Loss Of Rare Alleles Research Articles

Intraspecific genetic variability, differentiation and evolutionary relationships revealed through microsatellite loci in seven economically important Calamus species

Population density, species richness and critical population parameters are crucial in determining the levels of gene diversity in dioecious species of the genus Calamus. The extent of intraspecific and intrageneric genetic variability in Calamus from the southern Western Ghats of India was studied using 26 microsatellite markers by sampling 227 individuals belonging to seven economically important species. The heterozygosity of microsatellite loci ranged from zero to 0.78. Average gene diversity within species was 0.13; in all species it was 0.18 and amongst species was 0.06. The Shannon Information Index was the lowest for Calamus metzianus (0.11), whereas it ranged from 0.16 to 0.26 for other species. The expected heterozygosity varied from 0.08 to 0.18. Calamus hookerianus and Calamu travancoricus showed the highest genetic differentiation (44%) revealed through Fst values, whereas the lowest (22%) was observed between Calamus gamblei and Calamu thwaitesii. Population structuring and phylogenetic analysis differentiated the seven species. Due to overexploitation and loss of rare alleles, small populations could lead to fertilization between closely related individuals, resulting in inbreeding and increasing the risk of extinction. This could be important for species such as C. metzianus where allelic polymorphism was 23%, whereas for all other species it was 38% to 46%. Genetic diversity “micro-hotspots” were identified from the protected area network of the southern and central Western Ghats with highest observed heterozygosity. Four micro-hotspots from the Agasthyamalai Biosphere Reserve and the Pushpagiri Wildlife Sanctuary may be possible for long-term conservation programs. The findings of this study lay a strong foundation for strengthening protected area networks, especially areas with intermediate levels of disturbance.

Genetic Variation of the Siberian Sturgeon (Acipenser baerii Brandt, 1869) in Aquaculture

Genetic variation of aquaculture broodstocks of the Siberian sturgeon of different origin from 13 farms across the Russian Federation was assessed at five tetraploid microsatellite loci and the mitochondrial DNA control region. At present, in aquaculture stocks of Siberian sturgeon originating from the Lena and Ob rivers, a sharp decline of haplotype diversity is observed. The most part of aquaculture individuals carry two major haplotypes characteristic of the European part of Russia (the Lena aquaculture) and two haplotypes characteristic of the western part of Siberia (the Ob aquaculture). According to the results of the microsatellite analysis, in sturgeon aquaculture stock originating from the Lena River, two genetic clusters can be distinguished. One of these clusters is represented by the stocks composed of inbred individuals and, because of this, is characterized by depleted allelic variation and the loss of rare alleles.

Concerns and evidence on genetic diversity in planted forests

Planted forests are an important source of various services (economic, environmental, and social) with increasing portion in the total world’s forest area. Genetic diversity is fundamental for success and sustainability of planted forests. Facing the concern of the reduction of genetic diversity in planted forests, this study offers a review of evidence on comparisons between the levels of genetic diversity in forests established by different regeneration methods. A total of 34 papers comparing genetic diversity in natural forests versus various regeneration methods of 24 tree species examined by the range of markers are reviewed. In most cases, there are no significant differences in genetic diversity between natural and planted forests, followed by an almost equal number of cases with decreased and increased level of genetic diversity. The loss of rare alleles, but also new alleles are reported in planted forests. Although the origin of planting material in the most cases are unknown, the size of parental population is determinant for the level of genetic diversity in the new forest, with the provenancing and seed collection strategy as the most important management practices in planting projects.

Analysis of population-genetic processes in different cattle breeds by microsatellite loci of DNA

Aim. The aim of our research was to analyze the population-genetic processes in different dairy breeds using highly polymorphic molecular and genetic markers (DNA microsatellites). Methods. We used 10 loci recommended by the International Society for Animal Genetics (ISAG) to analyze 88 DNA samples of the two most abundant dairy breeds of cattle in Ukraine – Ukrainian red-motley dairy and Ukrainian black-and-white dairy breeds. Using formulae that related the expected linkage disequilibrium (LD) to the effective population size (Ne), Ne was estimated. Results. The work presents the results of the study on genetic processes in the populations of Ukrainian red-and-motley breed using 10 microsatellite loci of DNA. It was shown that, being highly polymorphic multilocus genetic systems, microsatellites of DNA are highly informative markers of populationgenetic processes, occurring in the populations of cattle. Conclusions. The studied populations of Ukrainian dairy cattle breeds are impacted by population-genetic and genetic-automatic processes. In particular, the effect of the latter on Ukrainian red-and-motley dairy breed was noted. These animals had notable signifi cant loss of rare alleles and the manifestation effect of “bottle neck”. The values obtained testify to a low level of inbredness in these populations. The effective population size in the studied Ukrainian dairy cattle breeds was estimated in the approximate range of 397–555 heads which testifi ed to a favorable condition of the population of Ukrainian red-and-motley dairy cattle and a critical condition of the Ukrainian black-and-white dairy breed.

The effect of tending and commercial thinning on the genetic diversity of Scots pine stands

The objective of this study was to estimate the effect of pre-commercial tending and commercial thinning on the genetic diversity parameters, especially rare allele loss and diameter–heterozygosity associations, in Scots pine stands by retrospectively modelling the removal of inferior/superior trees. Modelling was based on empirical data of DNA polymorphism in (a) a 60-year-old natural stand and (b) a 20-year-old young stand planted with seeds collected in a seed orchard. Within each of these stands, approximately 400 trees were systematically sampled within 1-ha plots (800 trees in total) and genotyped at 5 neutral and 7 EST-derived nuclear microsatellite markers. There was no significant association between heterozygosity, common allele number and tree diameter in either stand. Even at a high intensity, both simulated tending and commercial thinning had minor effects on the heterozygosity and allelic diversity but caused a significant loss of rare alleles. However, there was a nonlinear relationship between the loss of rare alleles and the thinning intensity in the young stand, such that below 30 % thinning intensity, the rare alleles were lost at a markedly lower rate. In conclusion, the association between commercial value and genetic diversity is weak in Scots pine. Thinning causes loss of rare alleles; however, for specific cases, it could be possible to identify the margins for a slow rate of rare allele loss.

Allozyme Based Genetic Variation between Hatchery and Natural Populations of Sahar (Tor putitora)

Sahar (Tor putitora) formed a substantial natural fishery in the major riverine and lacustrine ecosystem of Nepal. Biological diversity of this species is being threatened by various anthropogenic activities. In view of the conservational value and the aquaculture potential of T. putitora, significant development in artificial propagation of this species has been achieved. The successful hatchery production of T. putitora brought to the forefront problematic questions regarding genetic variation of the hatchery stocks. A study was, therefore, conducted to determine the genetic variability within and between hatchery stocks and their wild counterparts of T. putitora using allozyme markers.Analyses of seven enzyme systems resuled in 11 loci being resolved from lake population and two consecutive generations of hatchery populations of T. putitora. Based on five polymorphic loci, all populations had percentage polymorphic loci 45.45. Significant reduction (P<0.01) in number of alleles per locus was evident in hatchery populations (1.45 ±0.181) compared to lake population (1.72 ±0.90). Loss of rear alleles, EST-2*74, IDH*70 and GDH*33 occurred in both of the hatchery populations which were present in wild counterparts- the lake population. All populations under study conform to the Hardy-Weinberg equilibrium at the 1% level. Although not significant (P>0.05), observed heterozygosity increased in first generation of hatchery population (Ho= 0.181 ±0.233) compared to natural population (Ho=0.179±0.221). The Ho of second generation of hatchery population was lowest (0.119 ±0.143) among the populations studied. Loss of rare alleles from the two generations of hatchery population, while these alleles were present in corresponding natural populations suggested the founders (20-30 individuals) of the hatchery populations probably represented bottlenecks to very small effective population size (Ne).J. Nat. Hist. Mus. Vol. 26, 2012: 212-223

Genetic differences between broodstock and offspring of seven-band grouper in a hatchery

The seven-band grouper (Epinephelus septemfasciatus) is an important fishery resource of a target for prospective aquaculture diversification and maintenance of stock quality is thus important. To explore the sustainability of fry production, genetic variations in 83 seven-band groupers from two broodstock and offspring populations of a hatchery strain were analyzed using 13 polymorphic nuclear microsatellite DNA loci; 133 alleles were identified. Allelic variability ranged from 4 to 18 in the broodstock and from 3 to 11 in the offspring. The average observed and expected heterozygosities were 0.669 and 0.734 in broodstock and 0.674 and 0.649 in offspring, respectively. Although no statistically significant reductions in heterozygosity or allelic diversity were evident in offspring, considerable loss of rare alleles was apparent. The broodstock and offspring populations exhibited significant genetic differences (F ST = 0.033, P < 0.001) indicating that genetic drift has likely promoted differentiation between the two populations, which may have negative effects on sustainable fry production. Therefore, genetic variations between broodstock and offspring should be monitored, and inbreeding should be controlled, to ensure the success of commercial breeding programs. Our data provide a useful genetic basis for future planning of sustainable culture and management of E. septemfasciatus in fisheries.

Molecular markers reveal narrow genetic base and culturing-associated genetic drift inTeretrius nigrescensLewis populations released for the biological control of the larger grain borer in Africa

In biological control, successful establishment of a natural enemy species depends on its adaptability in the introduced range including its ability to re-establish desired ecological interactions with the pest. These are affected by genetic parameters hitherto largely unresolved in biological control. The larger grain borer (LGB), Prostephanus truncatus, an invasive species from meso-America, is the most important post-harvest pest of maize in Africa. We studied the genetic structure of Teretrius nigrescens, a predatory beetle previously released for the control of the pest in Africa, to test the hypothesis that establishment patterns were a result of ecotype-environment mismatch and to follow up on our earlier reports of distinct lineages of the predator. We studied 13 populations of T. nigrescens, using 16 polymorphic microsatellite markers. Five genetic populations with a hierarchical structure and significant isolation by distance were detected. The most diverse population was found in southern Mexico, consistent with earlier lineage coexistence observations. Populations introduced to Africa maintained genetic similarity to local geographic populations of their area of origin. The more successful Benin releases were also more genetically diverse. Loss of rare alleles and a higher frequency of existing private alleles in some populations indicated population expansions following bottleneck events. Sustainable biological control should accommodate pest and natural enemy species, and monitor genetic changes associated with introduction and release.

Two colonisation stages generate two different patterns of genetic diversity within native and invasive ranges of Ulex europaeus.

Genetic diversity and the way a species is introduced influence the capacity of populations of invasive species to persist in, and adapt to, their new environment. The diversity of introduced populations affects their evolutionary potential, which is particularly important for species that have invaded a wide range of habitats and climates, such as European gorse, Ulex europaeus. This species originated in the Iberian peninsula and colonised Europe in the Neolithic; over the course of the past two centuries it was introduced to, and has become invasive in, other continents. We characterised neutral genetic diversity and its structure in the native range and in invaded regions. By coupling these results with historical data, we have identified the way in which gorse populations were introduced and the consequences of introduction history on genetic diversity. Our study is based on the genotyping of individuals from 18 populations at six microsatellite loci. As U. europaeus is an allohexaploid species, we used recently developed tools that take into account genotypic ambiguity. Our results show that genetic diversity in gorse is very high and mainly contained within populations. We confirm that colonisation occurred in two stages. During the first stage, gorse spread out naturally from Spain towards northern Europe, losing some genetic diversity. During the second stage, gorse was introduced by humans into different regions of the world, from northern Europe. These introductions resulted in the loss of rare alleles but did not significantly reduce genetic diversity and thus the evolutionary potential of this invasive species.

Using molecular markers for pedigree reconstruction of the greater amberjack (Seriola dumerili) in the absence of parental information

Ensuring appropriate levels of genetic diversity in captive populations is essential to avoid inbreeding and loss of rare alleles by genetic drift. Pedigree reconstruction and parentage analysis in the absence of parental genotypes can be a challenging task that relies in the assignment of sibship relationships among the offspring. Here, we used eight highly variable microsatellite markers and three different assignment methods to reconstruct the most likely genotypes of a parental group of wild Seriola dumerili fish based on the genotypes of six cohorts of their offspring, to assess their relative contributions to the offspring. We found that a combination of the four most variable microsatellites was enough to identify the number of parents and their contribution to the offspring, suggesting that the variability of the markers can be more critical than the number of markers. Estimated effective population sizes were lower than the number of breeders and variable among years. The results suggest unequal parental contribution that should be accounted for breeding programs in the future.

Comparative genetic variability between broodstock and offspring populations of Korean starry flounder used for stock enhancement in a hatchery by using microsatellite DNA analyses

Korean starry flounder, Platichthys stellatus (Pleuronectidae), is one of the most economically important fishery resources in Korea. We investigated the effect of current artificial reproduction in a hatchery facility, genetic divergence between the broodstock and their offspring populations of starry flounder in a hatchery strain to be stocked into natural sea areas was accessed using 9 polymorphic nuclear microsatellite DNA loci. High levels of polymorphism were observed between the 2 populations. A total of 96 alleles were detected at the loci, with some alleles being unique in the broodstock. Allelic variability ranged from 8 to 17 in the broodstock and from 7 to 12 in the offspring population. Average observed and expected heterozygosities were estimated at 0.565 and 0.741 in the broodstock samples and 0.629 and 0.698 in the offspring population, respectively. Although no statistically significant reductions were found in heterozygosity or allelic diversity in the offspring population, a considerable loss of rare alleles was observed in the offspring population compared with that in the broodstock. Significant genetic difference was detected between the broodstock and offspring populations (FST = 0.021, P < 0.05). These results suggest that more intensive breeding practices for stock enhancement might have resulted in a further decrease of genetic diversity. Thus, genetic variations of broodstock and progeny should ideally be monitored in both breeding and release programs as a routine hatchery operation in order to improve the starry flounder hatchery management. This information might be useful for fishery management and aquaculture industry of P. stellatus.

Comparative genetic diversity of wild and hatchery-produced populations of tongue sole (Cynoglossus semilaevis) using multiplex PCR assays with polymorphic microsatellite markers

The tongue sole, Cynoglossus semilaevis (Cynoglossidae), is one of the most economically important fishery resources in Korea. This study presents a preliminary investigation of the future viability of the complete aquaculture of tongue sole in Korea. Specifically, possible differences in genetic variability between wild populations of tongue sole from Korea and hatchery-produced populations of tongue sole from China were assessed using multiplex assays with 12 polymorphic nuclear microsatellite DNA loci. High levels of polymorphism were observed between the 2 populations. A total of 135 different alleles were found, varying from 5-15 alleles per locus, with some alleles being unique. These findings indicate a high level of genetic variability in both the wild and hatchery-produced populations. Although a considerable loss of rare alleles was observed in hatchery samples, there were no statistically significant reductions of heterozygosity or allelic diversity in the hatchery population compared to the wild population. Moreover, the inbreeding coefficient was very low (FIS = -0.010-0.052) for both populations. However, significant genetic heterogeneity was found between the 2 populations. These findings indicate that genetic drift has likely promoted differentiation between these 2 populations, and might have negative effects on the reproductive capacity of the stock, because genetic factors are important in the production of high quality seed for complete aquaculture. Therefore, aquaculture management should incorporate basic genetic principles into existing molecular monitoring protocols. The information compiled by this study is anticipated to provide a useful genetic basis for future complete culturing plans and management of C. semilaevis in fisheries.

Comparative genetic diversity of wild and released populations of Pacific abalone Haliotis discus discus in Jeju, Korea, based on cross-species microsatellite markers including two novel loci

Pacific abalone Haliotis discus discus is an important fisheries resource in Jeju, Korea. For basic information about its current genetic status in relation to stock enhancement, the level and distribution of genetic variation between wild and released stocks of Pacific abalone in Jeju were examined at nine cross-species microsatellite markers including the use of two novel primers. High levels of polymorphism were observed between the two populations. A total of 146 different alleles were found at all loci, with some alleles being unique. The allelic variability ranged from five to 27 in the wild population and from four to 16 in the released sample. The average observed and expected heterozygosities were estimated to be 0.74 and 0.84 in the wild sample and 0.70 and 0.78 in the released sample, respectively. Although a considerable loss of rare alleles was observed in the released sample, no statistically significant reductions were found in heterozygosity or allelic diversity in the released sample compared to the wild population. Low but significant genetic differentiation was found between the wild and released populations. These results suggest that the intensive breeding practices for stock enhancement may have resulted in a further decrease in genetic diversity, and that the cross-species microsatellite markers used in this study represent a potentially efficient means for further genetic studies, providing beneficial information for the protection and management of H. discus discus.

Genome-Wide Loss of Diversity in the Critically Endangered Hawaiian Monk Seal

Threatened species often exhibit low genetic diversity as a result of selective sweeps, historical bottlenecks, or persistent small population size. Whereas selective sweeps create localized reduction of variation at a chromosome, population bottlenecks result in the loss of rare alleles throughout the genome. Heterozygosity is lost more slowly and is severely impacted only when populations are small for an extended period of time. We test the hypotheses of selective sweep, historical bottleneck and persistently small population size to explain extremely low genetic diversity in the critically endangered Hawaiian monk seal (Monachus schauinslandi). Of 163 microsatellite loci isolated from the species’ genome, only 17 are polymorphic. Mapping 98 monomorphic and 12 polymorphic loci to 35 chromosomes throughout the dog genome, we reject the selective sweep hypothesis. Genotyping 2,423 Hawaiian monk seals at the 17 polymorphic loci plus a locus previously isolated from another pinniped species, we find evidence for a recent bottleneck (P = 0.04). This is consistent with historical records describing intense hunting in the 19th century; however, the bottleneck was not of sufficient severity and duration to explain the genome-wide depletion of genetic diversity (HO = 0.05; A = 1.1). Long-term population size restriction is a more likely explanation. Though at least two of the polymorphic loci appear to be candidates for selection, the low genetic diversity of the species may further threaten chances for survival of this critically endangered species in a changing world.

Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae)

BackgroundCultivation of medicinal plants is not only a means for meeting current and future demands for large volume production of plant-based drug and herbal remedies, but also a means of relieving harvest pressure on wild populations. Scutellaria baicalensis Georgi (Huang-qin or Chinese skullcap) is a very important medicinal plant in China. Over the past several decades, wild resource of this species has suffered rapid declines and large-scale cultivation was initiated to meet the increasing demand for its root. However, the genetic impacts of recent cultivation on S. baicalensis have never been evaluated. In this study, the genetic diversity and genetic structure of 28 wild and 22 cultivated populations were estimated using three polymorphic chloroplast fragments. The objectives of this study are to provide baseline data for preserving genetic resource of S. baicalensis and to evaluate the genetic impacts of recent cultivation on medicinal plants, which may be instructive to future cultivation projects of traditional Chinese medicinal plants.ResultsThirty-two haplotypes of S. baicalensis (HapA-Y and Hap1-7) were identified when three chloroplast spacers were combined. These haplotypes constituted a shallow gene tree without obvious clusters for cultivated populations, suggesting multiple origins of cultivated S. baicalensis. Cultivated populations (hT = 0.832) maintained comparable genetic variation with wild populations (hT = 0.888), indicating a slight genetic bottleneck due to multiple origins of cultivation. However, a substantial amount of rare alleles (10 out of 25 haplotypes within wild populations) lost during the course of S. baicalensis cultivation. The genetic differentiation for cultivated group (GST = 0.220) was significantly lower than that of wild group (GST = 0.701). Isolation by distance analysis showed that the effect of geographical isolation on genetic structure was significant in wild populations (r = 0.4346, P < 0.0010), but not in cultivated populations (r = 0.0599, P = 0.2710). These genetic distribution patterns suggest that a transient cultivation history and the extensive seed change among different geographical areas during the course of S. baicalensis cultivation.ConclusionsAlthough cultivated S. baicalensis maintains comparable genetic diversity relative to wild populations, recent cultivation has still imposed profound impacts on genetic diversity patterns of the cultivated S. baicalensis populations, i.e., the loss of rare alleles and homogenization of cultivated populations. This study suggests that conservation-by-cultivation is an effective means for protecting genetic resources of S. baicalensis, however, the wild resources still need to be protected in situ and the evolutionary consequences of extensive seed exchange mediated by human being should be monitored carefully.

Genetic diversity of wild and farmed black sea bream populations in Jeju

Black sea bream, Acanthopagrus schlegelii, is a commercially important fish in Korea. As a preliminary investigation into the effect of hatchery rearing for stock enhancement, we examined genetic diversity between wild and farmed black sea bream populations from Jeju using six microsatellite markers. High levels of polymorphism were observed between the two populations. A total of 87 different alleles were found at the loci, with some alleles being unique. Allelic variability ranged from 8 to 22 in the wild population and from 7 to 17 in the farmed one. Average observed and expected heterozygosities were estimated at 0.87 and 0.88 in the wild sample. The corresponding estimates were 0.83 and 0.86 in the farmed sample. Although a considerable loss of rare alleles was observed in the farmed sample, no statistically significant reductions were found in heterozygosity or allelic diversity in the farmed sample, compared with the wild one. Significant genetic heterogeneity was found between the wild and farmed populations. These results suggest that more intensive breeding practices for stock enhancement may have resulted in a further decrease of genetic diversity. Thus, it is necessary to monitor genetic variation in bloodstock, progeny, and target populations and control inbreeding in a commercial breeding program for conservation. This information may be useful for fisheries management and the aquaculture industry.

Genetic structure of red-handed howler monkey populations in the fragmented landscape of Eastern Brazilian Amazonia.

We genotyped 15 microsatellite loci in order to evaluate the effects of habitat fragmentation, caused by flooding of the Tucuruí reservoir, on the genetic structure of Alouatta belzebul in eastern Amazonia. The analysis included two populations sampled in 1984, representing both margins of the Tocantins river, and three populations sampled 18 years later. Minimal differences in the diversity levels between present-day (Ho = 0.62-0.69 and A(R) = 6.07-7.21) and pre-flooding (Ho = 0.60-0.62 and A (R) = 6.27-6.77) populations indicated there was no significant loss of genetic variability, possibly because of successful management strategies applied during the flooding. The changes observed were limited to shifts in the composition of alleles, which presumably reflect the admixture of subpopulations during flooding. Given this, there were significant differences in the Rst values (p = 0.05) in all but one between-site comparison. Both present-day and original populations showed a deficit of heterozygotes, which suggests that this may be typical of the species, at least at a local level, perhaps because of specific ecological characteristics. The relatively large number of private alleles recorded in all populations may be a consequence of the Wahlund effect resulting from population admixture or a process of expansion rather than the loss of rare alleles through genetic drift. Additionally, the levels of genetic variability observed in this study were higher than those reported for other species of Neotropical primates, suggesting good fitness levels in these A. belzebul populations. Regular genetic monitoring of remnant populations, especially on islands, should nevertheless be an integral component of long-term management strategies.

Assessment of genetic diversity of accessions in Brassicaceae genetic resources by frequency distribution analysis of S haplotypes

Plant genetic resources are important sources of genetic variation for improving crop varieties as breeding materials. Conservation of such resources of allogamous species requires maintenance of the genetic diversity within each accession to avoid inbreeding depression and loss of rare alleles. For assessment of genetic diversity in the self-incompatibility locus (S locus), which is critically involved in the chance of mating, we developed a dot-blot genotyping method for self-incompatibility (S) haplotypes and applied it to indigenous, miscellaneous landraces of Brassica rapa, provided by the IPK Gene Bank (Gatersleben, Germany) and the Tohoku University Brassica Seed Bank (Sendai, Japan), in which landraces are maintained using different population sizes. This method effectively determined S genotypes of more than 500 individuals from the focal landraces. Although our results suggest that these landraces might possess sufficient numbers of S haplotypes, the strong reduction of frequencies of recessive S haplotypes occurred, probably owing to genetic drift. Based on these results, we herein discuss an appropriate way to conserve genetic diversity of allogamous plant resources in a gene bank.

Genetic effects of forest fragmentation in high-density Araucaria angustifolia populations in Southern Brazil

Araucaria angustifolia is an endangered tropical/subtropical coniferous of great interest for conservation due its economical, ecological, and social value. Only 3% of original Araucaria forests remain, which are generally confined to small forest fragments. Forest fragmentation can have serious consequences on genetic process in tree population, affecting long-term fitness and adaptability. To investigate the effects of forest fragmentation on genetic diversity and the structure of A. angustifolia populations, the genetic diversity of eight microsatellite loci was compared in four small fragmented populations (<22 ha), four tree groups (five to 11 trees) occurring in pastures and in three plots in a large continuous population. The clearest effect of fragmentation was the loss of rare alleles (p ≤ 0.05) in fragmented populations (19.4% to 47.2%) and intermediate frequency (0.05 < p ≤ 0.25) and rare alleles (p ≤ 0.05) in tree groups (19% to 86.1%) in comparison to continuous populations. Fragmented populations have significant higher fixation index (\( \widehat{F}_{\text{IS}} = 0.121 \), P < 0.05) than continuous populations (\( \widehat{F}_{\text{IS}} = 0.083 \), P < 0.05). High genetic differentiation was detected among tree groups (\( \widehat{G}_{{{\text{ST}}}}^{\prime } = 0.258 \), P < 0.01) and low among fragments (\( \widehat{G}_{{{\text{ST}}}}^{\prime } = 0.031 \), P < 0.05) and continuous populations (\( \widehat{G}_{{{\text{ST}}}}^{\prime } = 0.026 \), P < 0.05), showing a significant bottleneck effect in tree groups. Evidence that forest fragments have experienced a recent bottleneck was confirmed in at least two studied fragments. The implications of the results for conservation of the fragmented A. angustifolia populations are discussed.

Genetic effects of long-term stock enhancement programs

Since the 1980s, there has been growing concern about the deleterious genetic effects of hatchery fish on wild populations. The general awareness of the loss of genetic variation in hatchery-produced juveniles has increased. However, the genetic effects of hatchery fish on wild populations have not yet been fully evaluated, and their long-term effects remain largely unknown, with no data available for marine species. To address this issue, we have reviewed the scientific literature on large-scale marine fish stocking programs worldwide, conducted over multiple generations, in which the catches and genetic diversity of wild and hatchery-released fish were monitored. However, we found no published work apart from two Japanese reports of different types of stocking: red sea bream in Kagoshima Bay (KB) and Pacific herring in northern Japan. We investigated the genetic effects of hatchery fish on wild populations using a comparative analysis of these two stocking programs. The loss of rare alleles was observed in red sea bream in the inner KB and for Pacific herring in Honshu. A bottleneck test and numerical simulations revealed that the loss of rare alleles in the inner KB was caused by the extensive releases of juveniles produced from captive broodstock used to rear multiple generations, whereas a bottleneck at the southern limit of the species was responsible for these effects in herring in Honshu. There was no evidence that the herring release programs using native brood stock every year had a genetic impact. The recapture rate for one-year-old red sea bream decreased consistently, suggesting a decline in the survival rate of the hatchery fish. Nevertheless, the wild catch of red sea bream in KB has generally remained above the catch level at the commencement of the release program, with no evidence of fitness decline in the wild population. The genetic impact of hatchery fish on red sea bream localized in the bay was much smaller than that of the evolutionary forces affecting Pacific herring through their life history and environmental and fishing selection pressures. We discussed on precision of our divergence estimates in relation to the number of loci examined and how genetic diversity could be maintained in hatchery and stocked populations.