Epigenetic and Genetic Differentiation Between Coregonus Species Pairs.

Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation.

Environmental selection, rather than neutral processes, best explain regional patterns of diversity in a tropical rainforest fish.

To conserve the high functional and genetic variation in hotspots such as tropical rainforests, it is essential to understand the forces driving and maintaining biodiversity. We asked to what extent environmental gradients and terrain structure affect morphological and genomic variation across the wet tropical distribution of an Australian rainbowfish, Melanotaenia splendida splendida. We used an integrative riverscape genomics and morphometrics framework to assess the influence of these factors on both putative adaptive and non-adaptive spatial divergence.

Design and validation of a high-density single nucleotide polymorphism array for the Eastern oyster (Crassostrea virginica).

Dense single nucleotide polymorphism (SNP) arrays are essential tools for rapid high-throughput genotyping for many genetic analyses, including genomic selection and high-resolution population genomic assessments. We present a high-density (200 K) SNP array developed for the Eastern oyster (Crassostrea virginica), which is a species of significant aquaculture production and restoration efforts throughout its native range. SNP discovery was performed using low-coverage whole-genome sequencing of 435 F1 oysters from families from 11 founder populations in New Brunswick, Canada.

Genome-wide DNA methylation predicts environmentally driven life history variation in a marine fish.

Epigenetic modifications are thought to be one of the molecular mechanisms involved in plastic adaptive responses to environmental variation. However, studies reporting associations between genome-wide epigenetic changes and habitat-specific variations in life history traits (e.g.

Landscape genomics of the American lobster (Homarus americanus).

In marine species experiencing intense fishing pressures, knowledge of genetic structure and local adaptation represent a critical information to assist sustainable management. In this study, we performed a landscape genomics analysis in the American lobster to investigate the issues pertaining to the consequences of making use of putative adaptive loci to reliably infer population structure and thus more rigorously delineating biological management units in marine exploited species. Toward this end, we genotyped 14,893 single nucleotide polymorphism (SNPs) in 4190 lobsters sampled across 96 sampling sites distributed along 1000 km in the northwest Atlantic in both Canada and the USA.

Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads.

Nascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) such as insertions, deletions and other rearrangements, allowing further insights into the genetic architecture of speciation and how different types of variants are involved in species differentiation.

Epigenomic modifications induced by hatchery rearing persist in germ line cells of adult salmon after their oceanic migration.

Human activities induce direct or indirect selection pressure on natural population and may ultimately affect population's integrity. While numerous conservation programs aimed to minimize human-induced genomic variation, human-induced environmental variation may generate epigenomic variation potentially affecting fitness through phenotypic modifications. Major questions remain pertaining to how much epigenomic variation arises from environmental heterogeneity, whether this variation can persist throughout life, and whether it can be transmitted across generations.

Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly.

Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale.

Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish.

Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be used to infer neutral and/or adaptive population genetic structure, whose study has been restricted to microsatellites, mitochondrial DNA and Amplified fragment length polymorphism markers in the past and more recently the use of single nucleotide polymorphisms (SNPs).

Adaptive and maladaptive genetic diversity in small populations: Insights from the Brook Charr (Salvelinus fontinalis) case study.

Investigating the relative importance of neutral versus selective processes governing the accumulation of genetic variants is a key goal in both evolutionary and conservation biology. This is particularly true in the context of small populations, where genetic drift can counteract the effect of selection. Using Brook Charr (Salvelinus fontinalis) from Québec, Canada, as a case study, we investigated the importance of demographic versus selective processes governing the accumulation of both adaptive and maladaptive mutations in closed versus open and connected populations to assess gene flow effect.

Demography, genetics, and decline of a spatially structured population of lekking bird.

Understanding the mechanisms underlying population decline is a critical challenge for conservation biologists. Both deterministic (e.g.

Latitudinal variation in climate-associated genes imperils range edge populations.

The ecological impacts of increasing global temperatures are evident in most ecosystems on Earth, but our understanding of how climatic variation influences natural selection and adaptive resilience across latitudes remains largely unknown. Latitudinal gradients allow testing general ecosystem-level theories relevant to climatic adaptation. We assessed differences in adaptive diversity of populations along a latitudinal region spanning highly variable temperate to subtropical climates.

Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species.

Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge of genotypic variation and evolution has largely been acquired by means of single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role of structural variants (SVs) and particularly that of CNVs has been overlooked in wild populations, partly due to their challenging identification.

Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish.

Gene flow has tremendous importance for local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of the evolutionary mechanisms impending or favouring local adaptation in the presence of gene flow is still limited to a restricted number of study systems.

The Epigenetics Dilemma.

This special issue of Genes demonstrates clearly that research in epigenetics has proceeded at a very rapid pace in the last decade. [..

Absence of founder effect and evidence for adaptive divergence in a recently introduced insular population of white-tailed deer (Odocoileus virginianus).

Islands are generally colonized by few individuals which could lead to a founder effect causing loss of genetic diversity and rapid divergence by strong genetic drift. Insular conditions can also induce new selective pressures on populations. Here, we investigated the extent of genetic differentiation within a white-tailed deer (Odocoileus virginianus) population introduced on an island and its differentiation with its source mainland population.

Evidence for host effect on the intestinal microbiota of whitefish ( sp.) species pairs and their hybrids.

Investigating relationships between microbiota and their host is essential toward a full understanding of how animal adapt to their environment. Lake Whitefish offers a powerful system to investigate processes of adaptive divergence where the dwarf, limnetic species evolved repeatedly from the normal, benthic species. We compared the transient intestinal microbiota between both species from the wild and in controlled conditions, including their reciprocal hybrids.

Kin-dependent dispersal influences relatedness and genetic structuring in a lek system.

Kin selection and dispersal play a critical role in the evolution of cooperative breeding systems. Limited dispersal increases relatedness in spatially structured populations (population viscosity), with the result that neighbours tend to be genealogical relatives. Yet the increase in neighbours' fitness-related performance through altruistic interaction may also result in habitat saturation and thus exacerbate local competition between kin.

Seascape genomics of eastern oyster () along the Atlantic coast of Canada.

Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq.

Impact of supplementation on deleterious mutation distribution in an exploited salmonid.

Deleterious mutations have important implications for the evolutionary trajectories of populations. While several studies recently investigated the dynamics of deleterious mutations in wild populations, no study has yet explored the fate of deleterious mutations in a context of populations managed by supplementation. Here, based on a dataset of nine wild and 15 supplemented Lake Trout populations genotyped at 4,982 single nucleotide polymorphisms (SNP)s by means of genotype by sequencing (GBS), we explored the effect of supplementation on the frequency of putatively deleterious variants.

Predicting the genetic impact of stocking in Brook Charr () by combining RAD sequencing and modeling of explanatory variables.

In fisheries management, intensive stocking programs are commonly used to enhance population abundance and maintain stock productivity. However, such practices are increasingly raising concerns as multiple studies documented adverse genetic and evolutionary impacts of stocking on wild populations. Improvement of stocking management relies on a better understanding of the dynamic of introgressive hybridization between wild and domestic population and on assessment of the genetic state of wild populations after stocking cessation.

Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon.

Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining fisheries. However, the beneficial role of this widely used management practice is highly debated since fitness decrease of hatchery-origin fish in the wild has been documented.