Neighbourhood size and the importance of barriers to gene flow in an intertidal snail

ALLOZYME VARIATION IN A SNAIL (LITTORINA SAXATILIS)-DECONFOUNDING THE EFFECTS OF MICROHABITAT AND GENE FLOW

It is commonly observed that a restricted gene flow among populations of a species generates genetic differentiation in, for example, allozyme markers. However, recent studies suggest that microhabitat-specific variation may contribute to the total differentiation. To appreciate the relative contributions of geographic variation and habitat-specific variation, we sampled 42 subpopulations of the intertidal snail Littorina saxatilis from three different microhabitats (boulders, low and high rocky intertidal) on five small islands within a distance of 15 km. We used a modified orthogonal version of Nei's gene diversity analysis with a modified analysis of variance (ANOVA) that estimated the significance of habitat and geographic separation and the interaction between them. Between subpopulation differentiation (G_ST ) was usually in the range of 5% to 10% but was exceptionally high in one locus (Aat; 53%). Genetic differentiation attributable to different habitats accounted for 10% to 81% (mean 35%) of the between subpopulation variation and was significant (P < 0.05) in six loci. Differentiation due to geographic separation accounted for 11% to 61% (mean 36%) and was significant (P < 0.05) in seven loci. Furthermore, three loci showed interactions between habitat and island, suggesting varying effects of habitat in different islands. Microhabitat-specific variation, probably through spatially varying fitness, seems particularly likely in Aat and Pgm-2. Moderate levels of habitat associated variation added to the observed differentiation due to gene flow in Pgi, Pnp, and Pgm-1, whereas in the remaining three loci either the habitat effect was confused by strong habitat-island interaction (Ark) or was virtually absent (Pep and Mpi).

Statistical analyses of population genetic data: new tools, old concepts

Several methods or tests and various software are currently being developed for analyzing data in population genetics and ecology, which often rely on computer-intensive algorithms. The potential user is thus confronted with the painful experience of freedom and, in particular, has to makea priori choices between different methods. Using examples drawn from population genetics, we explain some of these recently developed tools.

Long-term genetic monitoring reveals contrasting changes in the genetic composition of newly established populations of the intertidal snail Bembicium vittatum

Newly established populations are susceptible to founder events that reduce genetic variation. This may be counterbalanced by gene flow after populations become established or founders coming from genetically different populations. However, initial gains in genetic diversity may be short-lived if there is limited mixing between lineages and subsequent inbreeding, or if one lineage sweeps to fixation through selection or genetic drift. Here, we report on the genetic changes taking place within two newly established populations of intertidal snail over a 15-year period (∼ 10 generations). Each translocation was set up using multiple, genetically distinct source populations. Our data show that higher levels of variation in the translocated populations compared to the source populations were maintained over time for both nuclear (microsatellite) and mitochondrial genes. Small changes in allele and haplotype frequencies were observed in the source populations and in one of the translocated populations, but marked changes were evident in the other, where there was a dramatic shift towards the genetic make-up of one of the source populations. These genetic changes occurred despite relatively large numbers of founders (200-374 adults) and no evidence of the population experiencing a severe reduction in effective population size. Our study shows that the genetic composition of newly established populations can vary greatly over time and that genetic outcomes can be highly variable, and significantly different from initial expectations, even when they are established using high numbers of individuals and involve source populations from the same geographic regions.

Effect of anthropogenic landscape features on population genetic differentiation of Przewalski's gazelle: main role of human settlement

Anthropogenic landscapes influence evolutionary processes such as population genetic differentiation, however, not every type of landscape features exert the same effect on a species, hence it is necessary to estimate their relative effect for species management and conservation. Przewalski's gazelle (Procapra przewalskii), which inhabits a human-altered area on Qinghai-Tibet Plateau, is one of the most endangered antelope species in the world. Here, we report a landscape genetic study on Przewalski's gazelle. We used skin and fecal samples of 169 wild gazelles collected from nine populations and thirteen microsatellite markers to assess the genetic effect of anthropogenic landscape features on this species. For comparison, the genetic effect of geographical distance and topography were also evaluated. We found significant genetic differentiation, six genetic groups and restricted dispersal pattern in Przewalski's gazelle. Topography, human settlement and road appear to be responsible for observed genetic differentiation as they were significantly correlated with both genetic distance measures [F_ST/(1−F_ST) and F′_ST/(1−F′_ST)] in Mantel tests. IBD (isolation by distance) was also inferred as a significant factor in Mantel tests when genetic distance was measured as F_ST/(1−F_ST). However, using partial Mantel tests, AIC_c calculations, causal modeling and AMOVA analysis, we found that human settlement was the main factor shaping current genetic differentiation among those tested. Altogether, our results reveal the relative influence of geographical distance, topography and three anthropogenic landscape-type on population genetic differentiation of Przewalski's gazelle and provide useful information for conservation measures on this endangered species.

Mitochondrial DNA variation in the caramote prawn Penaeus (Melicertus) kerathurus across a transition zone in the Mediterranean Sea

In this study we analysed mitochondrial DNA variation in Penaeus kerathurus prawns collected from seven locations along a transect across the Siculo-Tunisian region in order to verify if any population structuring exists over a limited geographical scale and to delineate the putative transition zone with sufficient accuracy. Partial DNA sequences of COI and 16S genes were analysed. In contrast to the highly conservative 16S gene, the COI sequences exhibited sufficient diversity for population analysis. The COI gene revealed low levels of haplotype and nucleotide diversities. The size of the annual landings of this commercial species suggests large population sizes. Hence, the low genetic diversity detected in this study could indicate a possible reduction in effective population sizes in the past. We detected significant genetic differentiation between eastern and western populations likely due to restricted gene flow across the Siculo-Tunisian boundary. We discuss the different evolutionary forces that may have shaped the genetic variation and suggest that the genetic divide is probably maintained by present-day dispersal limitation.

Review. Sympatric, parapatric or allopatric: the most important way to classify speciation?

The most common classification of modes of speciation begins with the spatial context in which divergence occurs: sympatric, parapatric or allopatric. This classification is unsatisfactory because it divides a continuum into discrete categories, concentrating attention on the extremes, and it subordinates other dimensions on which speciation processes vary, such as the forces driving differentiation and the genetic basis of reproductive isolation. It also ignores the fact that speciation is a prolonged process that commonly has phases in different spatial contexts. We use the example of local adaptation and partial reproductive isolation in the intertidal gastropod Littorina saxatilis to illustrate the inadequacy of the spatial classification of speciation modes. Parallel divergence in shell form in response to similar environmental gradients in England, Spain and Sweden makes this an excellent model system. However, attempts to demonstrate 'incipient' and 'sympatric' speciation involve speculation about the future and the past. We suggest that it is more productive to study the current balance between local adaptation and gene flow, the interaction between components of reproductive isolation and the genetic basis of differentiation.

Adaptive responses of independent traits to the same environmental gradient in the intertidal snail Bembicium vittatum

The snail Bembicium vittatum occupies a wide range of intertidal habitats in the Houtman Abrolhos Islands, Western Australia. Allozyme variation reflects patterns of connectivity, which are independent of local habitat. In contrast, heritable differences in shell shape among 83 shore sites vary with habitat, indicating local adaptation. Here we examine dimorphisms of colour and spotting of the shell in the same populations, as a test of consistency and complexity of patterns of local adaptation. Within populations, the frequency of spotted shells is higher in dark shells. Despite this association, spatial variations of colour and spotting are only weakly correlated. As predicted for traits associated with local adaptation, subdivision is greater for colour, spotting and shape than for allozymes. Colour and shape are associated with local habitat, such that populations on vertical shores have higher frequencies of dark and relatively flatter shells than those on gently sloping shores. These associations are repeatable between three separate groups of islands. Spotting shows a weaker, but significant association with the same gradient. Although shape does not differ between colour morphs within populations, the proportion of dark shells is strongly associated with shape. Thus, the independent shell traits are apparently adapted to a common, biologically significant gradient, even though the adaptive mechanisms probably differ for colour and shape. The parallel variations of independent traits highlight both the complexity of local adaptation and the potential to reveal evolutionarily significant environmental contrasts by examining adaptively relevant traits.

Population biology of the invasive freshwater snail Physa acuta approached through genetic markers, ecological characterization and demography

Abstract The respective role of factors acting on population functioning can be inferred from a variety of approaches, including population genetics and demography. We here investigated the role of four of these factors (mating systems, population size, bottlenecks and migration) in the hermaphroditic freshwater snail Physa acuta. Twenty-four populations were sampled either around Montpellier (local scale), or at the scale of France (global scale). At local scale, eight populations were sampled twice, before and after summer drying out. The genetic structure of these populations was studied using microsatellite loci. Populations were classified according to openness (ponds vs. rivers) and water regime (permanent vs. temporary) allowing predictions on genetic patterns (e.g. diversity within populations and differentiation). At local scale, progeny-arrays analysis of the selfing rate was conducted, and size distributions of individuals were followed over two years. Results with regard to the four factors mentioned above were: (i) Estimates of population selfing rates derived from inbreeding coefficients were only slightly higher than those from progeny-arrays. (ii) More variation was detected in rivers than in ponds, but no influence of water regime was detected. One reason might be that permanent populations are not going less often through low densities than those from temporary habitats at the time scale studied. (iii) There was limited evidence for genetic bottlenecks which is compatible with the fact that even marked reduction in water availability was not necessarily associated with demographic bottlenecks. More generally, bottlenecks reducing genetic variation probably occur at population foundation. (iv) Lower genetic differentiation was detected among rivers than among ponds which might be related to limitations on gene flow. Demographic and temporal genetic data further indicates that flooding in rivers is unlikely to induce marked gene flow explaining the strong genetic differentiation at short geographical scale in such habitats. Finally, the demographic data suggest that some populations are transitory and subject to recurrent recolonization, a pattern that was also detected through genetic data.

Genetic differentiation within and between populations of a hermaphroditic freshwater planarian

Dispersal of individuals is an important factor that can influence genetic differentiation between populations. The hermaphroditic freshwater planarian Schmidtea polychroainhabits shallow regions of lakes and streams, in which they appear to be continuously distributed. In the present study we used three highly polymorphic markers for analysing small-scale and large-scale genetic structure within one, and between four natural lake populations. Genetic differentiation could already be observed between samples collected at least 13 m apart, but not between neighbouring samples, and was most pronounced between samples from different lakes. Probably due to the high variance in F(ST)values, a significant correlation between genetic differentiation and geographic distance could not be observed. These results show that individual dispersal of S. polychroa is limited, but that there is gene flow between subpopulations from the same lake. They further suggest that long-distance dispersal and gene flow between lakes, if present, is not a common process in S. polychroa.

Delayed prezygotic isolating mechanisms: evolution with a twist

Assortative mating characterizes the situation wherein reproducing individuals pair according to similarity. Usually, the impetus for this bias is attributed to some type of mate choice conferring benefits (e.g., increased fitness or genetic compatibility) and, thereby, promoting speciation and phenotypic evolution. We investigate, by computer simulation of an evolving deme-structured snail population, the ramifications ensuing from passive assortative mating wherein couples exhibiting opposite shell coil direction phenotypes experience a physical constraint on mating success: putative mating partners inhabiting stout dextral and sinistral shells are unable to exchange sperm. Because shell coil chirality genotype is encoded at a single locus by shell coil alleles that are inherited maternally, snails containing sinistral alleles can present the typical dextral phenotype. Consequently, the incidence of a sinistral allele in as few as one snail can be manifested as prezygotic reproductive isolation within a deme in a subsequent generation. However, because the efficacy of achieving this type of prezygotic reproductive isolation is affected by shell form, the likelihood and product of single-gene speciation should be determined by deme interaction (migration) and composition (morphological distribution). We test this hypothesis and show how stochastic migration interacts with passive assortative mating yielding morphologically induced prezygotic reproductive isolation to produce new species phenotypes. The results show that demes can achieve rapid macroscopic phenotypic transformation and indicate that sympatric speciation might be more plausible than naturalists recognize conventionally.

Clinal variation at microsatellite loci reveals historical secondary intergradation between glacial races of Coregonus artedi (Teleostei: Coregoninae)

Classical models of the spatial structure of population genetics rely on the assumption of migration-drift equilibrium, which is seldom met in natural populations having only recently colonized their current range (e.g., postglacial). Population structure then depicts historical events, and counfounding effects due to recent secondary contact between recently differentiated lineages can further counfound analyses of association between geographic and genetic distances. Mitochondrial polymorphisms have revealed the existence of two closely related lineages of the lake cisco, Coregonus artedi, whose significantly different but overlaping geographical distributions provided a weak signal of past range fragmentation blurred by putative subsequent extensive secondary contacts. In this study, we analyzed geographical patterns of genetic variation at seven microsatellite loci among 22 populations of lake cisco located along the axis of an area covered by proglacial lakes 12,000-8,000 years ago in North America. The results clearly confirmed the existence of two genetically distinct races characterized by different sets of microsatellite alleles whose frequencies varied clinally across some 3000 km. Equilibrium and nonequilibrium analyses of isolation by distance revealed historical signal of gene flow resulting from the nearly complete admixture of these races following neutral secondary contacts in their historical habitat and indicated that the colonization process occurred by a stepwise expansion of an eastern (Atlantic) race into a previously established Mississippian race. This historical signal of equilibrium contrasted with the current migration-drift disequilibrium within major extant watersheds and was apparently maintained by high effective population sizes and low migration regimes.

Population subdivision in marine environments: the contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus

The relative importance of factors that may promote genetic differentiation in marine organisms is largely unknown. Here, contributions to population structure from a biogeographic boundary, geographical distance and the distribution of suitable habitat were investigated in Axoclinus nigricaudus, a small subtidal rock-reef fish, throughout its range in the Gulf of California. A 408-bp fragment of the mitochondrial control region was sequenced from 105 individuals. Variation was significantly partitioned between 28 of 36 possible combinations of population pairs. Phylogenetic analyses, hierarchical analyses of variance and a modified Mantel test substantiated a major break between two putative biogeographic regions. This genetic discontinuity coincides with an abrupt change in ecological characteristics, including temperature and salinity, but does not coincide with known oceanographic circulation patterns or any known historic barriers. There was an overall relationship of increasing genetic distance with increasing geographical distance between population pairs, in a manner consistent with isolation-by-distance. A significant habitat-by-geographical-distance interaction term indicated that, for a given geographical distance, populations separated by discontinuous habitat (sand) are more distinct genetically than are populations separated by continuous habitat (rock). In addition, populations separated by deep open waters were more genetically distinct than populations separated by continuous habitat (rock). These results indicate that levels of genetic differentiation among populations of A. nigricaudus cannot be explained by a single factor, but are due to the combined influences of biogeography, geographical distance and availability of suitable habitat.

Isolation by distance in the Atlantic cod, Gadus morhua, at large and small geographic scales

Genetic isolation by distance (IBD) has rarely been described in marine species with high potential for dispersal at both the larval and adult life-history stages. Here, we report significant relationships between inferred levels of gene flow and geographic distance in the Atlantic cod, Gadus morhua, at 10 nuclear restriction-fragment-length-polymorphism (RFLP) loci at small regional scales in the western north Atlantic region (< 1,600 km) that mirror those previously detected over its entire geographic range (up to 7,300 km). Highly significant allele frequency differences were observed among eight northwestern Atlantic populations, although the mean FST for all 10 loci was only 0.014. Despite this weak population structuring, the distance separating populations explained between 54% and 62% of the variation in gene flow depending on whether nine or 10 loci were used to estimate Nm. Across the species' entire geographic range, highly significant differences were observed among six regional populations at nine of the 10 loci (mean FST = 0.068) and seven loci exhibited significant negative relationships between gene flow and distance. At this large geographic scale, natural selection acting in the vicinity of one RFLP locus (GM798) had a significant effect on the correlation between gene flow and distance, and eliminating it from the analysis caused the coefficient of determination to increase from 17% to 62%. The role of vicariance was assessed by sequentially removing populations from the analysis and was found to play a minor role in contributing to the relationship between gene flow and distance at either geographic scale. The correlation between gene flow and distance detected in G. morhua at small and large spatial scales suggests that dispersal distances and effective population sizes are much smaller than predicted for the species and that the recent age of populations, rather than extensive gene flow, may be responsible for its weak population structure. Our results suggest that interpreting limited genetic differences among populations as reflecting high levels of ongoing gene flow should be made with caution.

Large scale population structure and gene flow in the planktonic developing periwinkle, Littorina striata, in Macaronesia (Mollusca: Gastropoda)

Allozymes were used to investigate the genetic structure of 42 populations of the planktonic developing, Macaronesian periwinkle Littorina striata, throughout its entire geographic range (Azores, Madeira, Canary Islands and Cape Verde Islands). This periwinkle is presumed to have a high dispersal and gene flow potential, because it has a planktonic development. It is therefore expected to show little population genetic differentiation. Indeed, based on Wright's hierarchical F-statistics, no significant genetic differentiation could be detected among populations, at any of the specified hierarchical levels (i.e. population, island, and archipelago). Nevertheless, the Cape Verde Islands seemed genetically more diverse (highest mean number of alleles per locus). The number of loci revealing a significant genetic heterogeneity increased with increasing distance between populations, while private alleles based gene flow (Nm) estimates also revealed a tendency towards a geographical pattern. The distribution of rare and private alleles, might account for these observations which suggested some geographical effect. Because of the low frequency at which these alleles occur, their influence on the genetic population structure is negligible, and not picked up by F-statistics.

Influence of landscape on the population genetic structure of the alpine butterfly parnassius smintheus (Papilionidae)

Four microsatellite DNA markers were developed which were used to examine the relationship between landscape and population genetic structure among a set of populations of the butterfly Parnassius smintheus located in the foothills of the Canadian Rockies. Detailed information on the dispersal of adult butterflies among this same set of populations was available. Simple and partial Mantel tests were used to examine the relationships between genetic distances, predicted rates of dispersal, and a number of landscape variables, all measured pairwise for 17 sample sites. Nei's standard genetic distance was negatively correlated with predicted dispersal. We observed a significant pattern of isolation by distance at a very small spatial scale. The distance between sites that was through forest was a stronger predictor of genetic distance than the distance through open meadow, indicating a significant effect of landscape on population genetic structure beyond that of simple isolation by distance. Our results suggest that rises in the tree-line in alpine areas, caused by global warming, will lead to reduced gene flow among populations of P. smintheus.