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• Klemetsen, Terje; Endresen, Dag; Johnsen, Arild; Boer, Hugo de; Fossøy, Frode & Ekrem, Torbjørn [Show all 11 contributors for this article] (2026). Strengthening molecular biodiversity research and monitoring in Norway – connecting tools, data and people. F1000 Research. 15, p. (ELIXIR)–(ELIXIR). doi: 10.12688/f1000research.179210.1. Full text in Research Archive Show summary

  Background Norway’s diverse ecosystems and strong research community are well-positioned to leverage molecular approaches (DNA barcoding, eDNA, whole-genome sequencing) for biodiversity research and monitoring. However, progress is constrained by gaps in data accessibility, standardisation, and interoperability across molecular, ecological, and biobank datasets. Methods ELIXIR’s Norwegian Molecular Biodiversity Working Group mapped national actors and networks through a desk review (2024–2025) and conducted a national survey (58 questions; open from 18 February to 8 March 2024) targeting data management, standards, tooling, infrastructures, and training. The survey was implemented in Nettskjema and received 58 responses from biodiversity-related researchers. Results We identified 19 Norwegian institutes active in molecular biodiversity and 28 relevant networks, with 11 networks involving three or more institutes. The survey results highlight gaps between policy and practice: 60% of respondents were familiar with the FAIR principles, but only 29% consistently made data fully open or FAIR-compliant. Data linkage with physical specimens was often reported as missing (38% of respondents), and taxonomic assignment was frequently challenging (39.3%). Most researchers reuse published datasets (90%), but data discovery and reuse are hindered: only 41% find it easy to locate relevant data, 32% struggle to find appropriate sequence databases, 54% cite insufficient metadata, and 72% need to harmonise combined datasets. Tool discoverability and documentation were limited (32% knew bio.tools; 5% WorkflowHub; 32% agreed tools are well documented and user-friendly). Data publication is not straightforward (63.8% find it hard or answered neutral). Conclusions Norway can strengthen molecular biodiversity research by 1) connecting molecular and ecological data, collections, and biobanks using persistent identifiers; 2) adhering to international metadata standards (e.g., DwC, MIxS) and rewarding data stewardship; 3) consolidating national collaborative networks; and 4) building capacity through targeted training and dedicated data steward roles. Implementing these measures will enhance interoperability, FAIR data sharing, and Norway’s leadership in biodiversity research and conservation.

• Baalsrud, Helle T; Tørresen, Ole K; Danneels, Bram; Ferrari, Giada; Tooming-Klunderud, Ave & Skage, Morten [Show all 12 contributors for this article] (2026). Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758). Journal of Heredity. ISSN 0022-1503. 117(4), p. 750–760. doi: https:/academic.oup.com/jhered/article/117/4/750/8497176. Full text in Research Archive Show summary

  The phylum Bryozoa is an understudied, yet commonly occurring, globally distributed bilaterian metazoan organismal group. They have a colonial lifestyle and an evolutionary history that spans at least 480 million years but likely longer. Despite their contentious phylogenetic affinities among metazoans, disproportionately few genomic investigations have been performed thus far. Here, we describe the first chromosome-level genome assembly of an individual Flustra foliacea colony belonging to the order Cheilostomatida, collected in southern Norway. The haplotype-resolved assembly of F. foliacea contains two pseudo-haplotypes spanning 956 megabases and 880 megabases, respectively. Both assemblies are highly complete both in terms of scaffolding (>90% of sequences placed in eight autosomal chromosomal pseudomolecules), and gene content (BUSCO completeness scores >90%). We also present gene and repeat annotations of the two assemblies. A comparison of our newly sequenced F. foliacea with five previously published bryozoan genomes supports the hypothesis that the group has undergone extensive genome rearrangements. This includes multiple chromosomal fusions in F. foliacea since their split with other cheilostome bryozoans. These fusions were enriched with long terminal repeat retrotransposons, highlighting the complex interplay between genome organization and genomic repeats. Our study contributes to a deeper understanding of bryozoan genome evolution and the role of repeats in metazoan genome organization.

• Baalsrud, Helle Tessand; Garmann-Aarhus, Benedicte; Enevoldsen, Emily Louise Gilbert; Krabberød, Anders Kristian; Dominik, Fischer, & Tooming-Klunderud, Ave [Show all 13 contributors for this article] (2026). Centromeric satellite expansion drives genome evolution in the snowy owl. Genome Biology. ISSN 1474-7596. doi: 10.1186/s13059-026-04175-y. Full text in Research Archive Show summary

  Comparative genomic studies in birds have revealed that bird genomes are relatively repeat-poor and stable in terms of karyotype, size, and gene synteny/collinearity compared to other vertebrates. One notable exception is the owls, with cytogenetic studies demonstrating large variations in karyotypes and the evolution of unusual centromeric satellite repeats in some species. However, there has so far not been an investigation into genome architecture and repeat landscape of owls. Here, we present a chromosome-level genome assembly for the snowy owl (Bubo scandiacus). We find that the repeat DNA content in the relatively large snowy owl genome (1.6 Gb) is among the highest reported for any bird genome to date (28.34% compared to an average of ~ 10% in other birds). The bulk of the snowy owl genomic repeat landscape consists of extensive centromeric satellite arrays that form large contiguous blocks across multiple chromosomes. These arrays represent one of the largest centromeric satellite expansions reported in birds and are consistent with rapid turnover and amplification of centromeric repeats. Using gene collinearity analyses we show that the position of the centromeres are not homologous with chicken centromeres, and are located in regions with collinearity breaks to other bird genomes due to chromosomal rearrangements. Our results support rapid satellite turnover at lineage-specific centromeres, which could have played a role in centromeric drive, reproductive isolation and speciation of the snowy owl. The extensive centromeric satellite arrays uncovered in this genome highlight centromere evolution as a potentially important driver of genome evolution in owls.

• Araya, Robin Aasegg; Reinar, William Brynildsen; Tørresen, Ole K; Goubert, Clément; Daughton, Tara Jane & Hoff, Siv Nam Khang [Show all 12 contributors for this article] (2025). Chromosomal Inversions Mediated by Tandem Insertions of Transposable Elements. Genome Biology and Evolution (GBE). 17(8). doi: 10.1093/gbe/evaf131. Full text in Research Archive Show summary

  Chromosomal inversions play a crucial role in evolution by influencing phenotypes through the linkage of coadapted alleles. While inversions have been found across a large number of taxa, mapping and characterizing inversion breakpoint regions remain challenging, often due to the presence of complex tandem repeats and transposable elements. Here, we identify and quantify transposable elements in the breakpoints of the four large-scale inversions previously reported in Atlantic cod, leveraging on three high-quality long-read-based reference genome assemblies for the Norwegian Coastal cod, the Northeast Arctic cod, and Celtic cod ecotypes. We detected a significant enrichment of transposable element orders and superfamilies with terminal inverted repeats within the inversion breakpoint regions of chromosomes 1, 7 and 12. Notably, we discovered a tandem accumulation of miniature inverted-repeat transposable elements belonging to a family of hAT transposons, exclusively residing in the breakpoints of the inverted haplotype on chromosomes 1 and 7 found in the Northeast Arctic cod. The accumulation of tandemly arranged transposable elements with high sequence similarity in breakpoint regions suggests that they have driven the appearance of inversions through ectopic recombination, further supporting the potential of transposable elements in facilitating chromosomal reorganizations with large evolutionary implications.

• Baalsrud, Helle Tessand; Byrtusova, Dana; To, Thu-Hien; Larsen, Ida Emilie; Bøe, Veronica Aarvik & Grønvold, Lars [Show all 10 contributors for this article] (2025). Calcium starvation leads to strain-specific gene regulation of lipid and carotenoid production in Mucor circinelloides. G3: Genes, Genomes, Genetics. 15(11). doi: 10.1093/g3journal/jkaf207. Full text in Research Archive Show summary

  Abstract Fungi are pivotal in transitioning to a bio-based, circular economy due to their ability to transform organic material into valuable products such as organic acids, enzymes, and drugs. Mucor circinelloides is a model organism for studying lipogenesis and is particularly promising for its metabolic capabilities in producing oils like TAGs and carotenoids, influenced by environmental factors such as nutrient availability. Notably, strains VI04473 and FRR5020 have been identified for their potential in producing single-cell oils and carotenoids, respectively. Calcium starvation has previously been shown to have strain-specific effects, with VI04473 accumulating more lipids and FRR5020 producing more carotenoids. Here, we used genome sequencing, comparative genomics, transcriptomics, and metabolite phenotyping to explore the genetic basis of lipid and carotenoid production under calcium starvation in these strains. We found extensive genomic rearrangements between these strains, as well as low conservation of gene regulatory responses to calcium depletion. This lack of conservation also applies to genes involved in lipid and carotenoid production, ie the lipidome. Crucially, we identified several metabolic pathways with distinct transcriptional responses to calcium depletion, suggesting the existence of a previously unrecognized, strain-dependent mechanism by which calcium signaling modulates metabolite production. This points to a potentially novel regulatory pathway linking calcium homeostasis to secondary metabolism in fungi, which may be linked to the complex gene family evolution of several lipidome-genes. Our study sheds light on the complexity of the evolution of metabolic networks in M. circinelloides. Understanding these genetic underpinnings can optimize the industrial use of M. circinelloides, enhancing lipid productivity and stress tolerance, and tailoring metabolic profiles for specific applications.

• Baalsrud, Helle Tessand; Garmann-Aarhus, Benedicte; Enevoldsen, Emily Louise Gilbert; Krabberød, Anders Kristian; Fischer, Dominik & Tooming-Klunderud, Ave [Show all 13 contributors for this article] (2024). Evolutionary new centromeres in the snowy owl genome putatively seeded from a transposable element. BioRxiv. ISSN 0362-4331. doi: 10.1101/2024.07.05.602039. Full text in Research Archive
• Matschiner, Michael; Barth, Julia Maria Isis; Tørresen, Ole K.; Star, Bastiaan; Baalsrud, Helle Tessand & Brieuc, Marine Servane Ono [Show all 10 contributors for this article] (2022). Supergene origin and maintenance in Atlantic cod. Nature Ecology and Evolution. 6(4), p. 469–481. doi: 10.1038/s41559-022-01661-x. Full text in Research Archive Show summary

  Abstract Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation.

• Pinsky, Malin L.; Eikeset, Anne Maria; Helmerson, Cecilia Jenny Margareta Thomas; Bradbury, Ian R.; Bentzen, Paul & Morris, Corey [Show all 17 contributors for this article] (2021). Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 118(15). doi: 10.1073/pnas.2025453118. Full text in Research Archive Show summary

  The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.

• Garcia, Lourdes Martinez; Ferrari, Giada; Oosting, Tom; Ballantyne, Rachel; Jagt, Inge van der & Ystgaard, Ingrid [Show all 20 contributors for this article] (2021). Historical demographic processes dominate genetic variation in ancient Atlantic cod mitogenomes. Frontiers in Ecology and Evolution. 9, p. 1–14. doi: 10.3389/fevo.2021.671281. Full text in Research Archive Show summary

  Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.

• Nilsson, Pernille; Solbakken, Monica Hongrø; Schmid, Boris Valentijn; Orr, Russell; Lv, Ruichen & Cui, Yujun [Show all 15 contributors for this article] (2020). The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene. Genome Biology and Evolution (GBE). 12(2), p. 3832–3849. doi: 10.1093/gbe/evaa008. Full text in Research Archive Show summary

  Abstract The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.

• Roth, Olivia; Solbakken, Monica Hongrø; Tørresen, Ole K.; Bayer, Till; Matschiner, Michael & Baalsrud, Helle Tessand [Show all 12 contributors for this article] (2020). Evolution of male pregnancy associated with remodeling of canonical vertebrate immunity in seahorses and pipefishes. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 117(17), p. 9431–9439. doi: 10.1073/pnas.1916251117. Full text in Research Archive Show summary

  A fundamental problem for the evolution of pregnancy, the most specialized form of parental investment among vertebrates, is the rejection of the nonself-embryo. Mammals achieve immunological tolerance by down-regulating both major histocompatibility complex pathways (MHC I and II). Although pregnancy has evolved multiple times independently among vertebrates, knowledge of associated immune system adjustments is restricted to mammals. All of them (except monotremata) display full internal pregnancy, making evolutionary reconstructions within the class mammalia meaningless. Here, we study the seahorse and pipefish family (syngnathids) that have evolved male pregnancy across a gradient from external oviparity to internal gestation. We assess how immunological tolerance is achieved by reconstruction of the immune gene repertoire in a comprehensive sample of 12 seahorse and pipefish genomes along the “male pregnancy” gradient together with expression patterns of key immune and pregnancy genes in reproductive tissues. We found that the evolution of pregnancy coincided with a modification of the adaptive immune system. Divergent genomic rearrangements of the MHC II pathway among fully pregnant species were identified in both genera of the syngnathids: The pipefishes (Syngnathus) displayed loss of several genes of the MHC II pathway while seahorses (Hippocampus) featured a highly divergent invariant chain (CD74). Our findings suggest that a trade-off between immunological tolerance and embryo rejection accompanied the evolution of unique male pregnancy. That pipefishes survive in an ocean of microbes without one arm of the adaptive immune defense suggests a high degree of immunological flexibility among vertebrates, which may advance our understanding of immune-deficiency diseases.

• Ferrari, Giada; Neukamm, Judith; Baalsrud, Helle Tessand; Breidenstein, Abagail; Ravinet, Mark & Phillips, Carina [Show all 9 contributors for this article] (2020). Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox. Philosophical Transactions of the Royal Society of London. Biological Sciences. ISSN 0962-8436. 375(1812), p. 1–9. doi: 10.1098/rstb.2019.0572. Full text in Research Archive Show summary

  Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

• Hoff, Siv Nam Khang; Baalsrud, Helle Tessand; Tooming-Klunderud, Ave; Skage, Morten; Richmond, Todd & Obernosterer, Gregor [Show all 10 contributors for this article] (2018). Long‐read sequence capture of the haemoglobin gene clusters across codfish species. Molecular Ecology Resources. ISSN 1755-098X. 19(1), p. 245–259. doi: 10.1111/1755-0998.12955. Full text in Research Archive
• Baalsrud, Helle Tessand; Voje, Kjetil L.; Tørresen, Ole Kristian; Solbakken, Monica Hongrø; Matschiner, Michael & Malmstrøm, Martin [Show all 10 contributors for this article] (2017). Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth. Scientific Reports. 7, p. 1–10. doi: 10.1038/s41598-017-08286-2. Full text in Research Archive Show summary

  Understanding the genetic basis of adaptation is one of the main enigmas of evolutionary biology. Among vertebrates, hemoglobin has been well documented as a key trait for adaptation to different environments. Here, we investigate the role of hemoglobins in adaptation to ocean depth in the diverse teleost order Gadiformes, with species distributed at a wide range of depths varying in temperature, hydrostatic pressure and oxygen levels. Using genomic data we characterized the full hemoglobin (Hb) gene repertoire for subset of species within this lineage. We discovered a correlation between expanded numbers of Hb genes and ocean depth, with the highest numbers in species occupying shallower, epipelagic regions. Moreover, we demonstrate that the Hb genes have functionally diverged through diversifying selection. Our results suggest that the more variable environment in shallower water has led to selection for a larger Hb gene repertoire and that Hbs have a key role in adaptive processes in marine environments.

• Baalsrud, Helle Tessand; Tørresen, Ole Kristian; Solbakken, Monica Hongrø; Salzburger, Walter; Hanel, Reinhold & Jakobsen, Kjetill Sigurd [Show all 7 contributors for this article] (2017). De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 35(3), p. 593–606. doi: 10.1093/molbev/msx311. Full text in Research Archive Show summary

  New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes (afgps) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgps evolved from an extant gene, yet the evolutionary origin of afgps in codfishes is unknown. Here, we demonstrate that afgps in codfishes have evolved de novo from non-coding DNA 13–18 Ma, coinciding with the cooling of the Northern Hemisphere. Using whole-genome sequence data from several codfishes and notothenioids, we find higher copy number of afgp in species exposed to more severe freezing suggesting a gene dosage effect. Notably, antifreeze function is lost in one lineage of codfishes analogous to the afgp losses in non-Antarctic notothenioids. This indicates that selection can eliminate the antifreeze function when freezing is no longer imminent. In addition, we show that evolution of afgp-assisting antifreeze potentiating protein genes (afpps) in notothenioids coincides with origin and lineage-specific losses of afgp. The origin of afgps in codfishes is one of the first examples of an essential gene born from non-coding DNA in a non-model species. Our study underlines the power of comparative genomics to uncover past molecular signatures of genome evolution, and further highlights the impact of de novo gene origin in response to a changing selection regime.

• Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole Kristian; Star, Bastiaan; Snipen, Lars-Gustav & Hansen, Thomas F [Show all 13 contributors for this article] (2016). Evolution of the immune system influences speciation rates in teleost fishes. Nature Genetics. ISSN 1061-4036. 48(10), p. 1204–1210. doi: 10.1038/ng.3645. Full text in Research Archive Show summary

  Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9–39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outside this clade. Moreover, we identify an association between high MHC I copy number and elevated speciation rates using trait-dependent diversification models. Our results extend current understanding of the plasticity of the adaptive immune system and suggest an important role for immune-related genes in animal diversification.

• Baalsrud, Helle Tessand; Sæther, Bernt-Erik; Hagen, Ingerid Julie; Myhre, Ane Marlene; Ringsby, Thor Harald & Pärn, Henrik [Show all 7 contributors for this article] (2014). Effects of population characteristics and structure on estimates of effective population size in a house sparrow metapopulation. Molecular Ecology. ISSN 0962-1083. 23(11), p. 2653–2668. doi: 10.1111/mec.12770. Full text in Research Archive Show summary

  Effective population size (Ne) is a key parameter to understand evolutionary processes and the viability of endangered populations as it determines the rate of genetic drift and inbreeding. Low Ne can lead to inbreeding depression and reduced population adaptability. In this study, we estimated contemporary Ne using genetic estimators (LDNE, ONeSAMP, MLNE and CoNe) as well as a demographic estimator in a natural insular house sparrow metapopulation. We investigated whether population characteristics (population size, sex ratio, immigration rate, variance in population size and population growth rate) explained variation within and among populations in the ratio of effective to census population size (Ne/Nc). In general, Ne/Nc ratios increased with immigration rates. Genetic Ne was much larger than demographic Ne, probably due to a greater effect of immigration on genetic than demographic processes in local populations. Moreover, although estimates of genetic Ne seemed to track Nc quite well, the genetic Ne-estimates were often larger than Nc within populations. Estimates of genetic Ne for the metapopulation were however within the expected range (

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• Baalsrud, Helle Tessand; Arnyasi, Mariann; To, Thu-Hien; Shapaval, Volha; Byrtusova, Dana & Andersstuen, Terese [Show all 13 contributors for this article] (2025). Chromosomal Chaos: Exploring a Dramatic Shift in the Evolution of Genome Organization in Mucoromycota. Full text in Research Archive
• Klemetsen, Terje; Petters, Sebastian; Åberg, espen; Baalsrud, Helle Tessand & Willassen, Nils Peder (2024). D6.6 (M24) - Report on the outreach and training activities produced (an ELIXIR Norway ELIXIR3 deliverable). doi: 10.5281/ZENODO.11202426. Full text in Research Archive
• Kersten, Oliver Sven; Garcia, Lourdes Martinez; Pulido, Angélica; Ferrari, Giada; Baalsrud, Helle Tessand & Helmerson, Cecilia [Show all 18 contributors for this article] (2024). Long-term population dynamics of Atlantic cod revealed by Ancient DNA and Genomics. Full text in Research Archive
• Baalsrud, Helle Tessand; Arnyasi, Mariann; To, Thu-Hien; Shapaval, Volha; Byrtusova, Dana & Andersstuen, Terese [Show all 13 contributors for this article] (2024). Different modes of chromosomal evolution in fungi revealed by long-read sequencing. Full text in Research Archive
• Klemetsen, Terje; Åberg, Espen; Baalsrud, Helle Tessand; Petters, Sebastian & Willassen, Nils P (2024). D6.6 (M24) - Report on the outreach and training activities produced (an ELIXIR Norway ELIXIR3 deliverable). zenodo. doi: 10.5281/zenodo.11202427. Full text in Research Archive
• Tørresen, Ole Kristian & Baalsrud, Helle Tessand (2022). The Norwegian Earth Biogenome Project: the snowy owl genome assembly. Full text in Research Archive
• Tørresen, Ole K.; Baalsrud, Helle Tessand; Sandve, Simen Rød & Jakobsen, Kjetill Sigurd (2022). Bioinfomatic approaches for EBP-Nor. Full text in Research Archive
• Stenseth, Nils Christian; Baalsrud, Helle Tessand; Jakobsen, Kjetill Sigurd; Brautaset, Trygve; Goksøyr, Anders & Jensen, Nina [Show all 9 contributors for this article] (2021). Havgenomet – bevaring og bærekraftig bruk av marine genetiske ressurser i Norge. In Rist, Therese & Elvevoll, Edel O. (Ed.), Blått kompass - Stø kurs mot bærekraft i norske havnæringer. Senter for hav og Arktis. ISSN 9788293806080. Full text in Research Archive
• Stranden, Anne Lise & Baalsrud, Helle Tessand (2018). Slik fikk torsken herredømme i det iskalde vannet i Arktis. [Internet]. forskning.no. Full text in Research Archive
• Jensen, Henrik; Stubberud, Marlene Wæge; Baalsrud, Helle Tessand; Holand, Håkon; Kvalnes, Thomas & Hagen, Ingerid Julie [Show all 9 contributors for this article] (2018). Consequences of demographic processes for effective population size in house sparrows. Full text in Research Archive
• Jensen, Henrik; Stubberud, Marlene Wæge; Myhre, Ane Marlene; Baalsrud, Helle Tessand; Holand, Håkon & Kvalnes, Thomas [Show all 10 contributors for this article] (2017). Consequences of demographic processes for genetic drift in house sparrows. Full text in Research Archive
• Jensen, Henrik; Stubberud, Marlene Wæge; Myhre, Ane Marlene; Baalsrud, Helle Tessand; Holand, Håkon & Kvalnes, Thomas [Show all 10 contributors for this article] (2017). Consequences of demographic processes for effective population size in house sparrows. Full text in Research Archive
• Baalsrud, Helle Tessand (2017). Whole genome sequencing reveals de novo gene evolution of antifreeze glycoproteins in codfishes. Full text in Research Archive
• Baalsrud, Helle Tessand; Tørresen, Ole Kristian; Malmstrøm, Martin; Salzburger, Walter; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2015). The hemoglobin repertoire in the order of Gadiformes linked to depth adaptation. Full text in Research Archive
• Hoff, Siv; Baalsrud, Helle Tessand & Jentoft, Sissel (2014). The evolution of the hemoglobin clusters in Gadiformes. Full text in Research Archive
• Baalsrud, Helle Tessand; Barlow, S; Berenbrink, M & Jentoft, Sissel (2014). Evolution of red blood cell sickling in Gadiformes. Full text in Research Archive
• Jensen, Henrik; Pärn, Henrik; Hagen, Ingerid Julie; Husby, Arild; Baalsrud, Helle Tessand & Elgvin, Tore Oldeide [Show all 11 contributors for this article] (2014). Consequences of dispersal in house sparrows, and a glimpse of on-going work on house sparrow genomics. Full text in Research Archive
• Baalsrud, Helle Tessand (2013). Genomic insight into the evolution of cold adaptation in teleosts: the story of hemoglobin. Full text in Research Archive
• Jensen, Henrik; Baalsrud, Helle Tessand; Hagen, Ingerid Julie; Myhre, Ane Marlene; Holand, Anna Marie & Billing, Anna Maria [Show all 11 contributors for this article] (2013). Spatio-temporal dynamics of genetic variation and effective population size in fragmented house sparrow populations. Full text in Research Archive
• Baalsrud, Helle Tessand (2012). Characterization of antifreeze proteins in teleost lineages two poles apart: a unique example of convergent evolution. Full text in Research Archive
• Jacobsen, Karl-Otto; Baalsrud, Helle Tessand; Enevoldsen, Emily Louise Gilbert; Solheim, Roar; Øien, Ingar Jostein & Aarvak, Tomas (2025). Snøuglas økologi, genetikk og forekomst i Norge. Årsrapport 2025. Norsk institutt for naturforskning (NINA). ISSN 9788242655462. Full text in Research Archive Show summary

  Jacobsen, K.-O., Baalsrud, H.T., Enevoldsen, E.L.G., Solheim, R., Øien, I.J. & Aarvak, T. 2025. Snøuglas økologi, genetikk og forekomst i Norge. Årsrapport 2025. NINA Rapport 2715. Norsk institutt for naturforskning Lemensyklusen er styrende for om snøugla går til hekking eller ikke, og i 2025 ble det ikke dokumentert noen hekkinger i Norge eller Fennoskandia. I Norge var det åtte observasjoner av snøugler i 2025 som er vurdert som sikre. I tillegg er det henholdsvis to og seks antatt sikre observasjo-ner i Sverige og Finland. I 2022 ble referansegenomet til snøugla ferdig sekvensert, dette er offentlig tilgjengelig på Europena Nucleotide Archive og vil bli publisert i en artikkel som er i siste runde med revisjon. Dette refereansegenomet danner grunnlaget for sammenlikningen av 68 helgenom-sekvenserte snøugler fra ulike bestander. Basert på dette datasettet med helgenomdata og over en million markører, finner vi ingen antydning til populasjonsstruktur, på tross av den vidstrakte utbredelsen til snøugla (individene fra de ulike områdene er blandet). Dette mønsteret stemmer overens med funn i to tidligere studier. Antydningen er dermed at snøugla har en høy mobilitet, og at den globale populasjonen er tett sammenkoblet. Vi har estimert den effektive populasjonsstørrelsen til snøugla de siste 1600 årene, og ser at det har vært flere perioder med vekst og nedgang, med en tydelig nedgang de siste 100 årene. Basert på resultatene i denne analysen ligger dagens globale populasjonsstørrelse på rundt 15 000 individer. Raptor Research Foundation hadde lagt sin årlige konferanse til Costa Rica i oktober 2025. På denne konferansen deltok snøugleprosjektet, og vi presenterte resultatene fra vårt arbeid med satellitt telemetri på arten i Norge. Vi fikk også gjennomført et møte med de ti ISOWG-medlemmene som deltok på konferansen. Fokus var en statusoppdatering og prioritering for videre arbeid i arbeidsgruppa.

• Brorson, Ina Skaara; Baalsrud, Helle Tessand & Høglo, Thale Christine (2025). Functional Insights into Homologous Recombination Deficiency in Breast Cancer. Norges miljø- og biovitenskapelige universitet (NMBU). Full text in Research Archive Show summary

  Cancer is a leading cause of death worldwide, and breast cancer is the most common type worldwide among females. With over 2.2 million new cases reported globally in 2022, the disease accounted for 23% of all female cancer diagnoses between 2022 and 2024 in Norway. Specific genes are associated with a higher risk of developing breast cancer if harboring a pathogenic variant. The Breast Associated Cancer Gene 1 and 2 (BRCA1/2) are among the most well-categorized genes found to be accountable for around 20% of all hereditary breast cancers. Carriers of pathogenic variants in BRCA1 and BRCA2 have a cumulative lifetime risk of developing breast cancer of 72% and 69%, respectively. Both BRCA1/2 encode key proteins involved in the homologous recombination (HR) pathway, crucial for error free repairment of double stranded DNA breaks. Pathogenic variants in these genes are increasingly used to determine eligibility for PARP inhibitor (PARPi) therapy of BRCA-related cancer, owing to the heightened sensitivity conferred by HR deficiency (HRD). Although advances in sequencing technologies, such as next-generation sequencing, now allow us to sequence entire genomes, vast expanses of knowledge remain to be uncovered regarding the mutations in various genes. Genetic testing can be inconclusive or yield variants that are of uncertain significance. When such an event occurs, testing for HRD can strengthen the suspicion of pathogenic variants if it yields a high genomic instability. In this study, gDNA was isolated from breast tumor biopsies from 13 breast cancer patients and sequenced using whole exome sequencing. The sequencing data was processed with ASCAT, a computational method that estimates allele-specific copy number profiles. Subsequently, two HRD algorithms, scarHRD and ovaHRDscar, were applied to calculate their respective HRD score. Focusing on comparing their differences and similarities in calculating HRD scores in breast cancer tumors, this approach provides broader insight into their potential applicability in clinical practice.

• Jonsson, Alexandra; Johansen, Finn-Eirik; Qiao, Shuo-Wang & Baalsrud, Helle Tessand (2025). Humoral immunity in Atlantic cod: a tale of antibodies in a fish missing the MHC II-CD4 pathway. Universitetet i Oslo. Full text in Research Archive Show summary

  Vaccines are designed to stimulate immune memory and protection, and antibody titers remain key indicators of vaccine efficacy. The production of high-affinity, long-lived antibodies relies on T cell-dependent mechanisms, where B cells interact with CD4+ T helper cells via peptide-MHC II presentation. This interaction drives germinal center formation, class switching, and memory development. However, Atlantic cod (Gadus morhua) present an immunological paradox. Despite their capacity to thrive in pathogen-rich environments and receive functional protection from certain vaccines, cod mount weak antibody responses and lack both the mhc class II locus and a functional cd4 gene. Long before this was confirmed by whole-genome sequencing by Star et al. in 2011, Pilström posed a prescient question: “If we pose the hypothetical question: ‘What would an antibody response look like in the absence of MHC class II molecules?’ an acceptable answer would be: ‘Very much like the antibody response of the cod.’” — Pilström, 2005 This thesis explores how cod generate specific and protective antibodies in the absence of canonical T cell-dependent pathways. We first developed monoclonal and polyclonal antibodies against cod IgM, enabling sensitive detection across multiple immunological methods. Using these tools, we showed that cod produced strong and sustained IgM responses to T cell-independent type 2 antigens, while T cell-dependent and T cell-independent type 1 responses were minimal. We then vaccinated cod with Vibrio anguillarum O2a and challenged them with both O2a and O2b strains, observing full and partial protection, respectively. This immunization induced specific IgM antibodies against O2a that cross-reacted with O2b. These antibodies recognized proteinaceous rather than lipopolysaccharide antigens and conferred protection when transferred to naive recipients. Yet, our efforts to define antibody effector functions was challenging. We found that the V. anguillarum O2a strain was resistant to complement-mediated killing, and that there was no measured differences in phagocytic activity in presence of either naive or immune sera. Altogether, this work shows that cod possess a functional but unconventional humoral immune system. It challenges assumptions about the universality of the MHC II–CD4 axis and highlights the evolutionary plasticity of adaptive immunity.

• Braut-Solheim, Astrid; Baalsrud, Helle Tessand; Skrede, Inger & Methlie, Ine-Susanne Hopland (2024). A population genomic study of the effect of clear-cut forestry on the beetle Gyrophaena boleti. Norges miljø- og biovitenskapelige universitet (NMBU). Full text in Research Archive Show summary

  The boreal forest is the home to several thousands of species, and about 2/3 of the forests are under management, mostly for timber production. In Norway only two percent of the forests are natural, and only 21% of this area is protected. The main logging strategy in Norway is clear-cutting followed by planting, altering the composition of both living trees and dead wood. Clear-cut forests are in particular danger of losing biodiversity. Gyrophaena boleti is a small rove beetle inhabiting bracket fungi in these forests, living in both mature previously clear-cut and near-natural forests. How the different management strategies are affecting the genetic diversity of this beetle is currently unknown. Utilizing pooled whole genome sequencing to do a population genomic study of G. boleti from nine paired forest sites, we show that G. boleti in the clear-cut forests tend to have slightly lower genetic diversity than G. boleti from near-natural forests. Although generally the genetic diversity is high. We also found little genome-wide population structure between sites with paired forest stands. However, we found peaks of differentiation between populations in different forest sites and stands which could be genomic regions involved in local adaptation. This is the first genomic study of the species G. boleti, contributing to the knowledge of how small, specialized insect species are affected by habitat change. This understanding could help support the development of conservation strategies and management practices of the boreal forests.

• Jacobsen, Karl-Otto; Baalsrud, Helle Tessand; Enevoldsen, Emily Louise Gilbert; Solheim, Roar; Øien, Ingar Jostein & Aarvak, Tomas (2024). Snøuglas økologi, genetikk og forekomst i Norge. Årsrapport 2024. Norsk institutt for naturforskning (NINA). Full text in Research Archive
• Jacobsen, Karl-Otto; Baalsrud, Helle Tessand; Enevoldsen, Emily Louise Gilbert; Solheim, Roar; Øien, Ingar Jostein & Aarvak, Tomas (2024). Snøuglas økologi, genetikk & forekomst i Norge. Årsrapport 2024. Norsk institutt for naturforskning (NINA). ISSN 9788242653598. Full text in Research Archive Show summary

  Lemensyklusen er styrende for om snøugla går til hekking eller ikke, og i 2024 ble det ikke dokumentert noen hekkinger i Norge eller Fennoskandia. I Norge var det 26 observasjoner av snøugler i 2024 som er vurdert som sikre. I tillegg er det henholdsvis åtte og seks antatt sikre observasjoner i Sverige og Finland. I 2022 ble referansegenomet til snøugla ferdig sekvensert. Dette er nesten komplett og danner grunnlaget for senere analyser. Vi reanalyserte det fullstendige datasettet i 2024, som består av 68 helgenomsekvenserte snøugler fra ulike bestander. Basert på dette datasettet med helgenomdata og over en million markører, finner vi ingen antydning til populasjonsstruktur, på tross av den vidstrakte utbredelsen til snøugla (individene fra de ulike områdene er blandet). Dette mønsteret stemmer overens med funn i to tidligere studier. Antydningen er dermed at snøugla har en høy mobilitet, og at den globale populasjonen er tett sammenkoblet. Vi har estimert den effektive populasjonsstørrelsen til snøugla de siste 1600 årene, og ser at det har vært flere perioder med vekst og nedgang, med en tydelig nedgang de siste 100 årene. Basert på resultatene i denne analysen ligger dagens globale populasjonsstørrelse på rundt bare 25 000 individer.

• Bøe, Veronica Aarvik; Shapaval, Volha; Sandve, Simen Rød & Baalsrud, Helle Tessand (2023). The genomic basis of lipid accumulation in Mucor circinelloides VI 04473. Norges miljø- og biovitenskapelige universitet (NMBU). Full text in Research Archive Show summary

  Den dimorfe muggsopparten Mucor circinelloides kan akkumulere opp til 80% av ens egen biomasse i lipider som er av interesse for ernæring og fór (som for eksempel flerumettede fettsyrer). Derfor er den et lovende alternativ til dyr og planter som råmateriale. Å optimere utbyttet er dermed av stor industriell interesse. Dzurendova et al. (2021b) viste at fravær av kalsium, kombinert med ulike nivå av fosfor, økte lipid-produksjonen i Mucor circinelloides VI 04473. Målet med denne avhandlingen var å undersøke det genomiske grunnlaget for lipid akkumulering, og den regulatoriske gen-responsen på fravær av kalsium, i MC VI 04473. Fenotypiske data fra gasskromotografi og Fouriertransformasjon infrarød spektroskopi kombinert med genuttrykksdata fra RNA sekvensering ble analysert. Fenotypiske data viste at den største økningen i lipidakkumulering forekom i behandlingen hvor kalsium-fravær ble kombinert med lave nivå av fosfor. Interessante funn av nedregulerte gener i denne behandlingen omfattet nedbrytning av fettsyrer, lipid signalisering, lipid transport, og kalsium-bindende proteiner. Interessante funn blant oppregulerte gener var relatert til cellevekst, polyfosfat- og karbohydrat-metabolisme, og stresstoleranse. Analysen av differensielt uttrykte gener mellom kalsium-fravær og kalsium-nærvær resulterte i utpekningen av enkelte gener som var relatert til både lipidakkumulering og kalsium-fravær. Dog, videre forskning kreves for å kunne belyse sammenhengen mellom kalsium og lipidakkumulering. Forbedring av genom-annotasjonen til MC VI 04473 kan bidra til å belyse denne sammenhengen.

• Jacobsen, Karl-Otto; Solheim, Roar; Øien, Ingar Jostein; Aarvak, Tomas & Baalsrud, Helle Tessand (2023). Snøuglas økologi og forekomst i Norge. Norsk institutt for naturforskning (NINA). ISSN 9788242650283. Full text in Research Archive Show summary

  Snøugleprosjektet er et samarbeid mellom Norsk institutt for naturforskning (NINA), Naturmuseum og Botanisk hage ved Universitetet i Agder (NMB-UIA) og BirdLife Norge (tidligere Norsk Ornitologisk Forening) som startet opp i 2005. Prosjektet innledet i 2021 et samarbeid med postdoktor Helle Tessand Baalsrud ved Norges miljø- og biovitenskapelige universitet (NMBU). Hun har et forskningsprosjekt hvor hun ønsker å gjennomføre helgenomsekvensering av snøugler fra ulike deler av artens utbredelsesområde. Det har ikke vært rapportert om noen hekkinger av snøugler i Norge og Fennoskandia i 2022. Forrige hekkesesong var i 2015, og den forventede hekkesesongen i 2019 ble spolert da lemenbestanden kollapset pga. ising vinteren 2018/19. Lemen har en 3-5 års syklus, og det var forventet at bestanden skulle begynne å øke igjen i løpet av 2022. I løpet av denne høsten har vi fått inn meldinger fra ulike steder i det nordlige Fennoskandia om at det observeres lemen. Hvis det blir gunstige snøforhold for lemen i løpet av denne vinteren, er det sannsynlig at det blir hekkinger av snøugler i Norge i 2023. Hvor mange par og i hvilke geografiske områder de i tilfelle vil kunne hekke i er ikke mulig å forutsi, da det er avhengig av hvor mange ugler som evt. kommer trekkende vestover fra Russland, og om og hvor det vil være tilstrekkelige mengder mat i egnede hekkehabitater. Det har imidlertid vært relativt mange meldinger om mulige observasjoner av snøugler i Norge i 2022, men kun fem av disse ble godkjent av oss under kvalitetssikringen. Fire av disse var i Finnmark (4/4, 2/9, 28/9 og 11/10), og én i Troms (24/8). I tillegg er det fem sikre observasjoner i Finland. Vi har ingen sikre observasjoner fra Sverige.

• Jacobsen, Karl-Otto; Øien, Ingar Jostein; Aarvak, Tomas; Solheim, Roar; Baalsrud, Helle Tessand & Enevoldsen, Emily Louise Gilbert (2023). Snøuglas økologi og forekomst i Norge. Årsrapport 2023. Norsk institutt for naturforskning (NINA). ISSN 9788242652089. Full text in Research Archive Show summary

  Lemensyklusen er styrende for om snøugla går til hekking eller ikke, og sommeren 2023 skulle etter forventingene ha en lementopp. Det ble i 2023 kun dokumentert én hekking av snøugle i Norge – den eneste kjente hekkingen i Fennoskandia. Forrige hekkesesong var i 2015. Den forventede hekkesesongen i år ble stort sett spolert da lemenbestanden kollapset pga. ising vinteren 2022/2023, noe som også skjedde vinteren 2018/19. I Norge har vi 24 observasjoner av snøugler i 2023 som vi har vurdert som sikre. I tillegg ble det gjort 21 sikre observasjoner i Finland, og kun tre sikre snøugleobservasjoner i Sverige. Dette er langt færre enn i de gode hekkeårene 2011 og 2015. Det var også færre enn i 2019, da det ikke var noen kjente hekkinger. I 2023 er det ferdigstilt datasett for populasjonsgenomikk, som nå består av 68 helgenomsekvenserte snøugler fra ulike bestander. Vi har gjort en del foreløpige analyser basert på deler av datasettet, og finner ingen antydning til populasjonsstruktur eller genetiske forskjeller mellom individer fra ulike geografiske regioner. I 2024 vil vi undersøke den demografiske historien til snøuglene for å få innblikk i hvordan populasjonsstørrelsen har endret seg over tid, samt genetisk diversitet hos denne arten. Dette vil kunne gi en pekepinn på om snøugla kan tilpasse seg endringer i miljøet.

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