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International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity – so‐called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome‐wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's ϴ and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern‐most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long‐term viability of these populations. Inbreeding (FROH) spans 10%–30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected. [ABSTRACT FROM AUTHOR]

Exploited marine resources can be managed more effectively when accurate information on geographic population structure is available. Genetic markers offer a powerful tool for fisheries management, because they reveal biologically sound management units. Single nucleotide polymorphisms (SNPs) markers derived from restriction-site associated DNA sequencing (RAD-seq) were developed and used to investigate the stock structure of Greenland halibut (Reinhardtius hippoglossoides). A total of 96 SNPs were analyzed from 384 individuals and eight locations across the Atlantic. Our results suggest a subdivision of Greenland halibut into two populations, an eastern Atlantic population and a western Atlantic population, with a proposed border across the Denmark Strait. In general, Greenland halibut display weak but significant population structure (overall [F.sub.ST] = 0.003; p < 0.001), which can be explained by connectivity among populations owing to the migratory behavior or egg and larval drift. Les ressources marines exploitees peuvent etre gerees plus efficacement quand de l'information exacte sur la structure geographique de leurs populations est disponible. Les marqueurs genetiques constituent un puissant outil pour la gestion des peches parce qu'ils font ressortir des unites de gestion coherentes sur le plan biologique. Des marqueurs de polymorphismes mononucleotidiques (SNPs) derives du sequenqage d'ADN associe a un site de restriction (RAD-seq) ont ete developpes et utilises pour etudier la structure des stocks de fletan noir (Reinhardtius hippoglossoides). Un total de 96 SNP ont ete analyses de 384 individus et huit emplacements dans l'Atlantique. Nos resultats semblent indiquer le regroupement des fletans noirs en deux populations, une de l'est de l'Atlantique et l'autre de l'ouest de l'Atlantique, la frontiere proposee entre les deux traversant le detroit du Danemark. En general, les fletans noirs presentent une structure de populations faible mais significative ([F.sub.ST] global = 0,003; p < 0,001) qui peut s'expliquer par la connectivite des populations decoulant du comportement migratoire ou de la derive des reufs et des larves. [Traduit par la Redaction], Introduction Marine fish populations typically consist of large numbers of individuals with high dispersal potential in one or several life-history stages (Conover et al. 2006), which can result in a [...]

The sympatric existence of genetically distinguishable populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verified the existence of the two coexisting demes using a 96‐SNP fluidigm array. We then applied whole‐genome resequencing of pooled DNA to explore genome‐wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome‐wide FST ≈ 0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole‐genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene‐copies for LDH‐A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome‐wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management. [ABSTRACT FROM AUTHOR]

Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2,562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the 'shallow' and 'deep' groups, beyond the Irminger Sea where they were described previously. A third group , 'slope,' has an extended distribution on the East Greenland Shelf, in addition to earlier findings on the Icelandic slope. Furthermore, S. mentella from the Northeast Arctic and Northwest Atlantic waters are genetically different populations. In both areas, interspecific introgression may influence allele frequency differences among populations. Evidence of introgression was found for almost all the identified Sebastes gene pools, but to a much lower extent than suggested earlier. Greenland waters appear to be a sympatric zone for many of the genetically independent Sebastes groups. This study illustrates that the identified groups maintain their genetic integrity in this region despite introgression. [ABSTRACT FROM AUTHOR]

Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2,562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the "shallow" and "deep" groups, beyond the Irminger Sea where they were described previously. A third group , "slope," has an extended distribution on the East Greenland Shelf, in addition to earlier findings on the Icelandic slope. Furthermore, S. mentella from the Northeast Arctic and Northwest Atlantic waters are genetically different populations. In both areas, interspecific introgression may influence allele frequency differences among populations. Evidence of introgression was found for almost all the identified Sebastes gene pools, but to a much lower extent than suggested earlier. Greenland waters appear to be a sympatric zone for many of the genetically independent Sebastes groups. This study illustrates that the identified groups maintain their genetic integrity in this region despite introgression.