Natural selection on feralization genes contributed to the invasive spread of wild pigs throughout the United States.

Despite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa × domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci.

Analyzing Autopolyploid Genetic Data Using GenoDive.

Analyzing autopolyploid genetic data still presents numerous challenges due to, e.g., missing dosage information of genotypes and the presence of multiple ploidy levels within species or populations, but also because the choice of software is limited when compared to what is available for diploid data.

Biogeographic Population Structure of Chimeric Blades of in the Northeast Atlantic Reveals Southern Rich Gene Pools, Introgression and Cryptic Plasticity.

The genus (Bangiaceae, Rhodophyta), an important seaweed grown in aquaculture, is the most genetically diverse group of the Class Bangiophyceae, but has poorly understood genetic variability linked to complex evolutionary processes. Genetic studies in the last decades have largely focused on resolving gene phylogenies; however, there is little information on historical population biogeography, structure and gene flow in the Bangiaceae, probably due to their cryptic nature, chimerism and polyploidy, which render analyses challenging. This study aims to understand biogeographic population structure in the two abundant species in the Northeast Atlantic: (a dioecious annual) and (protandrous hermaphroditic winter annual), occupying distinct niches (seasonality and position on the shore).

History or demography? Determining the drivers of genetic variation in North American plants.

Understanding the impact of historical and demographic processes on genetic variation is essential for devising conservation strategies and predicting responses to climate change. Recolonization after Pleistocene glaciations is expected to leave distinct genetic signatures, characterised by lower genetic diversity in previously glaciated regions. Populations' positions within species ranges also shape genetic variation, following the central-marginal paradigm dictating that peripheral populations are depauperate, sparse and isolated.

Niche divergence contributes to geographical parthenogenesis in two dandelion taxa.

Many sexual-asexual complexes show a distinct pattern where the asexuals have larger and more northerly ranges than closely related sexuals. A prime candidate to explain this so-called "geographical parthenogenesis" is ecological niche divergence between the sexuals and asexuals. Modern niche modelling techniques allow testing niche divergence by directly comparing the niches of sexuals and asexuals.

genodive version 3.0: Easy-to-use software for the analysis of genetic data of diploids and polyploids.

genodive version 3.0 is a user-friendly program for the analysis of population genetic data. This version presents a major update from the previous version and now offers a wide spectrum of different types of analyses.

STRUCTURE is more robust than other clustering methods in simulated mixed-ploidy populations.

Analysis of population genetic structure has become a standard approach in population genetics. In polyploid complexes, clustering analyses can elucidate the origin of polyploid populations and patterns of admixture between different cytotypes. However, combining diploid and polyploid data can theoretically lead to biased inference with (artefactual) clustering by ploidy.

Subsampling reveals that unbalanced sampling affects STRUCTURE results in a multi-species dataset.

Studying the genetic population structure of species can reveal important insights into several key evolutionary, historical, demographic, and anthropogenic processes. One of the most important statistical tools for inferring genetic clusters is the program STRUCTURE. Recently, several papers have pointed out that STRUCTURE may show a bias when the sampling design is unbalanced, resulting in spurious joining of underrepresented populations and spurious separation of overrepresented populations.

Sex in the wild: How and why field-based studies contribute to solving the problem of sex.

Why and how sexual reproduction is maintained in natural populations, the so-called "queen of problems," is a key unanswered question in evolutionary biology. Recent efforts to solve the problem of sex have often emphasized results generated from laboratory settings. Here, we use a survey of representative "sex in the wild" literature to review and synthesize the outcomes of empirical studies focused on natural populations.

The Lesser Antillean Iguana (Iguana delicatissima) on St. Eustatius: Genetically Depauperate and Threatened by Ongoing Hybridization.

The Lesser Antillean Iguana (Iguana delicatissima) is an endangered species threatened by habitat loss and hybridization with non-native Green Iguanas (Iguana iguana). Iguana delicatissima has been extirpated on several islands, and the Green Iguana has invaded most islands with extant populations. Information is essential to protect this species from extinction.

The Analysis of Polyploid Genetic Data.

Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data-and the interpretation of the results-requires even more scrutiny than with diploid data. This is because of several polyploidy-specific complications in segregation and genotyping such as tetrasomy, double reduction, and missing dosage information.

Outbreeding depression and breeding system evolution in small, remnant populations of : consequences for genetic rescue.

Many species suffer from anthropogenic habitat fragmentation. The resulting small and isolated populations are more prone to extinction due to, amongst others, genetic erosion, inbreeding depression and Allee-effects. Genetic rescue can help mitigate such problems, but might result in outbreeding depression.

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines.

Accurately detecting signatures of local adaptation using genetic-environment associations (GEAs) requires controlling for neutral patterns of population structure to reduce the risk of false positives. However, a high degree of collinearity between climatic gradients and neutral population structure can greatly reduce power, and the performance of GEA methods in such case is rarely evaluated in empirical studies. In this study, we attempted to disentangle the effects of local adaptation and isolation by environment (IBE) from those of isolation by distance (IBD) and isolation by colonization from glacial refugia (IBC) using range-wide samples in two white pine species.

Seven common mistakes in population genetics and how to avoid them.

As the data resulting from modern genotyping tools are astoundingly complex, genotyping studies require great care in the sampling design, genotyping, data analysis and interpretation. Such care is necessary because, with data sets containing thousands of loci, small biases can easily become strongly significant patterns. Such biases may already be present in routine tasks that are present in almost every genotyping study.

Nonconvergence in Bayesian estimation of migration rates.

The estimation of migration rates using molecular markers is an important aspect of many population genetic studies. Several different methods are available for estimating migration, but most of these make multiple limiting assumptions. One method that is relatively free from assumptions is BAYESASS, which uses assignment methods in a Bayesian framework.

Dissimilarity of contemporary and historical gene flow in a wild carrot (Daucus carota) metapopulation under contrasting levels of human disturbance: implications for risk assessment and management of transgene introgression.

Background And Aims: Transgene introgression from crops into wild relatives may increase the resistance of wild plants to herbicides, insects, etc. The chance of transgene introgression depends not only on the rate of hybridization and the establishment of hybrids in local wild populations, but also on the metapopulation dynamics of the wild relative. The aim of the study was to estimate gene flow in a metapopulation for assessing and managing the risks of transgene introgression.

Quantifying introgression risk with realistic population genetics.

Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified crop regulation.

AMOVA-based clustering of population genetic data.

Determining the genetic structure of populations is becoming an increasingly important aspect of genetic studies. One of the most frequently used methods is the calculation of F-statistics using an Analysis of Molecular Variance (AMOVA). However, this has the drawback that the population hierarchy has to be known a priori.

The trouble with isolation by distance.

The genetic population structure of many species is characterised by a pattern of isolation by distance (IBD): due to limited dispersal, individuals that are geographically close tend to be genetically more similar than individuals that are far apart. Despite the ubiquity of IBD in nature, many commonly used statistical tests are based on a null model that is completely non-spatial, the Island model. Here, I argue that patterns of spatial autocorrelation deriving from IBD present a problem for such tests as it can severely bias their outcome.

The costs of sex: facing real-world complexities.

Understanding the maintenance of sexual reproduction constitutes a difficult problem for evolutionary biologists because of the immediate costs that sex seems to incur. Typically, general benefits to sex and recombination are investigated that might outweigh these costs. However, several factors can strongly influence the complex balance between costs and benefits of sex; these include constraints on the evolution of asexuality, ecological differentiation, and certain lif-history traits.

Ecology and life history affect different aspects of the population structure of 27 high-alpine plants.

A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem and historical factors. As a result, many different statistical methods exist that measure different aspects of species' genetic structure. However, little is known about how these methods are interrelated and how they are related to a species' ecology and life history.

Complex patterns of hybridization between exotic and native North American poplar species.

Premise Of The Study: Poplars and their hybrids are seen as important candidates for bioenergy initiatives. However, many concerns have been raised about large-scale plantations of new poplar cultivars. The deployment of such plants with novel traits brings the risk of potential spread of novel genome regions (including exotic genes, transgenes, or other heritable modifications) into natural populations of related species.

MARLIN, software to create, run, and analyse spatially realistic simulations.

MARLIN is a software to create, run, analyse, and visualize spatially explicit population genetic simulations. It provides an intuitive user interface with which the geographical layout of a metapopulation can be drawn by hand or loaded from a map. Furthermore, the interface allows easy selection of the many different simulation settings.