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Population genomic and phylogenomic analyses of Atlantic cod provide new insights into the origin and maintenance of supergenes and highlight the role of recombination and structural variants.

Understanding the adaptive potential of populations and species is pivotal for minimizing the loss of biodiversity in this era of rapid climate change. Adaptive potential has been estimated in various ways, including based on levels of standing genetic variation, presence of potentially beneficial alleles, and/or the severity of environmental change. Kokanee salmon, the non‐migratory ecotype of sockeye salmon (Oncorhynchus nerka), is culturally and economically important and has already been impacted by the effects of climate change. To assess its climate vulnerability moving forward, we integrated analyses of standing genetic variation, genotype‐environment associations, and climate modeling based on sequence and structural genomic variation from 224 whole genomes sampled from 22 lakes in British Columbia and Yukon (Canada). We found that variables for extreme temperatures, particularly warmer temperatures, had the most pervasive signature of selection in the genome and were the strongest predictors of levels of standing variation and of putatively adaptive genomic variation, both sequence and structural. Genomic offset estimates, a measure of climate vulnerability, were significantly correlated with higher increases in extreme warm temperatures, further highlighting the risk of summer heat waves that are predicted to increase in frequency in the future. Levels of standing genetic variation, an important metric for population viability and resilience, were not correlated with genomic offset. Nonetheless, our combined approach highlights the importance of integrating different sources of information and genomic data to formulate more comprehensive and accurate predictions on the vulnerability of populations and species to future climate change.

Despite widespread declines of many wildlife species, the effects of population decline on the genome and the recovery potential of affected species are still poorly understood, especially beyond a few charismatic species. The Northern abalone (or Pinto abalone; Haliotis kamtschatkana) is a marine gastropod mollusk of social, cultural and historical economic importance in the Pacific Northwest of North America that experienced a decline in population density due to commercial harvest, and is currently listed as endangered in Canada under the Species at Risk Act. Previous genetic investigations based on microsatellites and reduced‐representation approaches concluded that Northern abalone is panmictic throughout its range, from Alaska to California, and identified high levels of genetic variation with no indication of population decline. Using whole genome resequencing data from Northern abalone sampled across the northern part of the species range, we instead identified both: (1) significant differentiation between two genetic groups, albeit concentrated in few genomic regions, and (2) a strong signature of a dramatic population decline, without genomic evidence of genetic inbreeding. Demographic reconstructions showed a modest signal of recent population expansion, supported by an increasing number of juveniles observed during dive surveys. We also found evidence of historical, rather than current, connectivity throughout the area investigated. These results are important for management decisions and highlight the utility of whole genome data in conservation, especially in species with historically large effective population sizes like the Northern abalone.

Genomic tools are becoming increasingly necessary for mitigating biodiversity loss and guiding management decisions in the context of climate change. Freshwater fish species are particularly susceptible to the impacts of changing environments, including kokanee, the resident form of sockeye salmon (Oncorhynchus nerka), which has already been negatively impacted by increases in extreme temperature throughout its distribution. A previous study using whole genome resequencing of wild kokanee stocks identified 1412 environmentally associated SNPs and demonstrated genomic offset, a measure of climate vulnerability, to be significantly correlated with higher increases in extreme warm temperatures across much of the species' range in western Canada. Here, we aimed to operationalize this information for fisheries management by first developing a Genotyping‐in‐Thousands by sequencing (GT‐seq) panel populated exclusively with environment associated SNPs. We then evaluated the robustness of the GT‐seq panel relative to the signal in the whole genome resequencing baseline and demonstrated a novel application of donor and recipient importance (DI/RI) analysis to inform recreational fisheries stocking decisions. We found that a reduced GT‐seq panel of 616 SNPs exhibited a significant positive correlation with those calculated from the full set of 1412 SNPs across the climate change scenarios tested; similar results were obtained when adding new reference populations not included in the original whole genome resequencing baseline. The DI/RI analysis revealed clear spatial trends, with populations situated in the warmest regions of southern interior British Columbia (Canada) having the highest probability for successful translocations to different recipient locations to the north. Similarly, candidate recipient lakes for stocking at the center of the distribution had higher recipient importance values than those located towards the eastern and western range peripheries. Although further refinement is required, pairing targeted genotyping with genomic offset and DI/RI predictions holds great promise for informing freshwater fisheries management moving forward.

The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and recombination landscapes in shaping genetic diversity across genomes and among populations. This is particularly relevant when local adaptation occurs despite gene flow, where clustering of differentiated loci can maintain locally adapted variants by reducing recombination between them. However, the limited genomic resources for nonmodel species, including reference genomes and recombination maps, have constrained our understanding of these patterns. In this study, we leverage the Atlantic silverside—a nonmodel fish with extensive local adaptation across a steep latitudinal gradient—as an ideal system to explore how genome structure influences adaptation under varying levels of gene flow, using a newly available reference genome and multiple recombination maps. Analyzing 168 genomes from four populations, we found a continuum of genome-wide differentiation increasing from south to north, reflecting higher connectivity among southern populations and reduced gene flow at northern latitudes. With increasing gene flow, the number and clustering of FST outlier loci also increased, with differentiated loci found exclusively within large haploblocks harboring inversions and smaller peaks overlapping putative centromeric regions. Notably, sequence divergence was only evident in inversions, supporting their role in adaptive divergence with gene flow, whereas centromeric regions appeared differentiated because of low recombination and diversity, with no indication of elevated divergence. Our results support the hypothesis that clustered genomic architectures evolve with high gene flow and enhance our understanding of how inversions and centromeres are linked to different evolutionary processes.

Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes. The effects of BGS reflect the interplay of the rates and fitness effects of deleterious mutations with recombination. A fundamental assumption of BGS models is that recombination rates are invariant over time. However, in some lineages, recombination rates evolve rapidly, violating this central assumption. Here, we investigate how recombination rate evolution affects genetic variation under BGS. We show that recombination rate evolution modifies the effects of BGS in a manner similar to a localized change in the effective population size, potentially leading to underestimation or overestimation of the genome-wide effects of selection. Furthermore, we find evidence that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.

Hybridization can negatively impact one or both taxa involved and therefore pose conservation concerns. Climate change is expected to increase the rate of hybridization particularly in polar regions, and so investigating hybridization in Arctic and Antarctic species is important for conservation. Hybridization and genetic introgression have been observed between Pacific populations of thick-billed (Uria lomvia) and common murres (Uria aalge), species of seabirds with arctic and low arctic/temperate distributions, respectively. We employed double-digest restriction site-associated DNA sequencing (ddRADseq) to generate thousands of genome-wide markers to investigate hybridization and introgression in 133 thick-billed and 119 common murres sampled from 15 colonies throughout the North Atlantic. We used molecular assignments and principal components analysis to identify hybrids and quantify genetic introgression. Despite previous reports of hybridization between murre species in the Atlantic, we found no evidence for hybrid individuals in our dataset, and limited evidence for introgression. Our results suggest that hybridization between Atlantic murre species is rare, and does not currently pose a conservation concern for either species. Our study provides baseline data for monitoring hybridization between murres in the Atlantic to assess future impacts of climate change on these species.

The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different mammalian clades—Peromyscus rodents, Mus mice, and great apes—from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades but not the Mus clade, suggesting that the dramatic chromosomal rearrangements among Mus species may have masked the ancestral genomic landscape of divergence in many comparisons. Our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different sizes is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations revealed that chromosomal rearrangements, demography, and divergence times may also affect the relationship between chromosome size and divergence, thus deepening our understanding of the role of genome structure in the evolution of species divergence.

Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick‐billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick‐billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome‐wide markers mapped to a newly assembled thick‐billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non‐breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds. Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. To test whether thick‐billed murres from five colonies along the Eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genomewide markers mapped to a newly assembled thick‐billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide SNPs and 137 outlier SNPs. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their nonbreeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.

Avian migration is a widespread, complex behavior that has long fascinated both scientists and the general public. Nonetheless, we have not identified the genetic and environmental controls of migration. Comparisons of migratory strategies within and among species suggest that these differences are associated with genetic and personality variation. Recently, studies have identified possible candidate genes for personality and migration in several avian taxa. Partially migratory species—those in which only some individuals migrate, while others remain resident year round—provide good study systems to test whether variation at candidate loci covaries with variation in migratory behavior. Using both a population genetic and a linear model approach, we tested whether genetic variation at 2 candidate genes (adenylate cyclase activating polypeptide 1, ADCYAP1, and dopamine receptor, DRD4) underlies variation in migratory behavior in the Western Bluebird (Sialia mexicana), a partial migrant, and the closely related Mountain Bluebird (S. currucoides), an obligate migrant, breeding in the Okanagan Valley, British Columbia. Our analyses suggested that DRD4, a gene usually associated with personality, might explain some of the propensity to migrate, but provided no evidence that ADCYAP1, a gene usually associated with the propensity to migrate, explained variation in migratory behavior in these species. Our results join a growing body of literature suggesting the effects of candidate genes are not generalizable across species or populations.