Patterns Of Neutral Genetic Diversity Research Articles

Spatial phenotypic variability is higher between island populations than between mainland populations worldwide

Spatial isolation is a key driver of population‐level variability in traits and genotypes worldwide. Geographical distance between populations typically increases isolation, but organisms face additional environmental barriers when dispersing between suitable habitat patches. Despite the predicted universal nature of the causes of isolation, global comparisons of isolation effects across taxa and geographic systems are few. We assessed the strength of isolation due to geographic and macroclimatic distance for paired marine island and paired mainland populations within the same species. Our meta‐analysis included published measurements of phenotypic traits and neutral genetic diversity from 1608 populations of 108 plant and animal species at a global scale. As expected, phenotypic differentiation was higher between marine islands than between populations on the mainland, but we found no consistent signal for differences in spatial patterns of neutral genetic diversity between the two systems. Geographic distance had comparatively weak effects on the spatial patterns of phenotypes and neutral genetic diversity. These results suggest that spatial patterns of phenotypic variation are determined by eco‐evolutionary pressures that differ more between islands than between mainland populations, while the spatial variability of neutral genetic diversity might be shaped by rather similar processes in the two systems. Our approach demonstrates that global biodiversity models that include island biology studies may progress our understanding of the interacting effects of spatial habitat structure, geographic‐ and environmental distances on biological processes underlying spatial population variability. We formulate future research directions for empirical tests and global syntheses in the field.

The effects of inversion polymorphisms on patterns of neutral genetic diversity.

The strong reduction in the frequency of recombination in heterozygotes for an inversion and a standard gene arrangement causes the arrangements to become partially isolated genetically, resulting in sequence divergence between them and changes in the levels of neutral variability at nucleotide sites within each arrangement class. Previous theoretical studies on the effects of inversions on neutral variability have either assumed that the population is panmictic or that it is divided into two populations subject to divergent selection. Here, the theory is extended to a model of an arbitrary number of demes connected by migration, using a finite island model with the inversion present at the same frequency in all demes. Recursion relations for mean pairwise coalescent times are used to obtain simple approximate expressions for diversity and divergence statistics for an inversion polymorphism at equilibrium under recombination and drift, and for the approach to equilibrium following the sweep of an inversion to a stable intermediate frequency. The effects of an inversion polymorphism on patterns of linkage disequilibrium are also examined. The reduction in effective recombination rate caused by population subdivision can have significant effects on these statistics. The theoretical results are discussed in relation to population genomic data on inversion polymorphisms, with an emphasis on Drosophila melanogaster. Methods are proposed for testing whether or not inversions are close to recombination-drift equilibrium, and for estimating the rate of recombinational exchange in heterozygotes for inversions; difficulties involved in estimating the ages of inversions are also discussed.

Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species.

Habitat fragmentation is a major cause of biodiversity loss, responsible for an alteration of intraspecific patterns of neutral genetic diversity and structure. Although neutral genetic variation can be informative for demographic inferences, it may be a poor predictor of adaptive genetic diversity and thus of the consequences of habitat fragmentation on selective evolutionary processes. In this context, we contrasted patterns of genetic diversity and structure of neutral loci (microsatellites) and immune genes (i.e., toll-like receptors) in an understorey bird species, the wedge-billed woodcreeper Glyphorynchus spirurus. The objectives were (1) to investigate forest fragmentation effects on population genetic diversity, (2) to disentangle the relative role of demography (genetic drift and migration) and selection, and (3) to assess whether immunogenetic patterns could be associated with variation of ectoparasite (i.e., ticks) pressures. Our results revealed an erosion of neutral genetic diversity and a substantial genetic differentiation among fragmented populations, resulting from a decrease in landscape connectivity and leading to the divergence of distinct genetic pools at a small spatial scale. Patterns of genetic diversity observed for TLR4 and TLR5 were concordant with neutral genetic patterns, whereas those observed for TLR3 and TLR21 were discordant. This result underlines that the dominant evolutionary force shaping immunogenetic diversity (genetic drift vs. selection) may be different depending on loci considered. Finally, tick prevalence was higher in fragmented environments. We discussed the hypothesis that pathogen selective pressures may contribute to maintain adaptive genetic diversity despite the negative demographic effect of habitat fragmentation on neutral genetic diversity.

Anthropogenic disturbance drives dispersal syndromes, demography, and gene flow in amphibian populations

AbstractThere is growing evidence that anthropogenic landscapes can strongly influence the evolution of dispersal, particularly through fragmentation, and may drive organisms into an evolutionary trap by suppressing dispersal. However, the influence on dispersal evolution of anthropogenic variation in habitat patch turnover has so far been largely overlooked. In this study, we examined how human‐driven variation in patch persistence affects dispersal rates and distances, determines dispersal‐related phenotypic specialization, and drives neutral genetic structure in spatially structured populations. We addressed this issue in an amphibian, Bombina variegata, using an integrative approach combining capture–recapture modeling, demographic simulation, common garden experiments, and population genetics. B. variegata reproduces in small ponds that occur either in habitat patches that are persistent (i.e., several decades or more), located in riverine environments with negligible human activity, or in patches that are highly temporary (i.e., a few years), created by logging operations in intensively harvested woodland. Our capture–recapture models revealed that natal and breeding dispersal rates and distances were drastically higher in spatially structured populations (SSPs) in logging environments than in riverine SSPs. Population simulations additionally showed that dispersal costs and benefits drive the fate of logging SSPs, which cannot persist without dispersal. The common garden experiments revealed that toadlets reared in laboratory conditions have morphological and behavioral specialization that depends on their habitat of origin. Toadlets from logging SSPs were found to have higher boldness and exploration propensity than those from riverine SSPs, indicating transgenerationally transmitted dispersal syndromes. We also found contrasting patterns of neutral genetic diversity and gene flow in riverine and logging SSPs, with genetic diversity and effective population size considerably higher in logging than in riverine SSPs. In parallel, intrapatch inbreeding and relatedness levels were lower in logging SSPs. Controlling for the effect of genetic drift and landscape connectivity, gene flow was found to be higher in logging than in riverine SSPs. Taken together, these results indicate that anthropogenic variation in habitat patch turnover may have an effect at least as important as landscape fragmentation on dispersal evolution and the long‐term viability and genetic structure of wild populations.

Fine-scale assessment of genetic diversity of trembling aspen in northwestern North America.

BackgroundIn North America, the last ice age is the most recent event with severe consequences on boreal species’ ranges. Phylogeographic patterns of range expansion in trembling aspen (Populus tremuloides) suggested that Beringia is likely to be a refugium and the “ice-free corridor” in Alberta may represent a region where small populations persisted during the last glacial maximum (LGM). The purpose of this study was to ascertain whether the origins of trembling aspen in western North America are reflected in the patterns of neutral genetic diversity and population structure. A total of 28 sites were sampled covering the northwestern part of aspen’s distribution, from Saskatchewan to Alaska. Twelve microsatellite markers were used to describe patterns of genetic diversity. The genetic structure of trembling aspen populations was assessed by using multivariate analyses, Mantel correlograms, neighbor-joining trees and Bayesian analysis.ResultsMicrosatellite markers revealed little to no neutral genetic structure of P. tremuloides populations in northwestern North America. Low differentiation among populations and small isolation by distance (IBD) were observed. The most probable number of clusters detected by STRUCTURE was K = 3 (∆K = 5.9). The individuals in the populations of the 3 clusters share a common gene pool and showed a high level of admixture. No evidence was found that either Beringia or the “ice-free corridor” were refugia. Highest allelic richness (AR) and lowest heterozygosity (Ho) were observed in Alberta foothills of the Rocky Mountains.ConclusionsContrary to our hypothesis, our results showed that microsatellite markers revealed little to no genetic structure in P. tremuloides populations. Consequently, no divergent populations were observed near supposed refugia. The lack of detectable refugia in Beringia and in the “ice-free corridor” was due to high levels of gene flow between trembling apsen populations. More favorable environmental conditions for sexual reproduction and successful trembling aspen seedling establishment may have contributed to increase allelic richness through recombination in populations from the Albertan foothills of the Rocky Mountains.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0810-1) contains supplementary material, which is available to authorized users.

The architecture of river networks can drive the evolutionary dynamics of aquatic populations.

It is widely recognized that physical landscapes can shape genetic variation within and between populations. However, it is not well understood how riverscapes, with their complex architectures, affect patterns of neutral genetic diversity. Using a spatially explicit agent-based modeling (ABM) approach, we evaluate the genetic consequences of dendritic river shapes on local population structure. We disentangle the relative contribution of specific river properties to observed patterns of genetic variation by evaluating how different branching architectures and downstream flow regimes affect the genetic structure of populations situated within river networks. Irrespective of the river length, our results illustrate that the extent of river branching, confluence position, and levels of asymmetric downstream migration dictate patterns of genetic variation in riverine populations. Comparisons between simple and highly branched rivers show a 20-fold increase in the overall genetic diversity and a sevenfold increase in the genetic differentiation between local populations. Given that most rivers have complex architectures, these results highlight the importance of incorporating riverscape information into evolutionary models of aquatic species and could help explain why riverine fishes represent a disproportionately large amount of global vertebrate diversity per unit of habitable area.

Dendritic connectivity shapes spatial patterns of genetic diversity: a simulation-based study.

Landscape features notoriously affect spatial patterns of biodiversity. For instance, in dendritic ecological networks (such as river basins), dendritic connectivity has been proposed to create unique spatial patterns of biodiversity. Here, we compared genetic datasets simulated under a lattice-like, a dendritic and a circular landscape to test the influence of dendritic connectivity on neutral genetic diversity. The circular landscape had a level of connectivity similar to that of the dendritic landscape, so as to isolate the influence of dendricity on genetic diversity. We found that genetic diversity and differentiation varied strikingly among the three landscapes. For instance, the dendritic landscape generated higher total number of alleles and higher global Fst than the lattice-like landscape, and these indices also varied between the dendritic and the circular landscapes, suggesting an effect of dendricity. Furthermore, in the dendritic landscape, allelic richness was higher in highly connected demes (e.g. confluences in rivers) than in low-connected demes (e.g. upstream and downstream populations), which was not the case in the circular landscape, hence confirming the major role of dendricity. This led to bell-shaped distributions of allelic richness along an upstream-downstream gradient. Conversely, genetic differentiation (Fst ) was lower in highly than in low-connected demes (which was not observed in circular landscape), and significant patterns of isolation by distance (IBD) were also observed in the dendritic landscape. We conclude that in dendritic networks, the combined influence of dendricity and connectivity generates unique spatial patterns of neutral genetic diversity, which has implications for population geneticists and conservationists.

Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard.

Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test whether the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of postglacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian computation approach, but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonization abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.

Climate change reduces genetic diversity of Canada lynx at the trailing range edge

Shifts in species distributions due to environmental change may affect the spatial pattern of genetic structure within a species' range, including possible changes to the adaptive potential of populations. We investigated spatial patterns of neutral genetic diversity and differentiation at the southern edge of the Canada lynx Lynx canadensis distribution in Ontario, Canada. We analyzed provincial fur harvest records (1972–2010) and collected and genotyped lynx pelt samples (2007–2009) from 702 lynx at 14 microsatellite loci. We show that the southern range boundary of lynx in central Canada has contracted northward by > 175 km since the 1970s, and that high winter temperature, low snow depth, and low proportion of suitable habitat are strongly correlated with low neutral genetic diversity and high genetic differentiation at the trailing range edge. Our work tests fundamental ideas about species range limits and demonstrates that environmental conditions can have a marked influence on neutral genetic structure. Our results suggest that changes in environmental conditions will result in further loss of genetic diversity and possibly reduce adaptive potential in southern peripheral lynx populations.

Rejection of a serial founder effects model of genetic and linguistic coevolution

Recent genetic studies attribute the negative correlation between population genetic diversity and distance from Africa to a serial founder effects (SFE) evolutionary process. A recent linguistic study concluded that a similar decay in phoneme inventories in human languages was also the product of the SFE process. However, the SFE process makes additional predictions for patterns of neutral genetic diversity, both within and between groups, that have not yet been tested on phonemic data. In this study, we describe these predictions and test them on linguistic and genetic samples. The linguistic sample consists of 725 widespread languages, which together contain 908 distinct phonemes. The genetic sample consists of 614 autosomal microsatellite loci in 100 widespread populations. All aspects of the genetic pattern are consistent with the predictions of SFE. In contrast, most of the predictions of SFE are violated for the phonemic data. We show that phoneme inventories provide information about recent contacts between languages. However, because phonemes change rapidly, they cannot provide information about more ancient evolutionary processes.

The impact of founder effects, gene flow, and European admixture on native American genetic diversity

Recent studies have concluded that the global pattern of neutral genetic diversity in humans reflects a series of founder effects and population movements associated with our recent expansion out of Africa. In contrast, regional studies tend to emphasize the significance of more complex patterns of colonization, gene flow, and secondary population movements in shaping patterns of diversity. Our objective in this study is to examine how founder effects, gene flow, and European admixture have molded patterns of neutral genetic diversity in the Americas. Our strategy is to test the fit of a serial founder effects process to the pattern of neutral autosomal genetic variation and to examine the contribution of gene flow and European admixture to departures from fit. The genetic data consist of 678 autosomal microsatellite loci assayed by Wang and colleagues in 530 individuals in 29 widely distributed Native American populations. We find that previous evidence for serial founder effects in the Americas may be driven in part by high levels of European admixture in northern North America, intermediate levels in Central America, and low levels in eastern South America. Geographically patterned admixture may also account for previously reported genetic differences between Andean and Amazonian groups. Though admixture has obscured the precise details of precontact evolutionary processes, we find that genetic diversity is still largely hierarchically structured and that gene flow between neighboring groups has had surprisingly little impact on macrogeographic patterns of genetic diversity in the Americas.

Sexual Systems and Population Genetic Structure in an Annual Plant: Testing the Metapopulation Model

The need for reproductive assurance during dispersal, along with the pressure of local mate competition, means that the importance of frequent or repeated colonization is implicit in the literature on sexual system evolution. However, there have been few empirical tests of the association between colonization history and sexual system in plants, and none within a single species. Here we use patterns of genetic diversity to provide such a test in the Mercurialis annua species complex, which spans the range of systems from self-compatible monoecy through androdioecy to dioecy. This variation has been hypothesized to result from differing patterns of metapopulation turnover and recolonization. Because monoecy should be favored during colonization, androdioecy and dioecy will be maintained only in regions with low rates of local extinction and recolonization, and these differences should also be reflected in patterns of neutral genetic diversity. We show that monoecious populations of M. annua display lower within-population genetic diversity than androdioecious populations and higher genetic differentiation than dioecious and androdioecious populations, as predicted by metapopulation models. In contrast, regional diversity in M. annua appears to be primarily a product of postglacial range expansion from two refugia in the eastern and western Mediterranean Basin.