Atal Saha

• Saha, Atal; Kurland, Sara; Kutschera, Verena E.; Díez-del-Molino, David; Ekman, Diana & Ryman, Nils [Vis alle 7 forfattere av denne artikkelen] (2024). Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations. Conservation Genetics. ISSN 1566-0621. doi: 10.1007/s10592-023-01586-3.
• Kurland, Sara; Saha, Atal; Keehnen, Naomi; de la Paz Celorio-Mancera, Maria; Díez-del-Molino, David & Ryman, Nils [Vis alle 7 forfattere av denne artikkelen] (2023). New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data. Molecular Ecology. ISSN 0962-1083. doi: 10.1111/mec.17213. Fulltekst i vitenarkiv Vis sammendrag

  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.

• Myksvoll, Mari Skuggedal; Devine, Jennifer Ann; Quintela, Maria; Geffen, Audrey J.; Nash, Richard David Marriott & Sandvik, Anne Dagrun [Vis alle 12 forfattere av denne artikkelen] (2021). Linking dispersal connectivity to population structure and management boundaries for saithe in the Northeast Atlantic. Marine Ecology Progress Series. ISSN 0171-8630. 680, s. 177–191. doi: 10.3354/meps13862. Fulltekst i vitenarkiv
• Saha, Atal; Andersson, Anastasia; Kurland, Sara; Keehnen, Naomi L. P.; Kutschera, Verena E. & Hössjer, Ola [Vis alle 13 forfattere av denne artikkelen] (2021). Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes. Molecular Ecology. ISSN 0962-1083. doi: 10.1111/mec.16252. Fulltekst i vitenarkiv Vis sammendrag

  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.coexisting populations, conservation genetics, conservation genomics, hidden biodiversity, population genetic structure, salmonid

• Saha, Atal; Kent, Matthew Peter; Hauser, Lorenz; Drinan, Daniel P.; Nielsen, Einar E. & Westgaard, Jon-Ivar [Vis alle 8 forfattere av denne artikkelen] (2021). Hierarchical genetic structure in an evolving species complex: Insights from genome wide ddRAD data in Sebastes mentella. PLOS ONE. ISSN 1932-6203. 16(5). doi: 10.1371/journal.pone.0251976. Fulltekst i vitenarkiv
• Saha, Atal; Hauser, Lorenz; Hedeholm, Rasmus; Planque, Benjamin; Fevolden, Svein-Erik & Boje, Jesper [Vis alle 7 forfattere av denne artikkelen] (2017). Cryptic Sebastes norvegicus species in Greenland waters revealed by microsatellites. ICES Journal of Marine Science. ISSN 1054-3139. 74(8), s. 2148–2158. doi: 10.1093/icesjms/fsx039. Vis sammendrag

  Identification of cryptic species can have profound implications in fishery management, conservation and biodiversity contexts. In the North Atlantic, the genus Sebastes is currently represented by four species, although additional cryptic species have been assumed. The connectivity of the gene-pools within the genus in Greenland waters, in particular, remains largely unexplored. Using a panel of 13 microsatellite markers for 720 fish, we explored the species complex of Sebastes norvegicus in Greenland waters. Genetic analyses provided evidence for three cryptic species in samples that were morphologically identified as S. norvegicus. They were termed S. norvegicus-A, S. norvegicus-B, and S. norvegicusgiants. A few phenotypic features exist to identify adult S. norvegicus giants, but no characteristics have been identified for the two other cryptic species. The proposed cryptic species should be recognized in the management regime to ensure sustainable exploitation and conservation of Sebastes species in Greenland waters.

• Saha, Atal; Johansen, Torild; Hedeholm, Rasmus; Nielsen, Einar Eg; Westgaard, Jon-Ivar & Hauser, Lorenz [Vis alle 9 forfattere av denne artikkelen] (2017). Geographic extent of introgression in Sebastes mentella and its effect on genetic population structure. Evolutionary Applications. ISSN 1752-4571. 10(1), s. 77–90. doi: 10.1111/eva.12429. Fulltekst i vitenarkiv
• Westgaard, Jon-Ivar; Saha, Atal; Kent, Matthew Peter; Hansen, Hanne Hellerud; Knutsen, Halvor & Hauser, Lorenz [Vis alle 9 forfattere av denne artikkelen] (2017). Genetic population structure in Greenland halibut (Reinhardtius hippoglossoides) and its relevance to fishery management. Canadian Journal of Fisheries and Aquatic Sciences. ISSN 0706-652X. 74(4), s. 475–485. doi: 10.1139/cjfas-2015-0430. Fulltekst i vitenarkiv
• Saha, Atal; Hauser, Lorenz; Kent, Matthew Peter; Planque, Benjamin; Neat, Francis & Kirubakaran, Tina Graceline [Vis alle 11 forfattere av denne artikkelen] (2015). Seascape genetics of saithe (Pollachius virens) across the North Atlantic using single nucleotide polymorphisms. ICES Journal of Marine Science. ISSN 1054-3139. 72(9), s. 2732–2741. doi: 10.1093/icesjms/fsv139.

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• Christensen, Helle Torp; Riget, Frank; Backe, Marie Balslev; Saha, Atal; Johansen, Torild & Hedeholm, Rasmus (2018). Comparison of three methods for identification of redfish (Sebastes mentella and S. norvegicus) from the Greenland east coast. Fisheries Research. ISSN 0165-7836. 201, s. 11–17. doi: 10.1016/j.fishres.2018.01.003.

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