Pattern Of Isolation By Distance Research Articles

The role of neutral and adaptive evolutionary processes on patterns of genetic diversity across small cave-dwelling populations of Icelandic Arctic charr (Salvelinus alpinus).

Understanding the adaptability of small populations in the face of environmental change is a central problem in evolutionary biology. Solving this problem is challenging because neutral evolutionary processes that operate on historical and contemporary timescales can override the effects of selection in small populations. We assessed the effects of isolation by colonization (IBC), isolation by dispersal limitation (IBDL) as reflected by a pattern of isolation by distance (IBD), and isolation by adaptation (IBA) and the roles of genetic drift and gene flow on patterns of genetic differentiation among 19 cave-dwelling populations of Icelandic Arctic charr (Salvelinus alpinus). We detected evidence of IBC based on the genetic affinity of nearby cave populations and the genetic relationships between the cave populations and the presumed ancestral population in the lake. A pattern of IBD was evident regardless of whether high-level genetic structuring (IBC) was taken into account. Genetic signatures of bottlenecks and lower genetic diversity in smaller populations indicate the effect of drift. Estimates of gene flow and fish movement suggest that gene flow is limited to nearby populations. In contrast, we found little evidence of IBA as patterns of local ecological and phenotypic variation showed little association with genetic differentiation among populations. Thus, patterns of genetic variation in these small populations likely reflect localized gene flow and genetic drift superimposed onto a larger-scale structure that is largely a result of colonization history. Our simultaneous assessment of the effects of neutral and adaptive processes in a tractable and replicated system has yielded novel insights into the evolution of small populations on both historical and contemporary timescales and over a smaller spatial scale than is typically studied.

An evaluation of isolation by distance and isolation by resistance on genetic structure of the Persian squirrel (Sciurus anomalus) in the Zagros forests of Iran

AbstractFor the conservation of wild species, it is important to understand how landscape change and land management can affect gene flow and movement. Landscape genetic analyses provide a powerful approach to infer effects of various landscape factors on gene flow, thereby informing conservation actions. The Persian squirrel is a keystone species in the woodlands and oak forests of Western Asia, where it has experienced recent habitat loss and fragmentation. We conducted landscape genetic analyses of individuals sampled in the northern Zagros Mountains of Iran (provinces of Kurdistan, Kermanshah, and Ilam), focusing on the evaluation of isolation by distance (IBD) and isolation by resistance (IBR), using 16 microsatellite markers. The roles of geographical distance and landscape features including roads, rivers, developed areas, farming and agriculture, forests, lakes, plantation forests, rangelands, shrublands, and rocky areas of varying canopy cover, and swamp margins on genetic structure were quantified using individual‐based approaches and resistance surface modeling. We found a significant pattern of IBD but only weak support for an effect of forest cover on genetic structure and gene flow. It seems that geographical distance is an important factor limiting the dispersal of the Persian squirrel in this region. The results of the current study inform ongoing conservation programs for the Persian squirrel in the Zagros oak forest.

Where to draw the line? Expanding the delineation of conservation units to highly mobile taxa.

Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species' range for protection when implementing conservation and management measures. However, current workflows for identifying CUs on the basis of neutral and adaptive genomic variation largely ignore information contained in patterns of isolation by distance (IBD), frequently the primary signal of population structure in highly mobile taxa, such as birds, bats, and marine organisms with pelagic larval stages. While individuals located on either end of a species' distribution may exhibit clear genetic, phenotypic, and ecological differences, IBD produces subtle changes in allele frequencies across space, making it difficult to draw clear boundaries for conservation purposes in the absence of discrete population structure. Here, we highlight potential pitfalls that arise when applying common methods for delineating CUs to continuously distributed organisms and review existing methods for detecting subtle breakpoints in patterns of IBD that can indicate barriers to gene flow in highly mobile taxa. In addition, we propose a new framework for identifying CUs in all organisms, including those characterized by continuous genomic differentiation, and suggest several possible ways to harness the information contained in patterns of IBD to guide conservation and management decisions.

Genomic Data Clarify Aquarana Systematics and Reveal Isolation-by-Distance Dominates Phylogeography of the Wide-Ranging Frog Rana clamitans

Wide-ranging species often span geographic dispersal barriers, providing opportunity for divergence via genetic drift or natural selection. Such conditions can be favorable for speciation, and wide-ranging taxa are frequently subdivided into multiple species by modern molecular studies. However, with wide-ranging species, it is important to explicitly test for isolation-by-distance (IBD), which can produce continuous genetic variation that may be misinterpreted as discrete population structure or even distinct species. Here we examine the Green Frog (Rana clamitans), a wide-ranging species of the Aquarana clade distributed across much of North America. The broader phylogenetic context for R. clamitans within Aquarana is poorly understood, particularly its relationship with the closely related and IUCN Vulnerable Florida Bog Frog (Rana okaloosae). Additionally, although phenotypic variation within Rana clamitans previously merited description of two subspecies, patterns of genetic diversity remain unclear. Using genome-wide ddRAD markers, we largely resolve relationships within Aquarana and unambiguously identify R. okaloosae as the sister lineage to R. clamitans. Despite mtDNA introgression, we find little genomic evidence of hybridization between R. okaloosae and R. clamitans. Within R. clamitans there are two well-supported and geographically divided clades, which are identified as distinct species by a multispecies coalescent-based approach. However, the two clades exhibit low genealogical divergence. Population genetic analyses reveal that genetic variation within R. clamitans is best described by a pattern of IBD rather than independently evolving lineages. We conclude that R. clamitans is indeed a single species and the subspecies concept is of limited use. Our analysis demonstrates the importance of understanding continuous genetic variation when delimiting lineages and highlights the power of combining population genetic and phylogenetic perspectives to describe diversity within wide-ranging taxa.

Isolation-by-distance and isolation-by-oceanography in Maroon Anemonefish (Amphiprion biaculeatus).

Obtaining dispersal estimates for a species is key to understanding local adaptation and population dynamics and to implementing conservation actions. Genetic isolation-by-distance (IBD) patterns can be used for estimating dispersal, and these patterns are especially useful for marine species in which few other methods are available. In this study, we genotyped coral reef fish (Amphiprion biaculeatus) at 16 microsatellite loci across eight sites across 210 km in the central Philippines to generate fine-scale estimates of dispersal. All sites except for one followed IBD patterns. Using IBD theory, we estimated a larval dispersal kernel spread of 8.9km (95% confidence interval of 2.3-18.4km). Genetic distance to the remaining site correlated strongly with the inverse probability of larval dispersal from an oceanographic model. Ocean currents were a better explanation for genetic distance at large spatial extents (sites greater than 150 km apart), while geographic distance remained the best explanation for spatial extents less than 150 km. Our study demonstrates the utility of combining IBD patterns with oceanographic simulations to understand connectivity in marine environments and to guide marine conservation strategies.

Genome-Wide Screening of Aedes aegypti (Culicidae: Diptera) Populations From Northwestern Argentina: Active and Passive Dispersal Shape Genetic Structure.

Aedes aegypti is the primary vector of arboviruses of great impact on human health. Our goal was to assess the spatial genetic structure of Ae. aegypti at the regional and local levels in Northwestern Argentina, an area with high prevalence of dengue fever. We analyzed 59 Ae. aegypti individuals collected from six locations in Northwestern Argentina using nuclear genome-wide Single Nucleotide Polymorphisms (SNPs) generated with double digest Restriction-site Associated DNA Sequencing. We also performed an entomological survey in 70 households in the cities of Orán and Tartagal. An analysis at the regional level indicated that the populations of Ae. aegypti in Northwestern Argentina are spatially structured and present a significant IBD pattern. Our results suggest that passive transport of eggs/immature stages, in both northward and southward directions, plays an important role in structuring Ae. aegypti populations at a regional scale and also as a source for the introduction of novel genetic variants through migration events into established populations. At a local level, we found neither spatial genetic structure nor significant isolation by distance (IBD) in Tartagal, indicating high gene flow within the city and active dispersal. In contrast, samples from Orán formed two clusters with a significant IBD pattern, although weaker than that at a regional level. Both populations showed signs of recent bottleneck events, probably coincident with past eradication campaigns. The entomological survey revealed a high prevalence of Ae. aegypti in both cities, although significantly higher in Tartagal.

Genetic isolation by distance in the yellowfin goby populations revealed by RAD sequencing

Population genetic studies of marine species sometimes find no clear patterns of genetic differentiation, but signals of geographic gene flow typified by isolation by distance (IBD) due to high dispersal ability. A previous study of mitochondrial DNA of the yellowfin goby Acanthogobius flavimanus indicated that this species also does not have clearly differentiated population groups around the Japanese archipelago, in contrast with other coastal goby species that have highly differentiated groups between the Sea of Japan and Pacific Ocean populations. Here, to clearly reveal phylogeographic structures of the yellowfin goby around the Japanese archipelago, we conducted large-scale RAD-sequencing analysis of their nuclear genomic SNP loci. As a result, IBD patterns were confirmed across the yellowfin goby populations, and the larval dispersal distance of this species was revealed to be approximately 19 km on average. In addition, different larval dispersal distances were estimated for its Sea of Japan and Pacific Ocean populations, suggesting that different coastal environments and/or ecological features may affect its dispersal rates. These results would provide foundations for ecological and conservation studies of the yellowfin goby and coastal fishes having similar dispersal strategy to this species.

To what extent are bryophytes efficient dispersers?

Abstract Bryophytes are typically seen as extremely efficient dispersers. Experimental evidence suggests that efficient short‐distance dispersal coupled with random long‐distance dispersal (LDD) leads to an inverse isolation effect. Under the latter, a higher genetic diversity of colonizing propagules is expected with increasing isolation, counteracting differentiation beyond the range of short‐distance dispersal. This expectation is tested from a review of evidence on spatial genetic structure and analyses of isolation‐by‐distance (IBD) at different scales. A decay of the IBD signal, characterized by non‐significant slopes between kinship coefficients and geographic distance was observed beyond 100 m. A second slope shift was observed at distances larger than 1 km, with a proportion of significant slopes in more than one third of the datasets. The decay of the IBD signal beyond 100 m, which reflects efficient LDD, is consistent with the inverse isolation hypothesis. Persistence of a significant IBD signal at medium ranges in one third of the analysed cases suggests, however, that the inverse isolation effect is not a rule in bryophyte spore dispersal. Furthermore, the higher proportion of significant IBD patterns observed at scales over 100 km likely marks the limits of regional dispersal, beyond which an increasingly smaller proportion of spores travel. Synthesis. We discuss the differences between experimental and genetic estimates of spore dispersal and conclude that geographic distance remains a significant proxy of spore colonization rates, with major consequences for our understanding of actual migration capacities in bryophytes, and hence, our capacity to model range shifts in a changing world.

Genetic diversity and population structure of white-lipped peccaries (Tayassu pecari) in the Pantanal, Cerrado and Atlantic Forest from Brazil

In general, habitat fragmentation is associated with a reduction in gene flow that can reduce the genetic diversity, and, consequently, a species ability to survive environmental changes. The white-lipped peccary (Tayassu pecari) is a Neotropical ecosystem engineer that is vulnerable throughout its distribution area and under different degrees of threat in the Brazilian Pantanal (near threatened), Cerrado (endangered) and Atlantic Forest (critically endangered). We used 13 microsatellite loci to assess the genetic diversity and population structure of 361 white-lipped peccaries sampled in four areas in the Pantanal, two areas in the Cerrado, and one area in the Atlantic Forest. We found similar levels of genetic diversity in all localities. Bayesian clustering analysis indicated the presence of two (K = 2; all Pantanal localities plus the Cerrado locality at the Pantanal highlands versus the other Cerrado locality plus the Atlantic Forest one) or three (K = 3; with the additional differentiation between the Cerrado locality and the Atlantic Forest) genetically differentiated populations. We found a pattern of isolation by distance (IBD) limited by dispersal events of up to 180 km. This IBD pattern is congruent with gene flow between the geographically closer localities in the Pantanal and the Cerrado in the Pantanal highlands (25–137 km), while dispersal between the other Cerrado locality and the Atlantic Forest, that are 500 km apart, would not be as feasible. Therefore, we considered K = 3 as the best scenario to represent the genetic structure of the populations analyzed. As all populations of white-lipped peccary showed moderate levels of genetic diversity, conservation actions are recommended to maintain their diversity, as it is vital to the long-term viability of these populations, especially those in more threatened biomes.

Response of xerophytic plants to glacial cycles in southern South America.

Quaternary glaciations strongly affected the distribution of species from arid and semi-arid environments, as temperature drops were accompanied by strong fluctuations in rainfall. In this study, we examined the response of xerophytic species to glacial cycles, determining the genetic patterns and climatic niche of Echinopsis chiloensis var. chiloensis, an endemic columnar cactus of arid and semi-arid regions of Chile. We analysed 11 polymorphic microsatellites for 130 individuals from 13 populations distributed across the entire distribution of the species. We examined genetic diversity and structure, identified possible patterns of isolation by distance (IBD) and tested two competing population history scenarios using Approximate Bayesian Computation. The first scenario assumes a constant population size while the second includes a bottleneck in the southern population. The latter scenario assumed that the southernmost populations experienced a strong contraction during glaciation, followed by a postglacial expansion; by contrast, the area of the northernmost populations remained as a stable refugium. We also used ecological niche modelling (ENM) to evaluate the location and extension of suitable areas during the Last Glacial Maximum (LGM) and the mid-Holocene. We found a decline in genetic diversity towards high latitudes and a significant IBD pattern that together with ENM predictions suggest that E. chiloensis var. chiloensis experienced range contraction northwards during wet-cold conditions of the LGM, followed by expansion during aridification of the mid-Holocene. In addition to IBD, we detected the presence of a strong barrier to gene flow at 32°30'S, which according to coalescence analysis occurred 44 kyr BP. The resulting genetic clusters differed in realized climatic niche, particularly in the variables related to precipitation. Our results suggest that the cactus E. chiloensis var. chiloensis experienced range contraction and fragmentation during the wet-cold conditions of the LGM, which may have facilitated ecological differentiation between northern and southern populations, promoting incipient speciation.

Partitioning drivers of spatial genetic variation for a continuously distributed population of boreal caribou: Implications for management unit delineation.

Isolation by distance (IBD) is a natural pattern not readily incorporated into theoretical models nor traditional metrics for differentiating populations, although clinal genetic differentiation can be characteristic of many wildlife species. Landscape features can also drive population structure additive to baseline IBD resulting in differentiation through isolation‐by‐resistance (IBR). We assessed the population genetic structure of boreal caribou across western Canada using nonspatial (STRUCTURE) and spatial (MEMGENE) clustering methods and investigated the relative contribution of IBD and IBR on genetic variation of 1,221 boreal caribou multilocus genotypes across western Canada. We further introduced a novel approach to compare the partitioning of individuals into management units (MU) and assessed levels of genetic connectivity under different MU scenarios. STRUCTURE delineated five genetic clusters while MEMGENE identified finer‐scale differentiation across the study area. IBD was significant and did not differ for males and females both across and among detected genetic clusters. MEMGENE landscape analysis further quantified the proportion of genetic variation contributed by IBD and IBR patterns, allowing for the relative importance of spatial drivers, including roads, water bodies, and wildfires, to be assessed and incorporated into the characterization of population structure for the delineation of MUs. Local population units, as currently delineated in the boreal caribou recovery strategy, do not capture the genetic variation and connectivity of the ecotype across the study area. Here, we provide the tools to assess fine‐scale spatial patterns of genetic variation, partition drivers of genetic variation, and evaluate the best management options for maintaining genetic connectivity. Our approach is highly relevant to vagile wildlife species that are of management and conservation concern and demonstrate varying degrees of IBD and IBR with clinal spatial genetic structure that challenges the delineation of discrete population boundaries.

Postglacial range expansion shaped the spatial genetic structure in a marine habitat‐forming species: Implications for conservation plans in the Eastern Adriatic Sea

AbstractAimUnderstanding how historical and contemporary processes shaped and maintain spatial patterns of genetic diversity is a major goal for conservation biologists. Here, we characterized the pattern of neutral genetic diversity and we inferred underlying processes in the habitat‐forming octocoral Paramuricea clavata in the Adriatic Sea, a peculiar phylogeographic region of the Mediterranean Sea.LocationEastern coast of the Adriatic Sea.MethodsWe genotyped seven microsatellites in 454 individuals of P. clavata from 13 populations recolonized after the Last Glacial Maximum (LGM). We estimated the levels of contemporary connectivity and genetic drift and we reconstructed the demographic history of these populations.ResultsThe pattern of spatial genetic structure resulted from the combination of hierarchical genetic clusters and isolation by distance (IBD). A significant decrease in genetic diversity and an increase of the frequencies of individual alleles likely due to allele surfing from the south to the north of the area were observed as expected after a postglacial sequential recolonization. Based on maximum likelihood analyses, the foundation of these populations was not linked to dramatic change in population size.Main conclusionOceanographic barriers to gene flow combined to the restricted dispersal of P. clavata likely maintain the hierarchical structure and the IBD pattern. We suggest that the latitudinal genetic gradient results from a northward “serial founder events” recolonization. By integrating patterns and processes, we bridge the gap between the evolutionary and the conservation biology of P. clavata, providing management guidelines, which will benefit the associated coralligenous biodiversity.

The impact of floral morphology on genetic differentiation in two closely related biennial plant species.

The genetic diversity and structure of plant populations are determined by the interaction of three distinct processes: gene flow, genetic drift and natural selection. These processes are to some extent dependent on the mating system of plants, which in turn is largely determined by floral morphology and the level of herkogamy in particular. In this study, we used molecular markers to investigate the impact of floral morphology on genetic differentiation and structure in two closely related Centaurium species that display large variation in floral morphology across two distinct geographic regions in Europe (mainland Europe and the UK). Our results showed that genetic differences between regions and populations within regions were similar for both species, but that patterns of genetic structure largely depended on the observed variation in floral morphology. Populations of Centaurium erythraea showed higher genetic differentiation and clear isolation by distance (IBD) in mainland Europe, but limited IBD in the UK. Opposite patterns were found in Centaurium littorale, with higher genetic differentiation and significant IBD in populations sampled in the UK and lower genetic differentiation in Continental populations with no pattern of IBD. Overall, these results indicate that variation in floral morphology has a profound impact on structuring of genetic diversity, with populations displaying low levels of herkogamy showing the strongest patterns of genetic structuring and the reverse pattern in populations showing high levels of herkogamy.

Isolation by distance, not incipient ecological speciation, explains genetic differentiation in an Andean songbird (Aves: Furnariidae: Cranioleuca antisiensis, Line-cheeked Spinetail) despite near threefold body size change across an environmental gradient.

During the process of ecological speciation, reproductive isolation results from divergent natural selection and leads to a positive correlation between genetic divergence and adaptive phenotypic divergence, that is, isolation by adaptation (IBA). In natural populations, phenotypic differentiation is often autocorrelated with geographic distance, making IBA difficult to distinguish from the neutral expectation of isolation by distance (IBD). We examined these two alternatives in a dramatic case of clinal phenotypic variation in an Andean songbird, the Line-cheeked Spinetail (Cranioleuca antisiensis). At its geographic extremes, this species shows a near threefold difference in body mass (11.5 to 31.0g) with marked plumage differences. We analysed phenotypic, environmental and genetic data (5,154 SNPs) from 172 individuals and 19 populations sampled along its linear distribution in the Andes. We found that body mass was tightly correlated with environmental temperature, consistent with local adaptation as per Bergmann's rule. Using a PST -FST analysis, we found additional support for natural selection driving body mass differentiation, but these results could also be explained by environment-mediated phenotypic plasticity. When we assessed the relative support for patterns of IBA and IBD using variance partitioning, we found that IBD was the best explanation for genetic differentiation along the cline. Adaptive phenotypic or environmental divergence can reduce gene flow, a pattern interpreted as evidence of ecological speciation's role in diversification. Our results provide a counterexample to this interpretation. Despite conditions conducive to ecological speciation, our results suggest that dramatic size and environmental differentiation within C.antisiensis are not limiting gene flow.

Syntopic frogs reveal different patterns of interaction with the landscape: A comparative landscape genetic study of Pelophylax nigromaculatus and Fejervarya limnocharis from central China

Amphibians are often considered excellent environmental indicator species. Natural and man‐made landscape features are known to form effective genetic barriers to amphibian populations; however, amphibians with different characteristics may have different species–landscape interaction patterns. We conducted a comparative landscape genetic analysis of two closely related syntopic frog species from central China, Pelophylax nigromaculatus (PN) and Fejervarya limnocharis (FL). These two species differ in several key life history traits; PN has a larger body size and larger clutch size, and reaches sexual maturity later than FL. Microsatellite DNA data were collected and analyzed using conventional (F ST, isolation by distance (IBD), AMOVA) and recently developed (Bayesian assignment test, isolation by resistance) landscape genetic methods. As predicted, a higher level of population structure in FL (F ST′ = 0.401) than in PN (F ST′ = 0.354) was detected, in addition to FL displaying strong IBD patterns (r = .861) unlike PN (r = .073). A general north–south break in FL populations was detected, consistent with the IBD pattern, while PN exhibited clustering of northern‐ and southern‐most populations, suggestive of altered dispersal patterns. Species‐specific resistant landscape features were also identified, with roads and land cover the main cause of resistance to FL, and elevation the main influence on PN. These different species–landscape interactions can be explained mostly by their life history traits, revealing that closely related and ecologically similar species have different responses to the same landscape features. Comparative landscape genetic studies are important in detecting such differences and refining generalizations about amphibians in monitoring environmental changes.

Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea.

Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α (sensu Postaire et al., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive FIS values (from −0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (<10 km distance) and among islands (100 to >11,000 km distance), with significant pairwise FST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo‐Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.

One species for one island? Unexpected diversity and weak connectivity in a widely distributed tropical hydrozoan.

Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal capacities. This study reports the genetic structuring in the tropical hydrozoan Lytocarpia brevirostris α (sensu Postaire et al, 2016b), a brooding species, from 13 populations in the Western Indian Ocean (WIO) and one from New Caledonia (Tropical Southwestern Pacific). At the local scale, populations rely on asexual propagation at short distance, which was not found at larger scales; identical genotypes were restricted to single populations. After the removal of repeated genotypes, all populations presented significant positive FIS values (between 0.094*** and 0.335***). Gene flow was extremely low at all spatial scales, between sites within islands (<10 km distance) and among islands (100 to>11 000 km distance), with significant pairwise FST values (between 0.012*** and 0.560***). A general pattern of IBD was found at the Indo-Pacific scale, but also within sampled ecoregions of the WIO province. Clustering analyses identified each sampled island as an independent population, whereas analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. The high population differentiation might reflect the life cycle of this brooding hydrozoan, possibly preventing regular dispersal at distances more than a few kilometres and probably leading to high cryptic diversity, each island housing an independent evolutionary lineage.

Salinity and hydrological barriers have little influence on genetic structure of the mosquitofish in a coastal landscape shaped by climate change

Gradients in salinity and vegetation have been dramatically altered along shoreline of the northern Gulf of Mexico by both natural (i.e., erosion, fluctuating sea levels) and anthropogenic (i.e., dredging, habitat restoration) drivers. We gauged the impacts of salinity gradients and open water barriers on the genetic structure of a common marsh resident, western mosquitofish (Gambusia affinis) by sampling 15 populations along 440 km of Texas/Louisiana coast. We characterized 602 individuals (~40/population) using seven microsatellite loci and our results reflected significant isolation by distance (IBD) among populations, but without the hypothesized genetic substructure from local adaptation. Large tracts of open water, thought to inhibit mosquitofish movement, were apparently not significant deterrents of dispersal. There was no evidence of a significant relationship between salinity gradients and genetic divergence. Although mosquitofish dispersal is sufficiently limited to result in a strong pattern of IBD, it is high enough to maintain the connectedness of populations. Our results suggest that limited gene flow, combined with large effective size, creates conditions suitable to adaptation to local environment, suggesting that mosquitofish and other marsh residents with similar life histories will be able to adapt to changes occurring in coastal environments.

Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept.

Despite the recent upsurge of interest on natural epigenetic variation of nonmodel organisms, factors conditioning the spatial structure of epigenetic diversity in wild plant populations remain virtually unexplored. We propose that information on processes shaping natural epigenetic variation can be gained using the spatial structure of genetic diversity as null model. Departures of epigenetic isolation-by-distance (IBD) patterns from genetic IBD patterns for the same sample, particularly differences in slope of similarity-distance regressions, will reflect the action of factors that operate specifically on epigenetic variation, including imperfect transgenerational inheritance and responsiveness to environmental factors of epigenetic marks. As a proof of concept, we provide a comparative analysis of spatial genetic and epigenetic structure of 200mapped individuals of the perennial herb Helleborus foetidus. Plants were fingerprinted using nuclear microsatellites, amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP markers. Expectations from individual-level IBD patterns were tested by means of kinship-distance regressions. Both genetic and epigenetic similarity between H.foetidus individuals conformed to theoretical expectations under individual-level IBD models. Irrespective of marker type, there were significant negative linear relationships between the kinship coefficient for plant pairs and their spatial separation. Regression slopes were significantly steeper for epigenetic markers. Epigenetic similarity between individuals was much greater than genetic similarity at shortest distances, such epigenetic 'kinship excess' tending to decrease as plant separation increased. Results suggest that moderate-to-high heritability and responsiveness to local environments are major drivers of epigenetic spatial structure in H.foetidus, and illustrate the heuristic value of comparing genetic and epigenetic spatial structure for formulating and testing hypotheses on forces shaping epigenetic diversity in wild plant populations.

Reducing bias in population and landscape genetic inferences: the effects of sampling related individuals and multiple life stages

In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. Additionally, the removal of siblings from a data set is considered best-practice, but direct comparisons of inferences made with and without siblings are limited. In this study, we sampled embryos, larvae, and adult Ambystoma maculatum from five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (FST and DC) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. We also assessed the effect of reducing the number of microsatellites used to make inference. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. We found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when using DC, the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Further, power to detect an IBD relationship was reduced when fewer microsatellites were used in the analysis.