Atal Saha

Affiliated with UiA External

Email: atal.saha@uia.no
Office: J2002A (Universitetsveien 25, 4630 Kristiansand, Norway)

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I am a Post-Doctoral Research Fellow in population genomics at Centre for Coastal Research (CCR), affiliated to the Department of Natural Sciences, University of Agder, Norway.

My current project is about evolutionary and ecological genomics of marine species in Norwegian coastal waters. My research activities primarily involve bioinformatic and statistical analyses of genomic data from NGS sequencing (e.g. ddRAD) coupled with environmental and biological data, for the study of marine ecology and evolution.

Previously, I did a postdoc at Stockholm University (in the Division of Population Genetics) investigating genomic dynamics over space and time in salmonid (brown trout and Arctic char) metapopulations. My project was based on data from individual whole-genome sequencing and pool-sequencing of groups of individuals. In this work, we studied cryptic sympatry, genetic changes over time, local adaptation, hybridization and introgression in salmonids from mountain freshwater lake systems in Sweden.

In my PhD project, I investigated genetic population structure, cryptic speciation, hybridization and local adaptation, mainly in redfish (plus saithe and Greenland halibut) from the North Atlantic. Analysing data from microsatellite DNA and SNP markers, I found evidence of significant genetic population structure in beaked redfish, saithe and Greenland halibut. My data supported three novel cryptic species in golden redfish complex. A low but statistically significant extent of introgession was estimated in redfish. I also found an indication of local adaptation in groups of beaked redfish. I defended my PhD at University of Tromso and the project was coordinated by the Norwegian Institute of Marine Research (IMR). During my PhD period, I had a PhD internship at University of Washington. After completion of my PhD, I worked as a research assistant at IMR for a year.

As it is evident, my main research interest is to apply population genomic tools to support sustainable management and conservation of aquatic species.

Saha, Atal; Quintela, Maria; Nedreaas, Kjell Harald; Rodríguez-Ezpeleta, Naiara; Besnier, Francois & Gerritsen, Hans [Show all 11 contributors for this article] (2026). Genomic Insights Into Population Structure and Demographic History of White Anglerfish (Lophius piscatorius) Throughout Its Range. Evolutionary Applications. 19(7), p. 1–14. doi: 10.1111/eva.70288. Full text in Research Archive Show summary
Understanding population structure and clarifying species boundaries are essential for the sustainable management of exploited marine species. Although genomic resources for shallow-water taxa have expanded rapidly, open-water species remain comparatively understudied. Here, we present a comprehensive genomic analysis of the white anglerfish (Lophius piscatorius), a commercially important species that occupies a wide depth range. We examined genetic structuring and verified species identity across its distribution range in the North Atlantic and Mediterranean. We combined whole-genome sequencing of selected individuals with targeted SNP genotyping of 897 specimens from 35 locations. Our results support a panmictic or nearly panmictic population of white anglerfish throughout the Northeast Atlantic, consistent with earlier studies, here extended northward to about 68° N. We found no evidence of local adaptation or selection. Like earlier studies, we detected apparently misclassified specimens of the closely related black anglerfish (L. budegassa) and extensive hybridization with up to 20% hybrids in local samples from around the Celtic Sea and nearby waters. Most or all hybrids appear to be first generation (F1), with a few potential backcrossed individuals of less certain identification. Demographic analyses indicate a recent colonization of the North Atlantic, with black anglerfish diverging more recently and maintaining a smaller effective population size. These results underscore the value of integrating genomic tools into monitoring frameworks to improve species identification, delineate population units, and inform sustainable fisheries management.
Saha, Atal; Jorde, Per Erik; Sodeland, Marte; Albretsen, Jon; Korslund, Lars & Knutsen, Halvor (2025). Genomic population structure and local adaptation in the emerging commercially exploited Littorina littorea. ICES Journal of Marine Science. ISSN 1054-3139. 82(7). doi: 10.1093/icesjms/fsaf119. Full text in Research Archive Show summary
To address food deficit, stakeholders continuously diversify food systems by exploiting new commercially viable species. However, the absence of sustainable management measures often conflicts with global biodiversity policies. In light of this challenge, understanding genetic diversity and the geographic scale of population connectivity is essential. We employ ddRAD sequencing in Littorina littorea, a low-trophic, emerging commercial species, to investigate its genetic population structure in Norwegian coastal waters. From an initial detection of over two million SNPs (single nucleotide polymorphisms), 60 831 loci were retained for downstream genomic analyses in 189 individuals sampled across 17 coastal sites. Our results revealed significant isolation-by-distance across the study area, likely reflecting genetic divergence between populations along the west and southern coasts of Norway. While the overall genetic structure appears to be primarily shaped by genetic drift, our genome scan analyses provided evidence for selection acting on specific loci. We identified 39 SNPs potentially under selection, of which 16 overlapped with genes encoding proteins involved in transmembrane transport, metabolic processes, and pathogenesis-related functions. We found no evidence supporting the presence of chromosomal inversions. Oceanographic modelling suggests a likely link between observed genetic divergence and the prevailing ocean current in the region. Our findings demonstrate the adaptive potential of distinct populations to varying environmental conditions and highlight the importance of preserving their full genetic diversity to ensure long-term resilience and sustainability.
Saha, Atal; Jorde, Per Erik; Sodeland, Marte; Korslund, Lars & Knutsen, Halvor (2025). Pelagic Larval Duration and Isolation by Distance in Coastal Species. Evolutionary Applications. 18(12). doi: 10.1111/eva.70187. Full text in Research Archive Show summary
Dispersal among populations is crucial both for demographic stability and for the evolutionary potential of species. In marine organisms, dispersal has been shown to be prevalent during pelagic early life stages. Consequently, pelagic larval duration (PLD) has been proposed as an important driver of gene flow in marine species and is influencing genetic differentiation among populations. Despite this prediction, empirical studies have often failed to find the expected correlation between PLD and genetic metrics of gene flow. This could mean either that PLD is a poor predictor of gene flow or that differences in methodology, oceanography or sampling design across studies obscure the underlying mechanisms of gene flow. In the present study, we address these issues by using a consistent sampling design for 10 coastal species with previously published genetic data (ddRAD and microsatellites), and that differ in PLD. We investigate gene flow using an isolation-by-distance (IBD) model with pairwise FST-estimates regressed against distances measured along the prevailing coastal ocean current in the study region. We find a significant (p < 0.05) correlation between species' PLD and IBD slopes, with a moderately strong correlation (r2 > 0.5), These findings support the notion of PLD as a key factor determining dispersal and gene flow among populations of coastal species. Our findings reiterate genetics as a useful tool for inferring population dispersal in marine organisms when potentially confounding factors are eliminated by adopting a consistent sampling design.
Johansen, Torild; Hanebrekke, Tanja Lexau; Besnier, Francois; Westgaard, Jon-Ivar; Bruvold, Ingrid Marie & Dahle, Geir [Show all 9 contributors for this article] (2025). Development of SNP for Sebastes Species Identification With Special Focus on the Cryptic Species Complex of Sebastes norvegicus. Ecology and Evolution. 15(1). doi: 10.1002/ece3.70767. Full text in Research Archive Show summary
The genus Sebastes in the North Atlantic comprises of long lived deep-waters species that have been extensively fished upon, and many stocks are severely depleted across the Atlantic. This is particularly evident for the species Sebastes norvegicus. In recent papers, cryptic species have been indicated within this genus and molecular markers are therefore needed to provide identification for the Sebastes species, including the cryptic species as a basis for advice regarding management and rebuilding of the stocks. A suite of 2800 Single Nucleotide Polymorphism (SNP) markers were identified from ddRAD sequencing data, of which 56 SNPs were organized in two multiplex reactions and tested on 191 Sebastes spp. from different sampling locations from Norway and Greenland. Good-quality amplification products were successfully obtained from 49 SNP markers for Sebastes species ID, and 3 TaqMan probes were designed to successfully assign S. mentella, S. viviparus, and the two cryptic species S. norvegicus types A and B. A total 47 SNPs were biallelic, with averaged HE per locus ranging between 0.053 and 0.50. This SNP-based method establishes a foundation for genetically identifying the Northeast Atlantic Sebastes species. The findings presented should be followed by an effort to look for morphological characters to recognize the S. norvegicus cryptic species on site. In general, the SNP markers are a proper tool for monitoring the distribution of the species from a management perspective.
Bruvold, Ingrid Marie; Hansen, Agneta; Lynghammar, Arve; Höffle, Hannes; Hanebrekke, Tanja Lexau & Tranang, Caroline Aas [Show all 10 contributors for this article] (2025). Morphological evidence supports splitting of species in the North Atlantic Sebastes spp. complex. PLOS ONE. 20(2), p. 1–20. doi: 10.1371/journal.pone.0316988. Full text in Research Archive Show summary
The redfishes (genus Sebastes) are long-lived, commercial species in the North Atlantic. Excessive harvest through decades has led to a decline in the mature population of golden redfish (Sebastes norvegicus) in Norwegian waters, which is currently considered severely depleted. Accumulating genetic evidence suggests a more complex structure within this genus in the North Atlantic, which has recently inspired the hypotheses of cryptic species within S. norvegicus. Despite apparent genetic divergence between two types, they have yet to be verified morphologically. The morphology of genetically assigned fishes from Norwegian and Greenland waters was investigated using traditional morphometric methods, applying Linear Discriminant Analysis and Random Forest classification procedures to identify and evaluate the performance of descriptive characters. Combined with non-parametric meristic analysis, the results show that features such as beak length and eye diameter provide sufficient discrimination between the proposed cryptic species as well as separating them from the sympatric species S. mentella and S. viviparus. These findings support the presence of an additional redfish species in the North Atlantic, distinguishable both by morphological and genetic characters. This needs to be taken into consideration in future monitoring and management strategies for North Atlantic redfish.
Saha, Atal; Kurland, Sara; Kutschera, Verena E.; Díez-del-Molino, David; Ekman, Diana & Ryman, Nils [Show all 7 contributors for this article] (2024). Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations. Conservation Genetics. ISSN 1566-0621. 25, p. 513–531. doi: 10.1007/s10592-023-01586-3. Full text in Research Archive
Kurland, Sara; Saha, Atal; Keehnen, Naomi; Paz Celorio-Mancera, Maria de la; Díez-del-Molino, David & Ryman, Nils [Show all 7 contributors for this article] (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. Full text in Research Archive Show summary
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.
Saha, Atal; Andersson, Anastasia; Kurland, Sara; Keehnen, Naomi L. P.; Kutschera, Verena E. & Hössjer, Ola [Show all 13 contributors for this article] (2021). Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes. Molecular Ecology. ISSN 0962-1083. 31(2). doi: 10.1111/mec.16252. Full text in Research Archive Show summary
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 [Show all 8 contributors for this article] (2021). Hierarchical genetic structure in an evolving species complex: Insights from genome wide ddRAD data in Sebastes mentella. PLOS ONE. 16(5). doi: 10.1371/journal.pone.0251976. Full text in Research Archive Show summary
The diverse biology and ecology of marine organisms may lead to complex patterns of intraspecific diversity for both neutral and adaptive genetic variation. Sebastes mentella displays a particular life-history as livebearers, for which existence of multiple ecotypes has been suspected to complicate the genetic population structure of the species. Double digest restriction-site associated DNA was used to investigate genetic population structure in S. mentella and to scan for evidence of selection. In total, 42,288 SNPs were detected in 277 fish, and 1,943 neutral and 97 tentatively adaptive loci were selected following stringent filtration. Unprecedented levels of genetic differentiation were found among the previously defined ‘shallow pelagic’, ‘deep pelagic’ and ‘demersal slope’ ecotypes, with overall mean FST = 0.05 and 0.24 in neutral and outlier SNPs, respectively. Bayesian computation estimated a concurrent and historical divergence among these three ecotypes and evidence of local adaptation was found in the S. mentella genome. Overall, these findings imply that the depth-defined habitat divergence of S. mentella has led to reproductive isolation and possibly adaptive radiation among these ecotypes. Additional sub-structuring was detected within the ‘shallow’ and ‘deep’ pelagic ecotypes. Population assignment of individual fish showed more than 94% agreement between results based on SNP and previously generated microsatellite data, but the SNP data provided a lower estimate of hybridization among the ecotypes than that by microsatellite data. We identified a SNP panel with only 21 loci to discriminate populations in mixed samples based on a machine-learning algorithm. This first SNP based investigation clarifies the population structure of S. mentella, and provides novel and high-resolution genomic tools for future investigations. The insights and tools provided here can readily be incorporated into the management of S. mentella and serve as a template for other exploited marine species exhibiting similar complex life history traits.
Myksvoll, Mari Skuggedal; Devine, Jennifer Ann; Quintela, Maria; Geffen, Audrey J.; Nash, Richard David Marriott & Sandvik, Anne Dagrun [Show all 12 contributors for this article] (2021). Linking dispersal connectivity to population structure and management boundaries for saithe in the Northeast Atlantic. Marine Ecology Progress Series. ISSN 0171-8630. 680, p. 177–191. doi: 10.3354/meps13862. Full text in Research Archive Show summary
Population connectivity is an increasingly important focal area for the understanding of how marine fish populations respond to anthropogenic pressures like climate change and fisheries. Our model species, the saithe Pollachius virens (Linnaeus, 1758), was chosen because genetic analyses have documented a mismatch between the assessed stocks and the biological populations. We combined laboratory experiments of saithe egg buoyancy and temperature-modulated development time, genetic field data, and high-resolution oceanographic models to disentangle the mechanisms causing isolation and mixing between the management units and the biological populations. Saithe egg buoyancy and development data were included in an individual-based model to simulate transport from all known spawning grounds in the Northeast Atlantic. The results show that interannual variability in the transport of early life stages is strongly influenced by wider climate systems (e.g. the North Atlantic Oscillation). One sample (Rockall) showed genetic differences from the other samples, and this finding was supported by the model showing low mixing with other populations and strong local retention. Strong retention of early life stages around Iceland could indicate an isolated population; however, this possible isolation is counteracted by active migration of adults westward from the Norwegian coast, and no genetic differentiation from other populations was found. Overall, the dispersal modeling supports the genetic analysis, showing a large and well-connected Central Northeast Atlantic population distributed across several management units. This mismatch between population structure and management units can potentially increase the risk for overexploitation of saithe.
Saha, Atal; Hauser, Lorenz; Hedeholm, Rasmus; Planque, Benjamin; Fevolden, Svein-Erik & Boje, Jesper [Show all 7 contributors for this article] (2017). Cryptic Sebastes norvegicus species in Greenland waters revealed by microsatellites. ICES Journal of Marine Science. ISSN 1054-3139. 74(8), p. 2148–2158. doi: 10.1093/icesjms/fsx039. Full text in Research Archive Show summary
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 [Show all 9 contributors for this article] (2017). Geographic extent of introgression in Sebastes mentella and its effect on genetic population structure. Evolutionary Applications. 10(1), p. 77–90. doi: 10.1111/eva.12429. Full text in Research Archive
Westgaard, Jon-Ivar; Saha, Atal; Kent, Matthew Peter; Hansen, Hanne Hellerud; Knutsen, Halvor & Hauser, Lorenz [Show all 9 contributors for this article] (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), p. 475–485. doi: 10.1139/cjfas-2015-0430. Full text in Research Archive
Saha, Atal; Hauser, Lorenz; Kent, Matthew Peter; Planque, Benjamin; Neat, Francis & Kirubakaran, Tina Graceline [Show all 11 contributors for this article] (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), p. 2732–2741. doi: 10.1093/icesjms/fsv139. Full text in Research Archive

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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, p. 11–17. doi: 10.1016/j.fishres.2018.01.003. Full text in Research Archive

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Published Mar. 25, 2026 5:53 AM - Last modified Mar. 25, 2026 5:53 AM