PATTERNS OF GENETIC ARCHITECTURE FOR LIFE-HISTORY TRAITS AND MOLECULAR MARKERS IN A SUBDIVIDED SPECIES

Abstract Understanding the utility and limitations of molecular markers for predicting the evolutionary potential of natural populations is important for both evolutionary and conservation genetics. To address this issue, the distribution of genetic variation for quantitative traits and molecular markers is estimated within and among 14 permanent lake populations of Daphnia pulicaria representing two regional groups from Oregon. Estimates of population subdivision for molecular and quantitative traits are concordant, with Q _ST generally exceeding G _ST. There is no evidence that microsatellites loci are less informative about subdivision for quantitative traits than are allozyme loci. Character-specific comparison of Q _ST and G _ST support divergent selection pressures among populations for the majority of life-history traits in both coast and mountain regions. The level of within-population variation for molecular markers is uninformative as to the genetic variation maintained for quantitative traits. In D. pulicaria , regional differences in the frequency of sex may contribute to variation in the maintenance of expressed within-population quantitative-genetic variation without substantially impacting diversity at the genic level. These data are compared to an identical dataset for 17 populations of the temporary-pond species, D. pulex .     

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.     

Population divergence in the amphicarpic species Amphicarpaea edgeworthii Benth. (Fabaceae): microsatellite markers and leaf morphology

Comparative analyses of the genetic differentiation in microsatellite markers ( F _ST) and leaf morphology characters ( Q _ST) of Amphicarpaea edgeworthii Benth. were conducted to gain insight into the roles of random processes and natural selection in the population divergence. Simple sequence repeat analyses on 498 individuals of 19 natural populations demonstrate that a significant genetic differentiation occurs among populations (mean F _ST = 0.578), and A. edgeworthii is a highly self-fertilized species (mean selfing rate s  = 0.989). The distribution pattern of genetic diversity in this species shows that central populations possess high genetic diversity (e.g. population WL with H _E = 0.673 and population JG with H _E = 0.663), whereas peripheral ones have a low H _E as in population JD (0.011). The morphological divergence of leaf shape was estimated by the elliptical Fourier analysis on the data from 11 natural and four common garden populations. Leaf morphology analyses indicate the morphological divergence does not show strong correlation with the genetic differentiation ( R  = 0.260, P  = 0.069). By comparing the 95% confidence interval of Q _ST with that of F _ST, Q _ST values for five out of 12 quantitative traits are significantly higher than the average F _ST value over eight microsatellite loci. The comparison of F _ST and Q _ST suggests that two kinds of traits can be driven by different evolutionary forces, and the population divergence in leaf morphology is shaped by local selections.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 505–516.     

Q ST MEETS THE G MATRIX: THE DIMENSIONALITY OF ADAPTIVE DIVERGENCE IN MULTIPLE CORRELATED QUANTITATIVE TRAITS

The Q _ST– F _ST comparison has become an increasingly common method for inferring adaptive quantitative trait divergence among populations. For cases in which there is divergence in multiple traits, most studies have applied the method by performing multiple univariate Q _ST– F _ST comparisons. However, because traits are often genetically correlated, such univariate analyses are likely to paint a simplified picture of adaptive divergence. Here we show how the multivariate analogue of Q _ST, F_STq, which accounts for genetic correlations among traits, can be used to supply a more detailed picture of multitrait divergence. We apply the method to naturally occurring genetic variation for a suite of sexually selected display traits in Drosophila serrata . The analyses suggest the operation of divergent multivariate selection that has influenced multiple independent axes of genetic variance in a sex-specific manner. Finally, we show how a comparison of the components of F_STq, the average within and among population genetic variance–covariance matrices, G_W and G_B, can be used as an additional test of the null expectation of neutral divergence, and allows for an investigation of whether natural populations have diverged along major or minor axes of genetic variance.     

Spatial and temporal scales of adaptive divergence in marine fishes and the implications for conservation

Knowledge of geographic and temporal scales of adaptive genetic variation is crucial to species conservation, yet understanding of these phenomena, particularly in marine systems, is scant. Until recently, the belief has been that because most marine species have highly dispersive or mobile life stages, local adaptation could occur only on broad geographic scales. This view is supported by comparatively low levels of genetic variation among populations as detected by neutral markers. Similarly, the time scale of adaptive divergence has also been assumed to be very long, requiring thousands of generations. Recent studies of a variety of species have challenged these beliefs. First, there is strong evidence of geographically structured local adaptation in physiological and morphological traits. Second, the proportion of quantitative trait variation at the among-population level ( Q _ST) is much higher than it is for neutral markers ( F _ST) and these two metrics of genetic variation are poorly correlated. Third, evidence that selection is a potent evolutionary force capable of sustaining adaptive divergence on contemporary time scales is summarized. The differing spatial and temporal scales of adaptive v. neutral genetic divergence call for a new paradigm in thinking about the relationship between phenogeography (the geography of phenotypic variation) and phylogeography (the geography of lineages) in marine species. The idea that contemporary selective processes can cause fine-scale spatial and temporal divergence underscores the need for a new emphasis on Darwinian fishery science.     

Microsatellite analysis of genetic population structure in an endangered salmonid: the coastal cutthroat trout (Oncorhynchus clarki clarki)

The genetic population structure of coastal cutthroat trout ( Oncorhynchus clarki clarki ) in Washington state was investigated by analysis of variation in allele frequencies at six highly polymorphic microsatellite loci for 13 anadromous populations, along with one outgroup population from the Yellowstone subspecies ( O. clarki bouvieri) (mean heterozygosity = 67%; average number of alleles per locus = 24). Tests for genetic differentiation revealed highly significant differences in genotypic frequencies for pairwise comparisons between all populations within geographical regions and overall population subdivision was substantial ( F _ST = 0.121, R _ST = 0.093), with 44.6% and 55.4% of the among-population diversity being attributable to differences between streams ( F _SR = 0.054) and between regions ( F _RT = 0.067), respectively. Analysis of genetic distances and geographical distances did not support a simple model of isolation by distance for these populations. With one exception, neighbour-joining dendrograms from the Cavalli-Sforza and Edwards' chord distances and maximum likelihood algorithms clustered populations by physiogeographic region, although overall bootstrap support was relatively low (53%). Our results suggest that coastal cutthroat trout populations are ultimately structured genetically at the level of individual streams. It appears that the dynamic balance between gene flow and genetic drift in the subspecies favours a high degree of genetic differentiation and population subdivision with the simultaneous maintenance of high heterozygosity levels within local populations. Results are discussed in terms of coastal cutthroat trout ecology along with implications for the designation of evolutionarily significant units pursuant to the US Endangered Species Act of 1973 and analogous conservation units.     

Subtle population structuring within a highly vagile marine invertebrate, the veined squid Loligo forbesi, demonstrated with microsatellite DNA markers

Microsatellite DNA markers were applied for the first time in a population genetic study of a cephalopod and compared with previous estimates of genetic differentiation obtained using allozyme and mitochondrial DNA (mtDNA) markers. Levels of genetic variation detected with microsatellites were much higher than found with previous markers (mean number of alleles per locus=10.6, mean expected heterozygosity ( H _E)=0.79; allozyme H _E=0.08; mtDNA restriction fragment length polymorphism (RFLP) H _E=0.16). In agreement with previous studies, microsatellites demonstrated genetic uniformity across the population occupying the European shelf seas of the North East Atlantic, and extreme genetic differentiation of the Azores population ( R _ST/ F _ST=0.252/0.245; allozyme F _ST=0.536; mtDNA F _ST=0.789). In contrast to other markers, microsatellites detected more subtle, and significant, levels of differentiation between the populations of the North East Atlantic offshore banks (Rockall and Faroes) and the shelf population ( R _ST=0.048 and 0.057). Breakdown of extensive gene flow among these populations is indicated, with hydrographic (water depth) and hydrodynamic (isolating current regimes) factors suggested as possible barriers to migration. The demonstration of genetic subdivision in an abundant, highly mobile marine invertebrate has implications for the interpretation of dispersal and population dynamics, and consequent management, of such a commercially exploited species. Relative levels of differentiation indicated by the three different marker systems, and the use of measures of differentiation (assuming different mutation models), are discussed.     

Geographic patterns of genetic differentiation and plumage colour variation are different in the pied flycatcher (Ficedula hypoleuca)

The pied flycatcher is one of the most phenotypically variable bird species in Europe. The geographic variation in phenotypes has often been attributed to spatial variation in selection regimes that is associated with the presence or absence of the congeneric collared flycatcher. Spatial variation in phenotypes could however also be generated by spatially restricted gene flow and genetic drift. We examined the genetic population structure of pied flycatchers across the breeding range and applied the phenotypic Q _ST ( P _ST)– F _ST approach to detect indirect signals of divergent selection on dorsal plumage colouration in pied flycatcher males. Allelic frequencies at neutral markers were found to significantly differ among populations breeding in central and southern Europe whereas northerly breeding pied flycatchers were found to be one apparently panmictic group of individuals. Pairwise differences between phenotypic ( P _ST) and neutral genetic distances ( F _ST) were positively correlated after removing the most differentiated Spanish and Swiss populations from the analysis, suggesting that genetic drift may have contributed to the observed phenotypic differentiation in some parts of the pied flycatcher breeding range. Differentiation in dorsal plumage colouration however greatly exceeded that observed at neutral genetic markers, which indicates that the observed pattern of phenotypic differentiation is unlikely to be solely maintained by restricted gene flow and genetic drift.     

Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce

Conifers are characterized by a large genome size and a rapid decay of linkage disequilibrium, most often within gene limits. Genome scans based on noncoding markers are less likely to detect molecular adaptation linked to genes in these species. In this study, we assessed the effectiveness of a genome-wide single nucleotide polymorphism (SNP) scan focused on expressed genes in detecting local adaptation in a conifer species. Samples were collected from six natural populations of white spruce ( Picea glauca ) moderately differentiated for several quantitative characters. A total of 534 SNPs representing 345 expressed genes were analysed. Genes potentially under natural selection were identified by estimating the differentiation in SNP frequencies among populations ( F _ST) and identifying outliers, and by estimating local differentiation using a Bayesian approach. Both average expected heterozygosity and population differentiation estimates ( H _E = 0.270 and F _ST = 0.006) were comparable to those obtained with other genetic markers. Of all genes, 5.5% were identified as outliers with F _ST at the 95% confidence level, while 14% were identified as candidates for local adaptation with the Bayesian method. There was some overlap between the two gene sets. More than half of the candidate genes for local adaptation were specific to the warmest population, about 20% to the most arid population, and 15% to the coldest and most humid higher altitude population. These adaptive trends were consistent with the genes' putative functions and the divergence in quantitative traits noted among the populations. The results suggest that an approach separating the locus and population effects is useful to identify genes potentially under selection. These candidates are worth exploring in more details at the physiological and ecological levels.     

Widespread gene flow and high genetic variability in populations of water voles Arvicola terrestris in patchy habitats

Theory predicts that the impact of gene flow on the genetic structure of populations in patchy habitats depends on its scale and the demographic attributes of demes (e.g. local colony sizes and timing of reproduction), but empirical evidence is scarce. We inferred the impact of gene flow on genetic structure among populations of water voles Arvicola terrestris that differed in average colony sizes, population turnover and degree of patchiness. Colonies typically consisted of few reproducing adults and several juveniles. Twelve polymorphic microsatellite DNA loci were examined. Levels of individual genetic variability in all areas were high ( H _O= 0.69–0.78). Assignments of juveniles to parents revealed frequent dispersal over long distances. The populations showed negative F _IS values among juveniles, F _IS values around zero among adults, high F _ST values among colonies for juveniles, and moderate, often insignificant, F _ST values for parents. We inferred that excess heterozygosity within colonies reflected the few individuals dispersing from a large area to form discrete breeding colonies. Thus pre-breeding dispersal followed by rapid reproduction results in a seasonal increase in differentiation due to local family groups. Genetic variation was as high in low-density populations in patchy habitats as in populations in continuous habitats used for comparison. In contrast to most theoretical predictions, we found that populations living in patchy habitats can maintain high levels of genetic variability when only a few adults contribute to breeding in each colony, when the variance of reproductive success among colonies is likely to be low, and when dispersal between colonies exceeds nearest-neighbour distances.     

RST Calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance

R _ST, an analogue of F _ST, provides a convenient approach for estimating levels of genetic differentiation from microsatellite data. This paper examines current approaches for calculating estimates of R _ST and suggests a weighting scheme based on the transformation of allele sizes at loci across data sets. Combined within an analysis of variance framework this scheme yields an estimator of R _ST analogous to the θ estimator of F _ST. Software for the IBM-PC is described which carries out such calculations and assesses the significance of R _ST or Nm estimates using bootstrap and permutation tests.     

The effect of natural selection on estimates of genetic divergence among populations of the Atlantic salmon

The effect of natural selection on the _mMEP-2 * locus on measures of genetic divergence among Atlantic salmon populations was investigated by examining the pattern of change in the level of genetic differentiation (F_ST) averaged over loci when data on the _mMEP-2 * locus were either included or excluded. The level of F_ST among populations at various geographic scales was estimated from allele frequencies at up to four loci (_s AAT-4 *, IDDH-1 *, IDHP-3 *, and _mMEP-2 *). At smaller geographic scales (within river systems or limited geographic regions) levels of variance in _mMEP-2 * allele frequencies were reduced relative to mean levels. At larger geographic scales (across continents or the species range) variation in _mMEP-2 * allele frequencies was greater than mean levels. These results suggest an a priori hypothesis for the effect of selection on the _mMEP-2 * locus which may be applied in future studies on variation in protein coding or other (e.g. mini- and microsatellite) loci in the Atlantic salmon. It is recommended that estimates of gene flow among populations of the Atlantic salmon based on mean F _ST estimates which include data on the _mMEP-2 * locus should be viewed with caution.     

Small-Scale Fragmentation Effects on Local Genetic Diversity in Two Phyllostomid Bats with Different Dispersal Abilities in Panama

Habitat fragmentation is one of the greatest threats to biodiversity. Despite their importance for conservation, the genetic consequences of small-scale habitat fragmentation for bat populations are largely unknown. In this study, we linked genetic with ecological and demographic data to assess the effects of habitat fragmentation on two species of phyllostomid bats ( Uroderma bilobatum and Carollia perspicillata ) that differ in their dispersal abilities and demographic response to fragmentation. We hypothesized that population differentiation and the effect of habitat fragmentation on levels of genetic diversity will be a function of the species' mobility. We sequenced mtDNA from 232 bats caught on 11 islands in Gatún Lake, Panamá, isolated from the mainland for ca 90 yr, and in adjacent, continuous forest on the mainland. Populations of both species showed significant genetic differentiation ( F _ST). Consistent with our prediction, population subdivision was lower in the highly mobile U. bilobatum ( F _ST= 0.01) compared to the less vagile C. perspicillata ( F _ST= 0.06), and only the latter species showed a pattern indicative of isolation by distance and, in addition, an effect of fragmentation. Genetic erosion as a result of fragmentation was also only detectable in the less mobile species, C. perspicillata , where haplotype diversity was lower in island compared to mainland populations. Our results suggest that some Neotropical bat species are prone to loss of genetic variation in response to anthropogenic small-scale habitat fragmentation. In this context, our findings point toward mobility as a good predictor of a species' vulnerability to fragmentation and altered population genetic structure.     

Microsatellite data reveals weak population substructuring in Copadichromis sp.'virginalis kajose', a demersal cichlid from Lake Malawi, Africa

Small but significant differences were found in allele frequencies among five populations (overall F _ST estimate (θ)=0·004, P=0·006; overall R _ST estimate (RHO)=0·019, P <0·00001) of the demersal cichlid Copadichromis sp.'virginalis kajose', collected from five locations in Lake Malawi. Pairwise F _ST estimates revealed significant differences between the most southerly population (Cape Maclear), and the three most northerly populations (Mbamba Bay, Metangula and Chilola). Pairwise R _ST estimates also revealed significant differences between some populations, but no geographical pattern was discernible. There was no evidence of isolation by distance using either the shortest straight-line distance between samples, or the distance around the shoreline following a 50 m depth contour. F _ST estimates were considerably lower than found in previous studies on the mbuna (rock-dwelling species), but higher than those found in a study of three pelagic cichlid species from Lake Malawi. Substructuring in C. sp.'virginalis kajose' appears to be on a similar scale to the Atlantic cod.     

Genetic diversity and genetic structure of populations of Ranunculus japonicus Thunb. (Ranunculaceae)

Abstract In order to clarify the genetic diversity and population structure of Ranunculus japonicus , allozymic analysis was conducted on 60 populations in southwestern Japan. Considerable genetic variati ons were detected among the populations of R. japonicus . The genetic diversities within species ( H _es = 0.215) and within populations ( H _ep = 0.172) were slightly higher than those of other perennial herbs with widespread distribution and outcrossing plants. Significantly higher values of fixation index were detected in some populations, which might have arisen from restricted mating partners. The majority of genetic variation (approx. 80%) resided within a population and a moderate level of genetic differentiation ( G _ST = 0.203) was observed among populations. The F _ST value (0.203) suggests the existence of a substantial population structure in this species. The highly significant correlation between geographic distance and F _ST values indicates that isolation by distance has played an important role in the construction of the genetic structure of this species.     

Comparing geographical genetic differentiation between candidate and noncandidate loci for adaptation strengthens support for parallel ecological divergence in the marine snail Littorina saxatilis

The Galician sympatric ecotypes of Littorina saxatilis have been proposed as a model system for studying parallel ecological speciation. Such a model system makes a clear prediction: candidate loci (for divergent adaptation) should present a higher level of geographical differentiation than noncandidate (neutral) loci. We used 2356 amplified fragment length polymorphisms (AFLPs) and four microsatellite loci to identify candidate loci for ecological adaptation using the F _ST outlier method. Three per cent of the studied AFLP loci were identified as candidate loci associated with adaptation, after multitest adjustments, thus contributing to ecotype differentiation (candidate loci were not detected within ecotypes). Candidate and noncandidate loci were analysed separately at four different F _ST partitions: differences between ecotypes (overall and local), differences between localities and micro-geographical differences within ecotypes. The magnitude of F _ST differed between candidate and noncandidate loci for all partitions except in the case of microgeographical differentiation within ecotypes, and the microsatellites (putatively neutral) showed an identical pattern to noncandidate loci. Thus, variation in candidate loci is determined partially independent by divergent natural selection (in addition to stochastic forces) at each locality, while noncandidate loci are exclusively driven by stochastic forces. These results support the evolutionary history described for these particular populations, considered to be a clear example of incomplete sympatric ecological speciation.     

Genetic structure within and among regional populations of the Eurasian badger (Meles meles) from Denmark and the Netherlands

The Eurasian badger Meles meles has a wide distribution area ranging from Japan to Ireland. In western Europe badger habitats are severely disturbed by anthropogenic factors, leading to fragmentation into subpopulations and formation of a metapopulation substructuring of once continuous panmictic populations. We have examined the genetic structure of Dutch and Danish badger populations on a relatively small scale (within countries) and a larger scale (between countries). The levels of genetic variation of populations were moderate and did not differ significantly among populations (overall H _O=0.30, overall H _E=0.34). Considerable genetic differentiation between the Dutch and Danish populations was found (overall F _ST=0.32, mean pairwise Dutch–Danish F _ST=0.42), indicating a large-scale substructuring of these western European badger populations. Further analysis showed that the Danish badger population can be substructured into three clusters [ P _{( k =3)}=0.99], but the Dutch populations cluster into one more or less panmictic population [ P _{( k =1)}=0.99] with little or no substructuring. The presence of migration barriers, such as roads, together with the peninsular geography of Denmark, may have led to this structuring of badger populations. In contrast, measures that improve migration and connection to other populations from neighboring countries may have prevented substructuring of the Dutch badger population.     

Population genetic structure of the butterfly Melitaea didyma (Nymphalidae) along a northern distribution range border

The population genetic structure of the butterfly Melitaea didyma was studied along the northern distribution range border in Central Germany by means of allozyme electrophoresis. Individuals were sampled from a total of 21 habitat patches from four regions, and two provinces. Sampling was designed to estimate local vs. regional differentiation. High levels of variability were found, H _e= 0.14–0.21. The mean expected sample heterozygosity from one region, Mosel, was significantly lower than from the Hammelburg region, H _e= 0.17 and 0.19, respectively. Two hierarchical levels of genetic differentiation were found. Within regions individuals sampled from different patches behaved as belonging to one population with high levels of gene flow (Hammelburg F _ST= 0.015, Mosel F _ST= 0.044), though local isolation barriers did create a substructuring of these populations. The inbreeding coefficients, F _IS, were constant over all sample levels, suggesting a similar distribution of habitat patches within regions. Between regions gene flow was limited. An isolation by distance analysis indicated that the hierarchical structure, at the provincial level, may be breaking down due to isolation of regional populations. A more general observation was that the sampling design may greatly have influenced the estimation of genetic differentiation. Depending on which samples were included, overall F _ST estimates ranged from 0.059–0.090.     

History, chance and adaptation during biological invasion: separating stochastic phenotypic evolution from response to selection

Introduced species often exhibit changes in genetic variation, population structure, selection regime and phenotypic traits as they colonize and expand into new ranges. For these reasons, species invasions are increasingly recognized as promising systems for studying adaptive evolution over contemporary time scales. However, changes in phenotypic traits during invasion occur under non-equilibrium demographic conditions and may reflect the influences of prior evolutionary history and chance events, as well as selection. We briefly review the evidence for phenotypic evolution and the role of selection during invasion. While there is ample evidence for evolutionary change, it is less clear if selection is the primary mechanism. We then discuss the likelihood that stochastic events shift phenotypic distributions during invasion, and argue that hypotheses of adaptation should be tested against appropriate null models. We suggest two experimental frameworks for separating stochastic evolution from adaptation: statistically accounting for phenotypic variation among putative invasion sources identified by using phylogenetic or assignment methods and by comparing estimates of differentiation within and among ranges for both traits and neutral markers ( Q _ST vs. F _ST). Designs that incorporate a null expectation can reveal the role of history and chance in the evolutionary process, and provide greater insights into evolution during species invasions.     

Effects of a founder event and supplementary introductions on genetic variation in a captive breeding population of the endangered Spanish killifish

Twelve polymorphic allozyme loci were employed to assess the genetic change in a captive breeding population of the endangered killifish Aphanius baeticus in the Doñana National Park, south‐western Spain. The initial founder event did not significantly reduce the allelic richness or the expected heterozygosity. No genetic bottleneck signature was detected by tests for deviation from mutation‐drift equilibrium. The F _ST between the wild source and captive population, however, was relatively high (0·053 or 0·122 when excluding or including the locus IDHP‐1 * respectively), after just two to three generations in captivity. Two generations after the incorporation of 68 new wild specimens (greater than five generations after founding) decreased the genetic differences and the F _ST(0·041 excluding IDHP‐1 *). The restoration efforts appeared to be helpful and the study of 12 polymorphic loci and a sensitive parameter such as F _ST were useful for monitoring genetic changes in captivity. Nonetheless, future monitoring should include additional highly polymorphic loci (microsatellites) to achieve higher power to detect genetic change. Such restoration and monitoring efforts should help to avoid rapid inbreeding, adaptation to captivity, and to maintain the long‐term evolutionary potential in small isolated populations.