Evolutionary aspects of population structure for molecular and quantitative traits in the freshwater snail Radix balthica

Detecting the action of selection in natural populations can be achieved using the QST-FST comparison that relies on the estimation of FST with neutral markers, and QST using quantitative traits potentially under selection. QST higher than FST suggests the action of directional selection and thus potential local adaptation. In this article, we apply the QST-FST comparison to four populations of the hermaphroditic freshwater snail Radix balthica located in a floodplain habitat. In contrast to most studies published so far, we did not detect evidence of directional selection for local optima for any of the traits we measured: QST calculated using three different methods was never higher than FST. A strong inbreeding depression was also detected, indicating that outcrossing is probably predominant over selfing in the studied populations. Our results suggest that in this floodplain habitat, local adaptation of R. balthica populations may be hindered by genetic drift, and possibly altered by uneven gene flow linked to flood frequency.     

Contrasting patterns of divergence in quantitative traits and neutral DNA markers: analysis of clinal variation

Clinal variation in quantitative traits is often attributed to the effects of spatially varying selection. However, identical patterns can be produced by the interplay between purely stochastic processes (i.e. drift in combination with spatially restricted gene flow). One means of distinguishing between adaptive and nonadaptive causes of geographical variation is to compare relative levels of between-population divergence in quantitative traits and neutral DNA markers. Such comparisons can be used to test whether levels of trait divergence attributable to additive genetic effects (as measured by QST) exceed null expectations based on the level of divergence at neutral marker loci (as measured by FST). The purpose of this study was to use an approach based on 'QST vs. FST' contrasts to test for evidence of diversifying selection on body size of an Indian fruit bat, Cynopterus sphinx (Chiroptera: Pteropodidae). Specifically, relative levels of between-population divergence in body size and microsatellite DNA markers were compared to assess whether the observed pattern of clinal size variation could be explained by a neutral model of isolation by distance. QST for body size was calculated using unbiased estimators of within- and between-population variance of principal component scores. The association between body size variation and geographical/environmental distance was tested using pairwise and partial matrix correspondence tests (MCTs). Independent variables (representing causal hypotheses) were constructed as between-locality distance matrices. The effects of neutral genetic divergence were assessed by including a matrix of pairwise FST as an independent variable. Partial MCTs revealed highly significant associations between phenotypic divergence (QST) and both geographical and environmental distance, even when the effects of neutral genetic divergence (FST) were partialled out. Results of the tests confirmed that migration-drift equilibrium is not a sufficient explanation for the latitudinal pattern of clinal size variation in C. sphinx. The geographical patterning of pairwise QST is most likely attributable to spatially varying selection and/or the direct influence of latitudinally ordered environmental effects.     

Comparison of quantitative and molecular genetic variation of native vs. invasive populations of purple loosestrife (Lythrum salicaria L., Lythraceae)

Study of adaptive evolutionary changes in populations of invasive species can be advanced through the joint application of quantitative and population genetic methods. Using purple loosestrife as a model system, we investigated the relative roles of natural selection, genetic drift and gene flow in the invasive process by contrasting phenotypical and neutral genetic differentiation among native European and invasive North American populations ( Q _ST −  F _ST analysis). Our results indicate that invasive and native populations harbour comparable levels of amplified fragment length polymorphism variation, a pattern consistent with multiple independent introductions from a diverse European gene pool. However, it was observed that the genetic variation reduced during subsequent invasion, perhaps by founder effects and genetic drift. Comparison of genetically based quantitative trait differentiation ( Q _ST) with its expectation under neutrality ( F _ST) revealed no evidence of disruptive selection ( Q _ST >  F _ST) or stabilizing selection ( Q _ST <  F _ST). One exception was found for only one trait (the number of stems) showing significant sign of stabilizing selection across all populations. This suggests that there are difficulties in distinguishing the effects of nonadaptive population processes and natural selection. Multiple introductions of purple loosestrife may have created a genetic mixture from diverse source populations and increased population genetic diversity, but its link to the adaptive differentiation of invasive North American populations needs further research.     

Inferring local adaptation from QST-FST comparisons: neutral genetic and quantitative trait variation in European populations of great snipe

We applied a phenotypic QST (PST) vs. FST approach to study spatial variation in selection among great snipe (Gallinago media) populations in two regions of northern Europe. Morphological divergence between regions was high despite low differentiation in selectively neutral genetic markers, whereas populations within regions showed very little neutral divergence and trait differentiation. QST > FST was robust against altering assumptions about the additive genetic proportions of variance components. The homogenizing effect of gene flow (or a short time available for neutral divergence) has apparently been effectively counterbalanced by differential natural selection, although one trait showed some evidence of being under uniform stabilizing selection. Neutral markers can hence be misleading for identifying evolutionary significant units, and adopting the PST-FST approach might therefore be valuable when common garden experiments is not an option. We discuss the statistical difficulties of documenting uniform selection as opposed to divergent selection, and the need for estimating measurement error. Instead of only comparing overall QST and FST values, we advocate the use of partial matrix permutation tests to analyse pairwise QST differences among populations, while statistically controlling for neutral differentiation.     

Evolution in heterogeneous environments and the potential of maintenance of genetic variation in traits of adaptive significance

The maintenance of genetic variation in traits of adaptive significance has been a major dilemma of evolutionary biology. Considering the pattern of increased genetic variation associated with environmental clines and heterogeneous environments, selection in heterogeneous environments has been proposed to facilitate the maintenance of genetic variation. Some models examining whether genetic variation can be maintained, in heterogeneous environments are reviewed. Genetic mechanisms that constrain evolution in quantitative genetic traits indicate that genetic variation can be maintained but when is not clear. Furthermore, no comprehensive models have been developed, likely due to the genetic and environmental complexity of this issue. Therefore, I have suggested two empirical approaches to provide insight for future theoretical and empirical research. Traditional path analysis has been a very powerful approach for understanding phenotypic selection. However, it requires substantial information on the biology of the study system to construct a causal model and alternatives. Exploratory path analysis is a data driven approach that uses the statistical relationships in the data to construct a set of models. For example, it can be used for understanding phenotypic selection in different environments, where there is no prior information to develop path models in the different environments. Data from Brassica rapa grown in different nutrients indicated that selection changed in the different environments. Experimental evolutionary studies will provide direct tests as to when genetic variation is maintained.     

Life history traits variation in heterogeneous environment: The case of a freshwater snail resistance to pond drying

Ecologists and population geneticists have long suspected that the diversity of living organisms was connected to the structure of their environment. In heterogeneous environments, diversifying selection combined to restricted gene flow may indeed lead to locally adapted populations. The freshwater snail, Galba truncatula, is a good model to address this question because it is present in a heterogeneous environment composed of temporary and permanent waters. In order to test the selective importance of those environments, we proposed here to measure survival of lineages from both habitats during drought episodes. To this purpose, we experimentally submitted adults and juveniles individuals from both habitats to drought. We found a difference in desiccation resistance between temporary and permanents waters only for adults. Adults from temporary habitats were found more resistant to drought. This divergence in desiccation resistance seems to explain the unexpected life history traits differences between habitats observed.     

Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus)

The capelin (Mallotus villosus) is a widespread marine fish species for which previous work has identified geographically distinct mtDNA clades, the frontiers of which are well within adult and larval dispersal capabilities. Here, we use AFLPs to test for the presence of nuclear gene flow among clades. In addition, we evaluate genetic structuring within one clade, the Northwest Atlantic (NWA). We found that each of the mtDNA clades corresponds with a unique nuclear DNA genetic cluster. Within the NWA clade, we detected individuals with small but significant amounts of genetic ancestry from other clades, likely due to historical introgression. Further support for historical introgression comes from analyses of variance in locus-specific differentiation, which support introgression between some clades and divergence without gene flow between others. Within the NWA, we identified two genetic clusters that correspond to sites in geographically adjacent areas. However, these clusters differ primarily at 'outlier' loci, and a genetic subdivision (K=2) was not supported by genetic clustering programs using neutral loci. Significant neutral F(ST) differentiation was found only between sites that otherwise differed at outlier loci. Thus, these populations may be in the initial stages of 'isolation by adaptation'. These results suggest strong between-clade reproductive isolation despite opportunities for gene flow and support the hypothesis that selection can contribute to divergence in otherwise 'open' systems.     

Stable genetic polymorphism in heterogeneous environments: balance between asymmetrical dispersal and selection in the acorn barnacle

Elucidating the processes responsible for maintaining polymorphism at ecologically relevant genes is intimately related to understanding the interplay between selection imposed by habitat heterogeneity and a species' capacity for dispersal in the face of environmental constraints. In this paper, we used a model-based approach to solve equilibria of balanced polymorphism, given values of fitness and larval dispersal among different habitats in the acorn barnacle Semibalanus balanoides from the Gulf of St Lawrence. Our results showed that allele frequencies observed at both MPI* and GPI* loci represented stable equilibria, given empirical estimates of fitness values, and that considerably more larvae dispersed from one region (north) to the other (south) than vice versa. Dispersal conditions were predicted to be similar for the maintenance of polymorphism at both loci. Moreover, the values of asymmetrical dispersal required by the model to reach stable equilibria were compatible with empirical estimates of larval dispersal and oceanic circulation documented in this system. Overall, this study illustrated the usefulness of a modified and computable version of Bulmer's model (1972) in order to test hypotheses of balanced polymorphism resulting from interactions between spatial selection and asymmetrical dispersal.     

Genotype matrix mapping: searching for quantitative trait loci interactions in genetic variation in complex traits.

In order to reveal quantitative trait loci (QTL) interactions and the relationship between various interactions in complex traits, we have developed a new QTL mapping approach, named genotype matrix mapping (GMM), which searches for QTL interactions in genetic variation. The central approach in GMM is the following. (1) Each tested marker is given a virtual matrix, named a genotype matrix (GM), containing intersecting lines and rows equal to the total allele number for that marker in the population analyzed. (2) QTL interactions are then estimated and compared through virtual networks among the GMs. To evaluate the contribution of marker combinations to a quantitative phenotype, the GMM method divides the samples into two non-overlapping subclasses, S(0) and S(1); the former contains the samples that have a specific genotype pattern to be evaluated, and the latter contains samples that do not. Based on this division, the F-measure is calculated as an index of significance. With the GMM method, we extracted significant marker combinations consisting of one to three interacting markers. The results indicated there were multiple QTL interactions affecting the phenotype (flowering date). GMM will be a valuable approach to identify QTL interactions in genetic variation of a complex trait within a variety of organisms.     

Patterns of molecular genetic variation in Plantago major and P. intermedia in relation to ozone resistance

Patterns of molecular genetic variation were examined in seed collections of Plantago major and Plantago intermedia , used previously to investigate the variations in ozone (O₃) resistance of these species across Europe. Total genomic DNA was amplified with random primers (random amplied polymorphic DNA (RAPD) and inter- single sequence repeats (SSR)) to produce 73 genetic markers. In addition, allozyme and chloroplast variations were surveyed. Genetic markers were examined for association with O₃ resistance in 18 British populations of P. major as well as 27 continental European populations of P. major and P. intermedia . Two populations that exhibited increased resistance to O₃ following several years' exposure to high O₃ concentrations in the field showed decreased genetic variation over time. In addition, their genetic composition showed no drastic change, which suggests that the change in resistance to O₃ was probably the result of selection on genotypes already present in local populations (selection in situ ). It appears that selection for O₃ resistance may occur in independent populations, and also may involve a number of genetically determined traits. Consequently the finding that plants with similar degrees of O₃ resistance are not closely related was not unexpected. However, the finding of an association of several genetic markers with O₃ resistance merits further investigation.     

Temporal genetic differentiation: continuous v. discontinuous spawning runs in anadromous rainbow smelt Osmerus mordax (Mitchill)

Genetic differentiation was greater between 'early' and 'late' spawning rainbow smelt Osmerus mordax separated by a hiatus in spawning activity compared to a continuously spawning population over a similar time period. This magnitude of temporal differentiation was comparable to that seen among spatially separated populations.     

Adaptive divergence vs. environmental plasticity: tracing local genetic adaptation of metamorphosis traits in salamanders

In order to assess the significance of local adaptation relative to environmental plasticity on the evolution of life history traits, we analysed the possible genetic basis of differences between pond- and stream-breeding fire salamanders (Salamandra salamandra) in Germany. These salamanders typically deposit their larvae in small streams, where they grow until they are sufficiently large to metamorphose. However, some populations in Western Germany use ponds as larval habitat. Because habitat quality of streams differs from that of ponds one expects life history differences in the pond animals, which may result either from a plastic response or through genetic differentiation (i.e. local adaptation). Using a phylogeographical analysis of mitochondrial D-loop sequences, we show that both stream and pond populations in Western Germany are derived from a single lineage that recolonized following the last glaciation. This finding suggests that pond breeding originated very recently. Our studies of habitat quality and metamorphic behaviour of larvae in natural ponds and streams disclosed that pond larvae experience a significantly reduced food supply and greater risk of drying than do stream larvae. Pond larvae metamorphose earlier at the cost of reduced mass. Common-environment experiments with pond and stream larvae show that metamorphic behaviour of pond larvae under limited-food conditions is determined genetically and is not simply a plastic response to the differing habitat conditions. These results show that phenotypic plasticity is less important than local adaptation in explaining differences in ecological diversification within this species and suggests the possibility of rapid evolution of genetic adaptations when new habitats are exploited.     

Natural selection and quantitative genetics of life-history traits in Western women: a twin study

Whether contemporary human populations are still evolving as a result of natural selection has been hotly debated. For natural selection to cause evolutionary change in a trait, variation in the trait must be correlated with fitness and be genetically heritable and there must be no genetic constraints to evolution. These conditions have rarely been tested in human populations. In this study, data from a large twin cohort were used to assess whether selection will cause a change among women in a contemporary Western population for three life-history traits: age at menarche, age at first reproduction, and age at menopause. We control for temporal variation in fecundity (the "baby boom" phenomenon) and differences between women in educational background and religious affiliation. University-educated women have 35% lower fitness than those with less than seven years education, and Roman Catholic women have about 20% higher fitness than those of other religions. Although these differences were significant, education and religion only accounted for 2% and 1% of variance in fitness, respectively. Using structural equation modeling, we reveal significant genetic influences for all three life-history traits, with heritability estimates of 0.50, 0.23, and 0.45, respectively. However, strong genetic covariation with reproductive fitness could only be demonstrated for age at first reproduction, with much weaker covariation for age at menopause and no significant covariation for age at menarche. Selection may, therefore, lead to the evolution of earlier age at first reproduction in this population. We also estimate substantial heritable variation in fitness itself, with approximately 39% of the variance attributable to additive genetic effects, the remainder consisting of unique environmental effects and small effects from education and religion. We discuss mechanisms that could be maintaining such a high heritability for fitness. Most likely is that selection is now acting on different traits from which it did in pre-industrial human populations.     

Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population

Understanding the genetic architecture of phenotypic variation in natural populations is a fundamental goal of evolutionary genetics. Wild Soay sheep (Ovis aries) have an inherited polymorphism for horn morphology in both sexes, controlled by a single autosomal locus, Horns. The majority of males have large normal horns, but a small number have vestigial, deformed horns, known as scurs; females have either normal horns, scurs or no horns (polled). Given that scurred males and polled females have reduced fitness within each sex, it is counterintuitive that the polymorphism persists within the population. Therefore, identifying the genetic basis of horn type will provide a vital foundation for understanding why the different morphs are maintained in the face of natural selection. We conducted a genome-wide association study using ～36000 single nucleotide polymorphisms (SNPs) and determined the main candidate for Horns as RXFP2, an autosomal gene with a known involvement in determining primary sex characters in humans and mice. Evidence from additional SNPs in and around RXFP2 supports a new model of horn-type inheritance in Soay sheep, and for the first time, sheep with the same horn phenotype but different underlying genotypes can be identified. In addition, RXFP2 was shown to be an additive quantitative trait locus (QTL) for horn size in normal-horned males, accounting for up to 76% of additive genetic variation in this trait. This finding contrasts markedly from genome-wide association studies of quantitative traits in humans and some model species, where it is often observed that mapped loci only explain a modest proportion of the overall genetic variation.     

The quantitative genetic basis of sex ratio variation in Nasonia vitripennis: a QTL study

Our understanding of how natural selection should shape sex allocation is perhaps more developed than for any other trait. However, this understanding is not matched by our knowledge of the genetic basis of sex allocation. Here, we examine the genetic basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, a species well known for its response to local mate competition (LMC). We identified a quantitative trait locus (QTL) for sex ratio on chromosome 2 and three weaker QTL on chromosomes 3 and 5. We tested predictions that genes associated with sex ratio should be pleiotropic for other traits by seeing if sex ratio QTL co-occurred with clutch size QTL. We found one clutch size QTL on chromosome 1, and six weaker QTL across chromosomes 2, 3 and 5, with some overlap to regions associated with sex ratio. The results suggest rather limited scope for pleiotropy between these traits.     

Habitat differentiation vs. isolation-by-distance: the genetic population structure of Elymus athericus in European salt marshes

We investigated genetic differentiation among populations of the clonal grass Elymus athericus, a common salt-marsh species occurring along the Wadden Sea coast of Europe. While E. athericus traditionally occurs in the high salt marsh, it recently also invaded lower parts of the marsh. In one of the first analyses of the genetic population structure in salt-marsh species, we were interested in population differentiation through isolation-by-distance, and among strongly divergent habitats (low and high marsh) in this wind- and water-dispersed species. High and low marsh habitats were sampled at six sites throughout the Wadden Sea. Based on reciprocal transplantation experiments conducted earlier revealing lower survival of foreign genotypes we predicted reduced gene flow among habitats. Accordingly, an analysis with polymorphic cross-species microsatellite primers revealed significant genetic differentiation between high and low marsh habitats already on a very small scale (< 100 m), while isolation-by-distance was present only on larger scales (60-443 km). In an analysis of molecular variance we found that 14% of the genetic variance could be explained by the differentiation between habitats, as compared to only 8.9% to geographical (isolation-by-distance) effects among six sites 2.5-443 km distant from each other. This suggests that markedly different selection regimes between these habitats, in particular intraspecific competition and herbivory, result in habitat adaptation and restricted gene flow over distances as small as 80 m. Hence, the genetic population structure of plant species can only be understood when considering geographical and selection-mediated restrictions to gene flow simultaneously.     

Maintenance of genetic variation in sexual ornaments: a review of the mechanisms

Female preferences for elaborate male sexual traits have been documented in a number of species in which males contribute only genes to the next generation. In such systems, mate choice has been hypothesised to benefit females genetically. For the genetic benefits to be possible there must be additive genetic variation (V(A)) for sexual ornaments, such that highly ornamented males can pass fitter genes on to the progeny of choosy females. Here, I review the mechanisms that can contribute to the maintenance of this variation. The variation may be limited to sexual ornaments, resulting in Fisherian benefits in terms of the increased reproductive success of male progeny produced by choosy females. Alternatively, ornaments may capture V(A) in other life-history traits. In the latter case, "good genes" benefits may apply in terms of improved performance of the progeny of either sex. Some mechanisms, however, such as negative pleiotropy, sexually antagonistic variation or overdominance, can maintain V(A )in ornaments and other life-history traits with little variation in total fitness, leaving little room for any genetic benefits of mate choice. Distinguishing between these mechanisms has consequences not only for the theory of sexual selection, but also for evolution of sex and for biological conservation. I discuss how the traditional ways of testing for genetic benefits can usefully be supplemented by tests detecting benefits resulting from specific mechanisms maintaining V(A )in sexual ornaments.     

The genetic architecture of a niche: variation and covariation in host use traits in the Colorado potato beetle

The genetic basis of host plant use by phytophagous insects can provide insight into the evolution of ecological niches, especially phenomena such as specialization and phylogenetic conservatism. We carried out a quantitative genetic analysis of multiple host use traits, estimated on five species of host plants, in the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Mean values of all characters varied among host plants, providing evidence that adaptation to plants may require evolution of both behavioral (preference) and post-ingestive physiological (performance) characteristics. Significant additive genetic variation was detected for several characters on several hosts, but not in the capacity to use the two major hosts, a pattern that might be caused by directional selection. No negative genetic correlations across hosts were detected for any 'performance' traits, i.e. we found no evidence of trade-offs in fitness on different plants. Larval consumption was positively genetically correlated across host plants, suggesting that diet generalization might evolve as a distinct trait, rather than by independent evolution of feeding responses to each plant species, but several other traits did not show this pattern. We explored genetic correlations among traits expressed on a given plant species, in a first effort to shed light on the number of independent traits that may evolve in response to selection for host-plant utilization. Most traits were not correlated with each other, implying that adaptation to a novel potential host could be a complex, multidimensional 'character' that might constrain adaptation and contribute to the pronounced ecological specialization and the phylogenetic niche conservatism that characterize many clades of phytophagous insects.