Maintenance Of Genetic Diversity Research Articles

Characterization of the USDA Cucurbita pepo, C. moschata, and C. maxima germplasm collections.

The Cucurbita genus is home to a number of economically and culturally important species. We present the analysis of genotype data generated through genotyping-by-sequencing of the USDA germplasm collections of Cucurbita pepo, C. moschata, and C. maxima. These collections include a mixture of wild, landrace, and cultivated specimens from all over the world. Roughly 1,500 - 32,000 high-quality single nucleotide polymorphisms (SNPs) were called in each of the collections, which ranged in size from 314 to 829 accessions. Genomic analyses were conducted to characterize the diversity in each of the species. Analysis revealed extensive structure corresponding to a combination of geographical origin and morphotype/market class. Genome-wide associate studies (GWAS) were conducted using both historical and contemporary data. Signals were observed for several traits, but the strongest was for the bush (Bu) gene in C. pepo. Analysis of genomic heritability, together with population structure and GWAS results, was used to demonstrate a close alignment of seed size in C. pepo, maturity in C. moschata, and plant habit in C. maxima with genetic subgroups. These data represent a large, valuable collection of sequenced Cucurbita that can be used to direct the maintenance of genetic diversity, for developing breeding resources, and to help prioritize whole-genome re-sequencing.

Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola.

Klebsiella variicola is an emergent human pathogen causing diverse infections, some of which in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like (rough and dry) morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene (nac) or the type III fimbriae regulator, mrkH, suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of MrkH loss-of-function which reduces type 3 fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clones show that mutations in mrkH provide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and can socially exploit wild type strains. An exhaustive search for mrkH mutants in public databases revealed that ca 8% of natural isolates analysed had a truncated mrkH gene many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were rarely hypermucoid and often isolated from human, mostly from urine and blood. The decreased aggregation of these mutants could have important clinical implications as we hypothesize that such clones could better disperse within the host allowing colonisation of other body sites and potentially leading to systemic infections.

AUTOECOLOGIA, DIVERSIDADE E ESTRUTURA GENÉTICA INTERNA DE Ocotea porosa (NEES & MART.) BARROSO: SUBSÍDIOS PARA A COLETA DE SEMENTES

ABSTRACT Ecological restoration mitigates the negative effects of fragmentation and habitat loss. This practice allows the conservation of key species, such as Ocotea porosa, a tree native to the Araucaria Forest and extremely endangered. A key point in restoration projects is the source of seeds, as well as guidelines for collection. When carried out under technical criteria, the collection allows the maintenance of genetic diversity and adaptive potential in restoration plantations. Given the importance of seed source, genetic diversity, and adaptive potential, this study aimed to define areas and criteria for collecting seeds by characterizing the demography, genetics, and reproductive phenology of an O. porosa population. A plot of 16 hectares was installed in the municipality of Passos Maia, Santa Catarina, Brazil, and a demographic survey of trees with diameter at breast height (DBH) > 15 cm was carried out. Indices of diversity and internal genetic structure (IGS) were estimated using allozyme markers. The reproductive phenology of 67 individuals was evaluated during 8 months. The studied population showed a high density of individuals (10.7 ind. ha-1) with normal diametric distribution. The phenological pattern of the species is regular, seasonal, and annual. The evaluated population showed high genetic diversity, high fixation index, and significant IGS up to 80 meters away. Based on these results, the evaluated fragment can be used as a seed collection area. It has high genetic diversity, density, and area size sufficient to contain several demes. In addition, it is highly recommended that the matrices be at least 80 meters apart to avoid the effects of significant IGS.

Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing.

The common marmoset ( Callithrix jacchus) has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies. Epileptic marmosets have been independently reported in two Asian primate research centers. Nevertheless, the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated. Here, we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing. We identified 14 558 184 single nucleotide polymorphisms (SNPs) from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples. Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers. In addition, SNP and copy number variation (CNV) analyses suggested that the WW domain-containing oxidoreductase ( WWOX) and Tyrosine-protein phosphatase nonreceptor type 21 ( PTPN21) genes may be associated with epilepsy in marmosets. Notably, KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets. This study provides valuable population genomic resources for marmosets in two Asian primate centers. Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers, while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.

Genetic slippage after sex maintains diversity for parasite resistance in a natural host population.

Although parasite-mediated selection is a major driver of host evolution, its influence on genetic variation for parasite resistance is not yet well understood. We monitored resistance in a large population of the planktonic crustacean Daphnia magna over 8 years, as it underwent yearly epidemics of the bacterial pathogen Pasteuria ramosa. We observed cyclic dynamics of resistance: Resistance increased throughout the epidemics, but susceptibility was restored each spring when hosts hatched from sexual resting stages. Host resting stages collected across the year showed that largely resistant host populations can produce susceptible sexual offspring. A genetic model of resistance developed for this host-parasite system, based on multiple loci and strong epistasis, is in partial agreement with our findings. Our results reveal that, despite strong selection for resistance in a natural host population, genetic slippage after sexual reproduction can be a strong factor for the maintenance of genetic diversity of host resistance.

Oviposition behaviour in Drosophila melanogaster: Genetic and behavioural decoupling between oviposition acceptance and preference for natural fruits.

In phytophagous insects, oviposition behaviour is an important component of habitat selection and, given the multiplicity of genetic and environmental factors affecting its expression, is defined as a complex character resulting from the sum of interdependent traits. Here, we study two components of egg-laying behaviour: oviposition acceptance (OA) and oviposition preference (OP) in Drosophila melanogaster using three natural fruits as resources (grape, tomato and orange) by means of no-choice and two-choice experiments, respectively. This experimental design allowed us to show that the results obtained in two-choice assays (OP) cannot be accounted for by those resulting from no-choice assays (OA). Since the genomes of all lines used are completely sequenced, we perform a genome-wide association study to identify and characterize the genetic underpinnings of these oviposition behaviour traits. The analyses revealed different candidate genes affecting natural genetic variation of both OA and OP traits. Moreover, our results suggest behavioural and genetic decoupling between OA and OP and that egg-laying behaviour is plastic and context-dependent. Such independence in the genetic architectures of OA and OP variation may influence different aspects of oviposition behaviour, including plasticity, canalization, host shift and maintenance of genetic variability, which contributes to the adoption of adaptive strategies during habitat selection.

A diverse parasite pool can improve effectiveness of biological control constrained by genotype-by-genotype interactions.

The outcomes of biological control programs can be highly variable, with natural enemies often failing to establish or spread in pest populations. This variability has posed a major obstacle in use of the bacterial parasite Pasteuria penetrans for biological control of Meloidogyne species, economically devastating plant-parasitic nematodes for which there are limited management options. A leading hypothesis for this variability in control is that infection is successful only for specific combinations of bacterial and nematode genotypes. Under this hypothesis, failure of biological control results from the use of P. penetrans genotypes that cannot infect local Meloidogyne genotypes. We tested this hypothesis using isofemale lines of M. arenaria derived from a single field population and multiple sources of P. penetrans from the same and nearby fields. In strong support of the hypothesis, susceptibility to infection depended on the specific combination of host line and parasite source, with lines of M. arenaria varying substantially in which P. penetrans source could infect them. In light of this result, we tested whether using a diverse pool of P. penetrans could increase infection and thereby control. We found that increasing the diversity of the P. penetrans inoculum from one to eight sources more than doubled the fraction of M. arenaria individuals susceptible to infection and reduced variation in susceptibility across host lines. Together, our results highlight genotype-by-genotype specificity as an important cause of variation in biological control and call for the maintenance of genetic diversity in natural enemy populations.

Extended in vitro storage of eggs and milt increases maternal but not paternal variation in embryo viability of landlocked Atlantic salmon (Salmo salar m. sebago)

Appropriate fertilization practices play a crucial role in the maintenance of genetic diversity within captive fish broodstocks. We assessed the influence of in vitro storage of gametes (0-, 7- and 14-days post-stripping) at 1 °C on ovarian fluid pH, sperm motility, and embryo viability in the critically endangered Finnish landlocked salmon (Salmo salar m. sebago) population. A repeated full-factorial design used in both sperm-ovarian fluid activation analyses and fertilizations allowed us to separate the effects of female, male and their interaction on gamete quality and embryo survival across storage times. The ovarian fluid pH decreased most significantly during the first week of storage and showed considerable variation among females. The decrease of sperm motility varied across males, females and male–female (sperm-ovarian fluid) combinations. The mean proportion of viable embryos was initially 96.4%, but dropped to 45.5% after 7 days, and to 13.1% after 14 days of gamete storage. Embryo viability responses to gamete storage time predominantly increased among- and within-female variation but also showed major differences between female × male combinations (non-additive genetic effects). Interestingly, embryo viability showed virtually complete re-ranking (change of order) among full-sib families between the first two fertilization times (rs = − 0.03) but consistency between the first and last times (rs = 0.59). Overall, our results indicate that even when the primary aim is to maximize the genetic diversity of endangered fish populations, it may be advisable to prioritize minimal egg storage time rather than maximizing the number of parental combinations in fertilizations.

Reasons to move far away: studying the drivers of Carpetania matritensis (Hormogastridae: Crassiclitelatta) dispersal behaviour

Dispersal is a crucial process for animal populations as it allows the colonisation of new habitats and the maintenance of genetic diversity. However, it has not been studied enough for soil fauna, which is the basis for a wide variety of ecosystem services. Therefore, the study of their dispersal and the factors that trigger this behaviour is a relevant area of knowledge for the maintenance of the services they provide. For this work, Carpetania matritensis, an endogeic earthworm species endemic to the central Iberian Peninsula, has been used as a model to study the effect of habitat quality and conspecific density on dispersal and exploratory behaviour. The experiment was carried out in horizontal mesocosms divided into three sectors of the same dimensions: an inoculation section (left), a crossing section (centre) and a target sector (right). Those sectors were occupied by soil, a favourable habitat for earthworms, or sand, which represents an unsuitable habitat for earthworms and a physical barrier for their displacement. Earthworms were inoculated at two different densities (2 and 6 individuals per mesocosm; 848.86 and 2546.58 individuals/m3 respectively) and at two experimental durations (4 and 8 days) for each of the three different experimental treatments (unsuitable-unsuitable-suitable (U-U-S), suitable-unsuitable-suitable (S-U-S) and suitable-suitable-suitable (S-S-S), depending on the habitat type filling the inoculation, crossing and target section respectively). The results showed a large effect of treatment on the dispersal rate, being higher when earthworms were inoculated in an adverse environment, establishing habitat quality as a driver of the species’ dispersal behaviour. No significant effects of conspecific density, experimental duration or its interactions were found. Further studies are needed to clarify the species dispersal behaviour with a view to its conservation.

Polygenic signals of sex differences in selection in humans from the UK Biobank.

Sex differences in the fitness effects of genetic variants can influence the rate of adaptation and the maintenance of genetic variation. For example, "sexually antagonistic" (SA) variants, which are beneficial for one sex and harmful for the other, can both constrain adaptation and increase genetic variability for fitness components such as survival, fertility, and disease susceptibility. However, detecting variants with sex-differential fitness effects is difficult, requiring genome sequences and fitness measurements from large numbers of individuals. Here, we develop new theory for studying sex-differential selection across a complete life cycle and test our models with genotypic and reproductive success data from approximately 250,000 UK Biobank individuals. We uncover polygenic signals of sex-differential selection affecting survival, reproductive success, and overall fitness, with signals of sex-differential reproductive selection reflecting a combination of SA polymorphisms and sexually concordant polymorphisms in which the strength of selection differs between the sexes. Moreover, these signals hold up to rigorous controls that minimise the contributions of potential confounders, including sequence mapping errors, population structure, and ascertainment bias. Functional analyses reveal that sex-differentiated sites are enriched in phenotype-altering genomic regions, including coding regions and loci affecting a range of quantitative traits. Population genetic analyses show that sex-differentiated sites exhibit evolutionary histories dominated by genetic drift and/or transient balancing selection, but not long-term balancing selection, which is consistent with theoretical predictions of effectively weak SA balancing selection in historically small populations. Overall, our results are consistent with polygenic sex-differential-including SA-selection in humans. Evidence for sex-differential selection is particularly strong for variants affecting reproductive success, in which the potential contributions of nonrandom sampling to signals of sex differentiation can be excluded.

Genetic Analyses Reveal High Connectivity among Populations of the Honduran White Bat Ectophylla alba in the Caribbean Lowlands of Central Eastern Costa Rica

Vagility, ecological requirements, and forest patches can all influence gene flow among populations. These aspects are critical for the maintenance of genetic diversity in populations. Ectophylla alba is a fruit bat belonging to the family Phyllostomidae with specialized feeding and habitat requirements. Studies examining population genetics in this specialist bat are lacking. In this study, ten microsatellite loci were used to evaluate the current genetic structure of this bat species. Six localities in Costa Rica were evaluated. These localities are included in a landscape with remnants of lowland forests surrounded by cattle pastures, plantations, urban areas, and roads. Our results suggest a genetic population with moderate genetic diversity that was observed at most studied loci, with a statistically non-significant difference between the observed and expected heterozygosity. Most of the genetic variation was observed within rather than among sampled populations. The Mantel test showed a non-significant correlation between genetic diversity and geographic distance. These results suggest that E. alba populations have not shown an effect of habitat fragmentation in the studied area. We argue that the increase of forest patches is too recent to alter genetic diversity among sampled localities. Current migration among populations appears to be high enough to balance allele frequencies among localities.

The advantage of sex: Reinserting fluctuating selection in the pluralist approach.

The advantage of sex, and its fixation in some clades and species all over the eukaryote tree of life, is considered an evolutionary enigma, especially regarding its assumed two-fold cost. Several likely hypotheses have been proposed such as (1) a better response to the negative frequency-dependent selection imposed by the “Red Queen” hypothesis; (2) the competition between siblings induced by the Tangled Bank hypothesis; (3) the existence of genetic and of (4) ecological factors that can diminish the cost of sex to less than the standard assumed two-fold; and (5) a better maintenance of genetic diversity and its resulting phenotypic variation, providing a selective advantage in randomly fluctuating environments. While these hypotheses have mostly been studied separately, they can also act simultaneously. This was advocated by several studies which presented a pluralist point of view. Only three among the five causes cited above were considered yet in such a framework: the Red Queen hypothesis, the Tangled Bank and the genetic factors lowering the cost of sex. We thus simulated the evolution of a finite mutating population undergoing negative frequency-dependent selection on phenotypes and a two-fold (or less) cost of sexuality, experiencing randomly fluctuating selection along generations. The individuals inherited their reproductive modes, either clonal or sexual. We found that exclusive sexuality begins to fix in populations exposed to environmental variation that exceeds the width of one ecological niche (twice the standard deviation of a Gaussian response to environment). This threshold was lowered by increasing negative frequency-dependent selection and when reducing the two-fold cost of sex. It contributes advocating that the different processes involved in a short-term advantage of sex and recombination can act in combination to favor the fixation of sexual reproduction in populations.

Elevated inbreeding in Heliconia tortuosa is determined by tropical forest stand age, isolation and loss of hummingbird functional diversity.

Forest conversion and habitat loss are major threats to biological diversity. Forest regeneration can mitigate the negative effects of old-growth forest loss on species diversity, but less is known about the extent to which forest loss reduces genetic diversity in remnant populations and whether secondary forests play a role in the maintenance of genetic diversity. We quantified genetic diversity in a tropical hummingbird-pollinated understorey herb, Heliconia tortuosa, across a landscape mosaic of primary and secondary forest regrowth. Using microsatellite genotypes from >850 adult and juvenile plants within 33 forest patches and extensive bird surveys, we examined the effect of contemporary and historical landscape features including forest age (primary vs. secondary forest), stand isolation and pollinator assemblages on genetic diversity and levels of inbreeding in H. tortuosa. We found that inbreeding was up to three times higher in secondary forest, and this effect was amplified with reductions in primary forest in the surrounding landscape through reduced observed heterozygosity in isolated fragments. Inbreeding in forest patches was negatively correlated with the local frequency of specialist long-distance foraging traplining hummingbirds. Traplining hummingbirds therefore appear to facilitate mating among unrelated plants-an inference we tested using empirically parameterized simulations. Higher levels of inbreeding in H. tortuosa are therefore associated with reduced functional diversity of hummingbirds in secondary forests and forest patches isolated from primary forests. Our findings suggest a cryptic consequence of primary forest loss and secondary forest regeneration through the disruption of mutualistic interactions resulting in the erosion of genetic diversity in a common understorey plant.

Gene Flow and Recruitment Patterns among Disjunct Populations of Allocasuarina verticillata (Lam.) L.A.S. Johnson

Allocasuarina verticillata (Lam.) L.A.S. Johnson is a widespread species in south-eastern Australia providing vegetation cover, protecting fragile soils and providing food for birds. Understanding the effects of gene flow on the recruitment patterns, genetic differentiation and structure of fragmented populations provides fundamental guidelines to underpin plant conservation strategies and activities. In this study, four spatially disjunct populations of A. verticillata were sampled to explore the effects of population size, reproductive patterns and pollen and seed dispersal on among-population genetic diversity, genetic differentiation and structure, using field survey and microsatellite marker techniques. It was found that stands of A. verticillata were predominantly sexually reproductive, but asexual reproduction through root suckering was an additional mode of reproduction. The reproductive success of A. verticillata is positively correlated with the effective population size rather than actual population size. The reduction in effective population size and increment of spatial isolation resulted in lower genetic diversity and higher inbreeding coefficient of progenies. Moderate pairwise genetic differentiation and weak genetic structure were identified. The results suggest that exogenous, wind-mediated pollen flow provides some maintenance of genetic diversity in the isolated stands. Seed dispersal appears mainly to be over short distances (i.e., within populations), but the infrequent transport of seeds between disjunct locations cannot be ruled out as another factor that may help maintain genetic diversity.

The roles of balancing selection and recombination in the evolution of rattlesnake venom.

The origin of snake venom involved duplication and recruitment of non-venom genes into venom systems. Several studies have predicted that directional positive selection has governed this process. Venom composition varies substantially across snake species and venom phenotypes are locally adapted to prey, leading to coevolutionary interactions between predator and prey. Venom origins and contemporary snake venom evolution may therefore be driven by fundamentally different selection regimes, yet investigations of population-level patterns of selection have been limited. Here, we use whole-genome data from 68 rattlesnakes to test hypotheses about the factors that drive genomic diversity and differentiation in major venom gene regions. We show that selection has resulted in long-term maintenance of genetic diversity within and between species in multiple venom gene families. Our findings are inconsistent with a dominant role of directional positive selection and instead support a role of long-term balancing selection in shaping venom evolution. We also detect rapid decay of linkage disequilibrium due to high recombination rates in venom regions, suggesting that venom genes have reduced selective interference with nearby loci, including other venom paralogues. Our results provide an example of long-term balancing selection that drives trans-species polymorphism and help to explain how snake venom keeps pace with prey resistance.

Evolution of toxins as a public good in phytoplankton.

Toxic phytoplankton blooms have increased in many waterbodies worldwide with well-known negative impacts on human health, fisheries and ecosystems. However, why and how phytoplankton evolved toxin production is still a puzzling question, given that the producer that pays the costs often shares the benefit with other competing algae and thus provides toxins as a 'public good' (e.g. damaging a common competitor or predator). Furthermore, blooming phytoplankton species often show a high intraspecific variation in toxicity and we lack an understanding of what drives the dynamics of coexisting toxic and non-toxic genotypes. Here, by using an individual-based two-dimensional model, we show that small-scale patchiness of phytoplankton strains caused by demography can explain toxin evolution in phytoplankton with low motility and the maintenance of genetic diversity within their blooms. This patchiness vanishes for phytoplankton with high diffusive motility, suggesting different evolutionary pathways for different phytoplankton groups. In conclusion, our study reveals that small-scale spatial heterogeneity, generated by cell division and counteracted by diffusive cell motility and turbulence, can crucially affect toxin evolution and eco-evolutionary dynamics in toxic phytoplankton species. This contributes to a better understanding of conditions favouring toxin production and the evolution of public goods in asexually reproducing organisms in general.

A new test suggests hundreds of amino acid polymorphisms in humans are subject to balancing selection.

The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald-Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection.

Hybridization and low genetic diversity in the endangered Alabama red-bellied turtle (Pseudemys alabamensis).

Pseudemys alabamensis is one of the most endangered freshwater turtle species in the United States due to its restricted geographic distribution in coastal Alabama and Mississippi. Populations of P. alabamensis are geographically isolated from one another by land and saltwater, which could act as barriers to gene flow. It is currently unknown how differentiated these populations are from one another and whether they have experienced reductions in population size. Previous work found morphological differences between Alabama and Mississippi populations, suggesting that they may be evolutionarily distinct. Other Pseudemys turtles such as P. concinna and P. floridana occur naturally within the same geographic area as P. alabamensis and are known to hybridize with each other. These more abundant species could threaten the unique genetic identity of P. alabamensis through introgression. In order to evaluate the endangered status of P. alabamensis and the level of hybridization with other species, we used mitochondrial and nuclear microsatellite markers to assess genetic variation within and among populations of P. alabamensis throughout its range and estimate admixture with co‐occurring Pseudemys species. In P. alabamensis, we found no variation in mitochondrial DNA and an excess of homozygosity in microsatellite data. Our results show genetic differentiation between Alabama and Mississippi populations of P. alabamensis, and low estimated breeding sizes and signs of inbreeding for two populations (Fowl River, Alabama and Biloxi, Mississippi). We also found evidence of admixture between P. alabamensis and P. concinna/P. floridana. Based on our results, P. alabamensis is highly endangered throughout its range and threatened by both low population sizes and hybridization. In order to improve the species’ chances of survival, focus should be placed on habitat preservation, maintenance of genetic diversity within both the Mississippi and Alabama populations, and routine population‐monitoring activities such as nest surveillance and estimates of recruitment.

Linking genetic diversity and species diversity through plant-soil feedback.

Genetic diversity and species diversity are typically studied in isolation despite theory showing they likely influence one another. Here, we used simplified communities of one or two populations of one or two species to test whether linkages between genetic and species diversity can be mediated by interactions between plants and their soil microbiota, or microbe-mediated plant-soil feedback (PSF). Interspecific PSF promotes the maintenance of species diversity when plants grow better with heterospecific soil microbes than with conspecific microbes. Similarly, intraspecific PSF promotes the maintenance of genetic diversity when plants grow better with heterogenotypic than with congenotypic microbes. In a two-phase greenhouse experiment, we conditioned the soil microbial community with pairs of plants that were either two individuals of the same species (lower species diversity) or one individual of each of two species (higher species diversity), and with pairs of plants that were either two individuals from the same population (lower genetic diversity) or one individual from each of two populations (higher genetic diversity). We then tested the effects of these microbial communities on plant growth in a second phase. We found that higher genetic diversity reduced the ability of interspecific PSF to promote plant species diversity, and for one of our two study species, higher species diversity reduced the ability of intraspecific PSF to promote plant genetic diversity. If these patterns occur in more diverse communities, then our results suggest that PSF may dampen the negative effects of diversity loss by promoting diversity at other levels of biological organization.

Maintenance of Genetic Diversity of Black Sea Bream despite Unmonitored and Large-Scale Hatchery Releases.

Simple SummaryStock enhancement aggressively replenishes depleted wild finfish populations. However, stock enhancement of black sea bream in Taiwan with complex genetic sources, especially when successful, maintains genetic diversity but dramatically changes the genetic structure within and among wild populations.Stock enhancement, used for replenishing depleted wild finfish populations, is an aggressive approach. Stock enhancement projects in Taiwan involve black sea bream (Acanthopagrus schlegelii), a major commercial species. During 2004–2015, even management agencies conducted stock enhancement projects, leading to numerous private releases that have not been recorded. Stock enhancement by a private hatchery without accurate genetic records may lead to a genetic structure change in wild populations. Using allele frequencies at nine microsatellite loci, we studied the genetic effects of stock enhancement in 19 samples collected from populations in the hatcheries and the wild. In 458 individuals from nine hatchery samples, most populations showed weak but significant genetic differences and complex clusters in structure analysis, indicating dramatic stock change within and among hatcheries. The 10 wild populations (n = 773) also had a complex genetic composition and were genetically different among sampling sites and times. However, a simple and clear cluster in structure analysis was found for only one sampling site, which had no release history. Thus, stock enhancement with complex genetic sources helps maintain genetic diversity but dramatically changes the genetic structure within and among wild populations, especially when stock enhancement is successful.