Quantitative genetic variation in Daphnia: temporal changes in genetic architecture

Nonadditive genetic variation and genetic disequilibrium are two important factors that influence the evolutionary trajectory of natural populations. We assayed quantitative genetic variation in a temporary-pond-dwelling population of Daphnia pulex over a full season to examine the role of nonadditive genetic variation and genetic disequilibrium in determining the short-term evolutionary trajectory of a cyclic parthenogen. Quantitative traits were influenced by three factors: (1) clonal selection significantly changed the population mean phenotype during the course of the growing season; (2) sexual reproduction and recombination led to significant changes in life-history trait means and the levels of expressed genetic variation, implying the presence of substantial nonadditive genetic variation and genetic disequilibrium; and (3) Egg-bank effects were found to be an important component of the realized year-to-year change. Additionally, we examined the impact of genetic disequilibria induced by clonal selection on the genetic (co)variance structure with a common principal components model. Clonal selection caused significant changes in the (co)variance structure that were eliminated by a single bout of random mating, suggesting that a build-up of disequilibria was the primary source of changes in the (co)variance structure. The results of this study highlight the complexity of natural selection operating on populations that undergo alternating phases of sexual and asexual reproduction.     

Misspecification in Mixed-Model-Based Association Analysis

Additive genetic variance in natural populations is commonly estimated using mixed models, in which the covariance of the genetic effects is modeled by a genetic similarity matrix derived from a dense set of markers. An important but usually implicit assumption is that the presence of any nonadditive genetic effect increases only the residual variance and does not affect estimates of additive genetic variance. Here we show that this is true only for panels of unrelated individuals. In the case that there is genetic relatedness, the combination of population structure and epistatic interactions can lead to inflated estimates of additive genetic variance.     

Change of Genetic Architecture in Response to Sex

A traditional view is that sexual reproduction increases the potential for phenotypic evolution by expanding the range of genetic variation upon which natural selection can act. However, when nonadditive genetic effects and genetic disequilibria underlie a genetic system, genetic slippage (a change in the mean genotypic value contrary to that promoted by selection) in response to sex may occur. Additionally, depending on whether natural selection is predominantly stabilizing or disruptive, recombination may either enhance or reduce the level of expressed genetic variance. Thus, the role of sexual reproduction in the dynamics of phenotypic evolution depends heavily upon the nature of natural selection and the genetic system of the study population. In the present study, on a permanent lake Daphnia pulicaria population, sexual reproduction resulted in significant genetic slippage and a significant increase in expressed genetic variance for several traits. These observations provide evidence for substantial genetic disequilibria and nonadditive genetic effects underlying the genetic system of the study population. From these results, the fitness function of the previous clonal selection phase is inferred to be directional and/or stabilizing. The data are also used to infer the effects of natural selection on the mean and the genetic variance of the population.     

Sex differences in the genetic architecture of aggressiveness in a sexually dimorphic spider

Sex differences in the genetic architecture of behavioral traits can offer critical insight into the processes of sex‐specific selection and sexual conflict dynamics. Here, we assess genetic variances and cross‐sex genetic correlations of two personality traits, aggression and activity, in a sexually size‐dimorphic spider, Nuctenea umbratica. Using a quantitative genetic approach, we show that both traits are heritable. Males have higher heritability estimates for aggressiveness compared to females, whereas the coefficient of additive genetic variation and evolvability did not differ between the sexes. Furthermore, we found sex differences in the coefficient of residual variance in aggressiveness with females exhibiting higher estimates. In contrast, the quantitative genetic estimates for activity suggest no significant differentiation between males and females. We interpret these results with caution as the estimates of additive genetic variances may be inflated by nonadditive genetic effects. The mean cross‐sex genetic correlations for aggression and activity were 0.5 and 0.6, respectively. Nonetheless, credible intervals of both estimates were broad, implying high uncertainty for these estimates. Future work using larger sample sizes would be needed to draw firmer conclusions on how sexual selection shapes sex differences in the genetic architecture of behavioral traits.     

Natural genetic variation in plant photosynthesis

Natural genetic variation in plant photosynthesis is a largely unexplored and as a result an underused genetic resource for crop improvement. Numerous studies show genetic variation in photosynthetic traits in both crop and wild species, and there is an increasingly detailed knowledge base concerning the interaction of photosynthetic phenotypes with their environment. The genetic factors that cause this variation remain largely unknown. Investigations into natural genetic variation in photosynthesis will provide insights into the genetic regulation of this complex trait. Such insights can be used to understand evolutionary processes that affect primary production, allow greater understanding of the genetic regulation of photosynthesis and ultimately increase the productivity of our crops.     

Genetic changes caused by restocking and hydroelectric dams in demographically bottlenecked brown trout in a transnational subarctic riverine system

Habitat discontinuity, anthropogenic disturbance, and overharvesting have led to population fragmentation and decline worldwide. Preservation of remaining natural genetic diversity is crucial to avoid continued genetic erosion. Brown trout (Salmo trutta L.) is an ideal model species for studying anthropogenic influences on genetic integrity, as it has experienced significant genetic alterations throughout its natural distribution range due to habitat fragmentation, overexploitation, translocations, and stocking. The Pasvik River is a subarctic riverine system shared between Norway, Russia, and Finland, subdivided by seven hydroelectric power dams that destroyed about 70% of natural spawning and nursing areas. Stocking is applied in certain river parts to support the natural brown trout population. Adjacent river segments with different management strategies (stocked vs. not stocked) facilitated the simultaneous assessment of genetic impacts of dams and stocking based on analyses of 16 short tandem repeat loci. Dams were expected to increase genetic differentiation between and reduce genetic diversity within river sections. Contrastingly, stocking was predicted to promote genetic homogenization and diversity, but also potentially lead to loss of private alleles and to genetic erosion. Our results showed comparatively low heterozygosity and clear genetic differentiation between adjacent sections in nonstocked river parts, indicating that dams prevent migration and contribute to genetic isolation and loss of genetic diversity. Furthermore, genetic differentiation was low and heterozygosity relatively high across stocked sections. However, in stocked river sections, we found signatures of recent bottlenecks and reductions in private alleles, indicating that only a subset of individuals contributes to reproduction, potentially leading to divergence away from the natural genetic state. Taken together, these results indicate that stocking counteracts the negative fragmentation effects of dams, but also that stocking practices should be planned carefully in order to ensure long‐term preservation of natural genetic diversity and integrity in brown trout and other species in regulated river systems.     

Genetic support groups in the delivery of comprehensive genetic services.

This research sought information about the services provided by genetic support groups, their members' experiences in obtaining genetic and related services, and members' recommendations for improving services. Results from a survey of 43 directors of genetic support groups showed that these organizations not only provide their members with a wide range of informational and supportive services but also address the need for education of both the public and health professionals about genetic disorders. A second survey of 931 members of genetic support groups found that, although they obtained genetic information from a variety of professional and informal sources, many of them experienced barriers to obtaining sufficient genetic information. Respondents called for professionals to improve their interpersonal skills in working with clients and to assist families in obtaining a wider variety of services. On the basis of these findings, a service model and priorities are proposed to bring together genetic specialists, community professionals, and genetic support groups for the delivery of comprehensive services to individuals and families with genetic disorders.     

Quantitative genetics in conservation biology

Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.     

Population structure and genetic diversity in four tropical tree species in Costa Rica

Despite intensified interest in conservation of tropical forests, knowledge of the population genetics of tropical forest trees remains limited. We used random amplified polymorphic DNA (RAPD) data to evaluate trends in genetic diversity and differentiation for four tropical tree species, Alchornea latifolia, Dendropanax arboreus, Inga thibaudiana and Protium glabrum . These species occur at contrasting population densities along an elevational gradient and we use RAPD and ecological data to examine natural levels of genetic diversity of each species, trends in genetic variability with population density and structure, genetic differentiation along the elevation gradient, and the relationship between genetic diversity and such factors as seed dispersal and pollination syndrome. At the distances we examined (plot distances ranging from 0.8 to 8.6 km) there was very little genetic structuring at any distance along the gradient. All four species exhibited levels of variation expected for spatial distribution, mating system and pollinator syndrome; greater than 96% of the genetic variation occurred within plots for Inga thibaudiana, Protium glabrum and Dendropanax arboreus. Alchornea latifolia only occurred in a single plot. The results of this study contribute to a growing database of genetic diversity data that can be utilized to make predictions about the effect of disturbance and subsequent reductions in population size on genetic variation and structure in tropical tree species.     

Identifying mechanisms of genetic differentiation among populations in vagile species: historical factors dominate genetic differentiation in seabirds

Elucidating the factors underlying the origin and maintenance of genetic variation among populations is crucial for our understanding of their ecology and evolution, and also to help identify conservation priorities. While intrinsic movement has been hypothesized as the major determinant of population genetic structuring in abundant vagile species, growing evidence indicates that vagility does not always predict genetic differentiation. However, identifying the determinants of genetic structuring can be challenging, and these are largely unknown for most vagile species. Although, in principle, levels of gene flow can be inferred from neutral allele frequency divergence among populations, underlying assumptions may be unrealistic. Moreover, molecular studies have suggested that contemporary gene flow has often not overridden historical influences on population genetic structure, which indicates potential inadequacies of any interpretations that fail to consider the influence of history in shaping that structure. This exhaustive review of the theoretical and empirical literature investigates the determinants of population genetic differentiation using seabirds as a model system for vagile taxa. Seabirds provide a tractable group within which to identify the determinants of genetic differentiation, given their widespread distribution in marine habitats and an abundance of ecological and genetic studies conducted on this group. Herein we evaluate mitochondrial DNA (mtDNA) variation in 73 seabird species. Lack of mutation–drift equilibrium observed in 19% of species coincided with lower estimates of genetic differentiation, suggesting that dynamic demographic histories can often lead to erroneous interpretations of contemporary gene flow, even in vagile species. Presence of land across the species sampling range, or sampling of breeding colonies representing ice‐free Pleistocene refuge zones, appear to be associated with genetic differentiation in Tropical and Southern Temperate species, respectively, indicating that long‐term barriers and persistence of populations are important for their genetic structuring. Conversely, biotic factors commonly considered to influence population genetic structure, such as spatial segregation during foraging, were inconsistently associated with population genetic differentiation. In light of these results, we recommend that genetic studies should consider potential historical events when identifying determinants of genetic differentiation among populations to avoid overestimating the role of contemporary factors, even for highly vagile taxa.     

Genetics of Mandible Form in the Mouse

The underlying determination of phenotypic variability and covariability is described for 14 traits that define the morphological size and shape of the mature mouse mandible. Variability is partitioned into components due to direct additive and dominance genetic effects, indirect maternal additive genetic effects, genetic covariance between direct additive and indirect maternal additive effects and common and residual environmental effects. Multivariate analyses of the dimensionality of genetic variability indicate several complex and independent genetic components underlie the morphological form of the mandible. The multidimensional nature of the genetic components suggests a complex picture with regard to the consequences of selection on mandibular form.     

Genetic variation and fitness in salmonids

Over the last quarter century, many studieshave attempted to clarify the relationshipbetween genetic variability and fitness, butfew of these have involved salmonid fishes. Examination of studies of salmonids revealsthat such a relationship varies both among andwithin species. A correlation between geneticvariability and fitness can be affected bygenetic background, environment, and age, andit also depends upon the genetic markers andphenotypes evaluated. The relationshipsbetween molecular genetic variation,quantitative genetic variation, and phenotypicvariation may be more relevant to conservationissues than those between genetic variation andaverage fitness or performance. Consequently,future work in salmonids should include moreintensive investigation of the correspondenceof molecular genetic variation within and amongpopulations to quantitative genetic andphenotypic variation for traits affectingfitness. In the absence of a more completeunderstanding of the relationship betweengenetic variation and fitness, maintenance ofgenetic and phenotypic variation within andamong conspecific populations should beconsidered a primary goal of conservingsalmonid fishes.     

RAPD-PCR analysis of genetic diversity in the Manchurian pheasant

The genetic diversity of a local population of the Manchurian pheasant Phasianus colchicus pallasi was studied using RAPD-PCR. Based on the DNA patterns obtained in PCR with five arbitrary decanucleotide primers, we assessed genetic polymorphism of this population, estimated genetic distances between individuals, and constructed an NJ phylogenetic tree, and an UPGMA dendrogram of genetic similarity. The population was shown to exhibit high average genetic polymorphism (P = 79.4%) and genetic distances (D = 0.267). Possible reasons for the high genetic diversity of this local population are discussed.     

Genetic consequences of group living in Mongolian gerbils

Social behavior can shape the local population genetic structure of mammals. Group living can increase pairwise genetic relatedness of mammals at a local level but differentiate the genetic structure at a population level through offspring philopatry and nonrandom mating. Our study aimed to test the hypothesis that social groups of Mongolian gerbils (Meriones unguiculatus) would consist of genetically related individuals due to offspring philopatry and would have distinct genetic structures because of restricted gene flow among social groups and nonrandom mating. We genotyped 327 wild gerbils, live captured from 28 social groups in Inner Mongolia, China, using nine microsatellite loci. The within-group pairwise genetic relatedness coefficient averaged 0.28 ± 0.14 (standard deviation), whereas the average pairwise genetic relatedness coefficient of the whole gerbil population was 0.0 ± 0.2. Additionally, the value of the global F statistic (F(st)) was 0.21, suggesting a substantial genetic differentiation among social groups of Mongolian gerbils. The Bayesian clustering divided the 327 gerbils into 23 distinct genetic clusters. Therefore, our results show that high within-group genetic relatedness and among-group genetic differentiation are the genetic consequences of group living in social mammals because of restricted gene flow, female philopatry, and nonrandom mating within social groups.     

Gender differences in attitudes among those at risk for Huntington's disease

This report presents and discusses selected findings regarding gender differences from an Australian-based study that investigated attitudes of individuals at risk for Huntington's disease (HD) towards genetic risk and predictive testing. Clear gender differences emerged regarding perceived coping capacity with regard to predictive testing, as well as disclosure of the genetic risk for HD to others. Female participants were more likely to disclose their genetic risk to others, including their medical practitioners, while male participants were three times more fearful of disclosing their genetic risk to others. These findings are of interest in light of gender differences that have consistently been reported regarding the uptake of predictive testing for HD, other genetic conditions, and health services more generally. While gender differences cannot provide a fully explanatory framework for differential uptake of predictive genetic testing, men and women may experience and respond differently to the genetic risk for HD and possibly other inherited disorders. The meanings of genetic risk to men and women warrants further exploration, given anticipated increases in genetic testing for more common conditions, especially if post-test interventions are possible. These issues are also relevant within the context of individuals' concerns about the potential for discrimination on the basis of genetic risk or genetic test information.     

注意植物迁地保护中的遗传风险

稀有濒危植物迁地保护的长期目标之一就是要保护物种的遗传多样性和进化潜力。介绍了稀有濒危植物在植物园迁地保护过程中存在的一系列遗传风险。由于引种或取样的不足,容易导致被保存的物种缺乏足够的遗传代表性;盲目的引种、不合理的定植以及材料的来源不清则会导致稀有濒危植物的遗传混杂、近交衰退或杂交衰退;人为选择和生长环境的改变也容易造成濒危物种对迁地保护的遗传适应。在实际的迁地保护工作中,这些遗传风险往往被忽视。植物迁地保护中遗传风险将严重影响稀有濒危物种的回归和恢复。植物园应当重视濒危植物的遗传管理,以降低或避免迁地保护中的遗传风险。Abstract: Conserving genetic diversity of rare and endangered species and their evolutionary potential is one of the long-term goals of ex-situ conservation. Some potential genetic risks in ex-situ conservation in botanical gardens are presented. The preserved species may lack genetic representativity because of poor sampling. Inappropriate plantations, inadequate records and unclear kinships jeopardize endangered species to genetic confusion, inbreeding depression or outbreeding depression. Artificial selection and habitat conversion also potentially result endangered plants in adapting to ex-situ conservation, which had been usually overlooked. All the genetic risks can decrease the success of reintroduction and recovery. Therefore, appropriate genetic management should be carried out in botanical gardens to decrease or avoid genetic risks in ex-situ conservation.     

Genetic variation in a network of natural and reintroduced populations of Griffon vulture (Gyps fulvus) in Europe

It is generally considered that limiting the loss of genetic diversity in reintroduced populations is essential to optimize the chances of success of population restoration. Indeed, to counter founder effect in a reintroduced population we should maximize the genetic variability within the founding group but also take into account networks of natural populations in the choice of the reintroduction area. However, assessment of relevant reintroduction strategies requires long-term post-release genetic monitoring. In this study, we analyzed genetic data from a network of native and reintroduced Griffon vulture (Gyps fulvus) populations successfully restored in Southern Europe. Using microsatellite markers, we characterized the level of genetic diversity and degree of genetic structure within and among three native colonies, four captive founding groups and one long-term monitored reintroduced population. We also used Bayesian assignment analysis to examine recent genetic connections between the reintroduced population and the other populations. We aimed to assess the level of fragmentation among native populations, the effectiveness of random choice of founders to retain genetic variability of the species, the loss of genetic diversity in the reintroduced population and the effect of gene flow on this founder effect. Our results indicate that genetic diversity was similar in all populations but we detected signs of recent isolation for one native population. The reintroduced population showed a high immigration rate that limited loss of genetic diversity. Genetic investigations performed in native populations and post-released genetic monitoring have direct implications for founder choice and release design.     

The neutral theory in an infinite population

Selective substitutions at one locus induce stochastic dynamics at a linked neutral locus that resemble genetic drift even when the population size is infinite. This new stochastic force, which is called genetic draft, causes genetic variation at the neutral locus to decrease with population size and the rate of deleterious substitution to increase with population size. The fact that heterozygosities in natural populations are only weakly dependent on population size suggests that genetic draft may be a much more important stochastic force than genetic drift in natural populations. Some of the mathematical properties of genetic draft are explored.     

Evidence of rapid change in genetic structure and diversity during range expansion in a recovering large terrestrial carnivore

Recovery of natural populations occurs often with simultaneous or subsequent range expansions. According to population genetic theory, genetic structuring emerges at the expansion front together with decreasing genetic diversity, owing to multiple founder events. Thereupon, as the expansion proceeds and connectivity among populations is established, homogenization and a resurgence of genetic diversity are to be expected. Few studies have used a fine temporal scale combined with genetic sampling to track range expansions as they proceed in wild animal populations. As a natural experiment, the historical eradication of large terrestrial carnivores followed by their recovery and recolonization may facilitate empirical tests of these ideas. Here, using brown bear (Ursus arctos) as model species, we tested predictions from genetic theory of range expansion. Individuals from all over Finland were genotyped for every year between 1996 and 2010 using 12 validated autosomal microsatellite markers. A latitudinal shift of about 110 km was observed in the distribution and delineation of genetic clusters during this period. As the range expansion proceeded, we found, as theory predicts, that the degree of genetic structure decreased, and that both genetic variation and admixture increased. The genetic consequences of range expansions may first be detected after multiple generations, but we found major changes in genetic composition after just 1.5 generations, accompanied by population growth and increased migration. These rapid genetic changes suggest an ongoing concerted action of geographical and demographic expansion combined with substantial immigration of bears from Russia during the recovery of brown bears within the large ecosystem of northern Europe.     

Stocking activities for the Arctic charr in Lake Geneva: Genetic effects in space and time

Artificial stocking practices are widely used by resource managers worldwide, in order to sustain fish populations exploited by both recreational and commercial activities, but their benefits are controversial. Former practices involved exotic strains, although current programs rather consider artificial breeding of local fishes (supportive breeding). Understanding the complex genetic effects of these management strategies is an important challenge with economic and conservation implications, especially in the context of population declines. In this study, we focus on the declining Arctic charr (Salvelinus alpinus) population from Lake Geneva (Switzerland and France), which has initially been restocked with allochtonous fishes in the early eighties, followed by supportive breeding. In this context, we conducted a genetic survey to document the evolution of the genetic diversity and structure throughout the last 50 years, before and after the initiation of hatchery supplementation, using contemporary and historical samples. We show that the introduction of exotic fishes was associated with a genetic bottleneck in the 1980–1990s, a break of Hardy–Weinberg Equilibrium (HWE), a reduction in genetic diversity, an increase in genetic structure among spawning sites, and a change in their genetic composition. Together with better environmental conditions, three decades of subsequent supportive breeding using local fishes allowed to re‐establish HWE and the initial levels of genetic variation. However, current spawning sites have not fully recovered their original genetic composition and were extensively homogenized across the lake. Our study demonstrates the drastic genetic consequences of different restocking tactics in a comprehensive spatiotemporal framework and suggests that genetic alteration by nonlocal stocking may be partly reversible through supportive breeding. We recommend that conservation‐based programs consider local diversity and implement adequate protocols to limit the genetic homogenization of this Arctic charr population.