatellite markers were applied to 72 individuals from 7 sites. A considerable degree of admixture was found between samples from the two islands Flores and Corvo, with 98 % of the genetic variability allocated within populations. Levels of heterozygosity were high and no evidence of inbreeding was found. Species distribution models based on climatic and topographic variables allowed the estimation of the potential distribution of V. dabneyi on Flores and Corvo using ecological niche factor analysis and Maxent. The inclusion of land-use variables only slightly increased the information explained by the models. Projection of the expected habitat in Faial largely coincided with the only historic record of V. dabneyi on that island. This research could be the basis for the design of a recovery plan, showing the pertinence of more holistic research approaches to plant conservation.

Microsatellite assessment of walrus (&lt;i&gt;Odobenus rosmarus rosmarus&lt;/i&gt;) stocks in Canada

Walruses in Canada are currently subdivided into seven stocks based on summering areas; Western Jones Sound (WJS), Baffin Bay (BB), Penny Strait-Lancaster Sound (PS-LS), North Foxe Basin (N-FB), Central Foxe Basin (C-FB), Hudson Bay Davis Strait (HB-DS) and Southern and Eastern Hudson Bay (SE-HB). In this study, walrus were sampled from six of the seven stocks (SE-HB samples were not available) and genotyped at 10 microsatellite loci. All stocks were genetically diverse (average heterozygosity of 0.58) with no evidence of inbreeding (average FIS of 0.03). We detected significant genetic differentiation among the stocks and a pattern of genetic spatial autocorrelation that suggests a moderate effect of geographic distance on gene flow among stocks. Bayesian clustering suggested the six recognized stocks were elements of two larger genetic clusters - a northern Arctic population (containing BB, WJS, and PS-LS stocks) and a central Arctic population (containing C-FB, N-FB, and HB-DS stocks). These populations are moderately differentiated (FST = 0.07), but based on evidence of contemporary movement from assignment tests, are not completely isolated. There was support for maintaining the WJS stock and a combined BB+PS-LS stock, although the latter conclusion is based on a small sample size. Similarly, there was some evidence suggesting separation of the Foxe Basin stocks from the HB-DS but not the N-FB from the C-FB stock. However, given that there are morphological and chemical differences between N-FB and C-FB stocks, there is currently insufficient evidence to support a revision of the current stock designations.

Population genetics of bisexual and unisexual populations of the scaly-winged bark louse Echmepteryx hageni (Insecta: Psocoptera).

The scaly-winged bark louse, Echmepteryx hageni, exhibits a unique pattern of co-existence of apparently differnt reproductive modes. Unisexuality is widespread in eastern North America, while sexual populations are restricted to isolated rock out-croppings in southern Illinois and eastern Kentucky. Three of the four nuclear loci examined show greater genetic diversity in the unisexual form compared to the sexual form of E. hageni, in accordance with the pattern previously shown in mitochondrial genetic data. Neutrality tests of the nuclear loci indicate a consistent signal of demographic expansion in asexual populations, but not in sexual populations. There was evidence of inbreeding in the isolated sexual populations at three of the nuclear loci, and one locus had signs of gene specific balancing selection. However, there is no significant genetic differentiation between bisexual and unisexual populations, possibly due to the greater effective population size of nuclear loci relative to mitochondrial loci. The mitochondrial differentiation of E. hageni populations in the northwestern part of their range (Minnesota and Wisconsin) was also not reflected in the nuclear data. We present three hypotheses that may explain the disparity in observed nuclear and mitochondrial genetic diversity between the reproductive forms of E. hageni.

A viable population of the European red squirrel in an urban park.

Whether urban parks can maintain viable and self-sustaining populations over the long term is questionable. In highly urbanized landscapes, urban parks could play a role in biodiversity conservation by providing habitat and resources to native species. However, populations inhabiting urban parks are usually small and isolated, leading to increased demographic stochasticity and genetic drift, with expected negative consequences on their viability. Here, we investigated a European red squirrel population located in an urban park close to Paris, France (Parc de Sceaux; 184 ha) to assess its viability. Using mitochondrial D-loop sequences and 13 microsatellite loci, we showed that the population presented high levels of genetic variation and no evidence of inbreeding. The size of the population was estimated at 100–120 individuals based on the comparison of two census techniques, Distance Sampling and Capture-Mark-Recapture. The estimated heterozygosity level and population size were integrated in a Population Viability Analysis to project the likelihood of the population's persistence over time. Results indicate that the red squirrel population of this urban park can be viable on the long term (i.e. 20 years) for a range of realistic demographic parameters (juvenile survival at least >40%) and immigration rates (at least one immigration event every two years). This study highlights that urban parks can be potential suitable refuges for the red squirrel, a locally threatened species across western European countries, provided that ecological corridors are maintained.

Population genetics of Formica aquilonia wood ants in Scotland: the effects of long-term forest fragmentation and recent reforestation

Formica aquilonia wood ants are forest specialists which play a key role in the ecology of forests in Europe. Many of the Scottish populations at the edge of the species distribution range occur in highly fragmented landscapes. We used ten microsatellite loci to study the genetic diversity and structure of populations from two contrasting regions (Inverpolly and the Trossachs) to set the Scottish populations in the context of conspecific populations in mainland Europe. Historically, both study regions have experienced extreme habitat loss and fragmentation over several centuries. Inverpolly has remained fragmented whereas large scale reforestation over the last century has greatly increased the forested area in the Trossachs. Despite the long history of fragmentation, genetic diversity in the Scottish populations was greater than in the populations in mainland Europe. Genetic diversity was similar in the two Scottish regions and no evidence of inbreeding was detected. However, the populations in Inverpolly showed more evidence of genetic bottlenecks, possibly due to more frequent stochastic events such as moorland fires. The ant populations in individual forests were genetically distinct and we detected no contemporary gene flow between forests. The most intensively studied forest where non-native conifer plantations now occupy the matrix between the remaining ancient woodland fragments showed evidence that admixture and gene flow between nests was reducing the past differentiation. This may reflect a dynamic response to the reconnection of previously isolated populations in forest fragments by recent reforestation.

Patterns of pollen dispersal in a small population of the Canarian endemic palm (Phoenix canariensis)

The genetic diversity of small populations is greatly influenced by local dispersal patterns and genetic connectivity among populations, with pollen dispersal being the major component of gene flow in many plants species. Patterns of pollen dispersal, mating system parameters and spatial genetic structure were investigated in a small isolated population of the emblematic palm Phoenix canariensis in Gran Canaria island (Canary Islands). All adult palms present in the study population (n=182), as well as 616 seeds collected from 22 female palms, were mapped and genotyped at 8 microsatellite loci. Mating system analysis revealed an average of 5.8 effective pollen donors (Nep) per female. There was strong variation in correlated paternity rates across maternal progenies (ranging from null to 0.9) that could not be explained by the location and density of local males around focal females. Paternity analysis revealed a mean effective pollen dispersal distance of ∼71 m, with ∼70% of effective pollen originating from a distance of <75 m, and 90% from <200 m. A spatially explicit mating model indicated a leptokurtic pollen dispersal kernel, significant pollen immigration (12%) from external palm groves and a directional pollen dispersal pattern that seems consistent with local altitudinal air movement. No evidence of inbreeding or genetic diversity erosion was found, but spatial genetic structure was detected in the small palm population. Overall, the results suggest substantial pollen dispersal over the studied population, genetic connectivity among different palm groves and some resilience to neutral genetic erosion and subsequently to fragmentation.

Evidence of Recessive Alzheimer Disease Loci in a Caribbean Hispanic Data Set

IMPORTANCE The search for novel Alzheimer disease (AD) genes or pathologic mutations within known AD loci is ongoing. The development of array technologies has helped to identify rare recessive mutations among long runs of homozygosity (ROHs), in which both parental alleles are identical. Caribbean Hispanics are known to have an elevated risk for AD and tend to have large families with evidence of inbreeding. OBJECTIVE To test the hypothesis that the late-onset AD in a Caribbean Hispanic population might be explained in part by the homozygosity of unknown loci that could harbor recessive AD risk haplotypes or pathologic mutations. DESIGN We used genome-wide array data to identify ROHs (&gt;1 megabase) and conducted global burden and locus-specific ROH analyses. SETTING A whole-genome case-control ROH study. PARTICIPANTS A Caribbean Hispanic data set of 547 unrelated cases (48.8% with familial AD) and 542 controls collected from a population known to have a 3-fold higher risk of AD vs non-Hispanics in the same community. Based on a Structure program analysis, our data set consisted of African Hispanic (207 cases and 192 controls) and European Hispanic (329 cases and 326 controls) participants. EXPOSURE Alzheimer disease risk genes. MAIN OUTCOMES AND MEASURES We calculated the total and mean lengths of the ROHs per sample. Global burden measurements among autosomal chromosomes were investigated in cases vs controls. Pools of overlapping ROH segments (consensus regions) were identified, and the case to control ratio was calculated for each consensus region. We formulated the tested hypothesis before data collection. RESULTS In total, we identified 17 137 autosomal regions with ROHs. The mean length of the ROH per person was significantly greater in cases vs controls (P = .0039), and this association was stronger with familial AD (P = .0005). Among the European Hispanics, a consensus region at the EXOC4 locus was significantly associated with AD even after correction for multiple testing (empirical P value 1 [EMP1], .0001; EMP2, .002; 21 AD cases vs 2 controls). Among the African Hispanic subset, the most significant but nominal association was observed for CTNNA3, a well-known AD gene candidate (EMP1, .002; 10 AD cases vs 0 controls). CONCLUSIONS AND RELEVANCE Our results show that ROHs could significantly contribute to the etiology of AD. Future studies would require the analysis of larger, relatively inbred data sets that might reveal novel recessive AD genes. The next step is to conduct sequencing of top significant loci in a subset of samples with overlapping ROHs.

Population Decline in a Long-Lived Species: The Wood Turtle in Michigan

Abstract: Populations of Wood Turtles, Glyptemys insculpta, have steadily decreased over the past 30 yr because of habitat destruction and degradation. We sampled Wood Turtles from three areas in Michigan, USA, to characterize populations, quantify demographic trends, and measure the effect of declining population size on genetic diversity. Wood Turtle samples (n = 68) were collected from three rivers in the Lower Peninsula of Michigan and analyzed at nine microsatellite loci. Bayesian clustering programs identified two populations that split the three sampling sites into North and South populations. In both populations, analysis of genealogies estimated r < 0, indicating population decline. However, no evidence of a bottleneck was detected (P = 0.30 North, P = 0.29 South), and little evidence of inbreeding was observed (average North FIS = 0.25, average South FIS = 0.23), relative to other Emydidae populations. The high genetic diversity observed in the North and South populations is likely due to immigr...

Genetic diversity and gene flow in Zostera marina populations surrounding Long Island, New York, USA: No evidence of inbreeding, genetic degradation or population isolation

Since the 1930s, eelgrass around Long Island, New York, USA, has experienced significant ecological and anthropogenic disturbances reducing areal coverage of the species. Patchiness, low density or isolation of these remaining populations increase susceptibility of this aquatic angiosperm to extinction. The loss of genetic diversity and patch connectivity, may contribute to lower fitness of eelgrass thus affecting recovery potential. Previous studies of eelgrass populations around Long Island report genetically isolated populations with low diversity. In contrast, this study found neither the evidence of inbreeding nor indications of genetic degradation for the same populations. Measures of genetic diversity such as average alleles (A=7.59) and fixation index (F=0.02) suggest no significant impediments to genetic connectivity among populations sampled. Gene flow (Nm=4.58) and bottleneck analyses suggest the major disturbances of the past have not strongly affected population structure in the Long Island system. These findings have significant implications for both management and restoration. Locally, eelgrass populations in Long Island waters are unlikely to decline through genetic erosion or inbreeding processes alone. Plants from within these populations possess adequate genetic diversity to undertake restoration activities. On a larger geographic scale, the ability of these plants to maintain such high levels of genetic diversity and connectivity despite the significant areal losses historically provides optimism for the recovery potential of this species despite recent global losses.

GENETIC VARIATION IN THE AFRICAN VLEI RAT OTOMYS IRRORATUS (MURIDAE: OTOMYINAE)

ABSTRACT Starch gel electrophoresis was used to analyse genetic variation at 24 enzyme and protein loci in 12 South African populations of vlei rats Otomys irroratus. Mean heterozygosity ([Hbar]: 0.071) was relatively high for a mammal. Allelic variation within populations conformed to Hardy-Weinberg expectations, and the mean value for Wright's F IS statistic (0.048) indicated no evidence of inbreeding within populations. There was significant local differentiation in allelic frequencies (Wright's F ST = 0.375). However, genetic distances between populations were low (mean for Nei's D = 0.034), and cluster analysis of genetic distances failed to identify groups consistent with geographical position or karyotypic differences between populations. A single population (Hogsback, eastern Cape), bearing a chromosomal tandem fusion and demonstrating a high measure of reproductive isolation, showed no allozymic differences from other populations, suggesting that chromosomally-mediated speciation may precede phen...

Genetic Diversity among Island and Mainland Populations of the California Trapdoor SpiderBothriocyrtum californicum(Araneae, Ctenizidae)

Trapdoor spiders (Bothriocyrtum californicum) from nine southern California sites, including three on Santa Catalina and Santa Cruz Islands, were compared, based on variation at nine allozyme loci. Populations were generally in Hardy-Weinberg equilibrium, with no evidence of inbreeding. Levels of genetic variability in the six mainland populations were relatively high (mean Ho = 10.8%, mean P = 42.6%), while it was reduced (Ho < 2.0%, P < 23.0%) in two of three island populations, consistent with the loss of variability usually associated with island colonization. Genotype frequency distributions indicated a recent reduction in effective population size for spiders from Webb School of California, perhaps a consequence of habitat destruction associated with school construction in 1920–1930. Interpopulation differentiation was generally substantial and did not bear a simple relationship to physical distance. These findings suggest that, while B. californicum populations generally possess ample levels of genetic variability relative to other invertebrates, bottlenecks do occur, and populations are usually genetically isolated. To foster preservation of the existing gene pool, management of B. californicum should focus on maintaining as many populations in situ as possible and facilitating connections between them, while also creating or restoring habitat for potential colonization.

The importance of population genetic information in formulatingex situconservation strategies for the freshwater pearl mussel (Margaritifera margaritiferaL.) inNorthernIreland

AbstractCaptive breeding is the last resort to protect a species that will become extinct because it is incapable of surviving in the wild without human intervention. The freshwater pearl musselMargaritifera margaritiferais a prime candidate for such action: the species has experienced a recent range‐wide decline, particularly inEurope. InNorthernIreland,M. margaritiferais now only found in six rivers and, because of a lack of natural recruitment in the wild, it has been predicted that these populations will become extinct within 80 years. Consequently, anex situbreeding program was established with the aim of using a semi‐natural method to propagate mussels for restocking. In the present study, we analysed the levels and patterns of genetic diversity in the captive‐bred mussels, as well as their parent broodstock and remnant populations from their natal and other rivers inNorthernIreland whereM. margaritiferais still found, to help develop best practice for the captive breeding program. Levels of genetic diversity were high, although there was a strong correlation between genetic diversity and census population sizes, as well as evidence of inbreeding in all populations. Small but significant levels of genetic differentiation were observed between both the captive‐bred juveniles and their parent broodstock, and the samples from their source river, indicating a possible founder effect. In addition, three groups of genetically distinct clusters were observed among the remaining natural populations that could be used as the basis for defining conservation units. These findings allow us to make recommendations for efficient management of the captive breeding program, including rotation of theex situbroodstock on a regular basis to avoid prolonged inbreeding, and the establishment of captive breeding of other populations to reflect genetic differences between putative conservation units inNorthernIreland and elsewhere.

Development of robust genomic simple sequence repeat markers for estimation of genetic diversity within and among bulb onion (Allium cepa L.) populations

Improved understanding of genetic diversity in onion and shallot (Allium cepa L.) is required to inform breeding and genetic resource conservation, and to enable development of association genetics and seed quality assurance methods. To develop quantitative estimates of diversity we estimated within- and among-population heterozygosity in a set of onion populations using genomic simple sequence repeat (SSR) markers developed by genomic skim sequencing. Primer sets (166) designed to flank SSR motifs identified were evaluated in a diverse set of lines, with 80 (48 %) being polymorphic. The 20 most robust single copy markers were scored in 12 individuals from 24 populations representing short-day to long-day adapted material from diverse environments. The average genetic diversity estimate (He) per population was 0.3 (SD 0.08) and the average per marker was 0.49 (SD 0.2). The onion populations assessed in this survey were distinct with moderate to large population differentiation but also had high within-population variation (Fst = 0.26). There was evidence of inbreeding (Fis = 0.22) with observed heterozygosities lower than the expected. This marker resource will be applicable for DNA fingerprinting, measuring levels of inbreeding in breeding lines, assessing population structure for association mapping and expanding linkage maps that are principally based on expressed sequence tag-based markers. A Galaxy workflow was developed to facilitate bulk SSR marker design from next-generation sequence data. This study provides one of the first quantitative views of population genetic variation in onion and a practical toolset for further genetics.