Biology subjects

Baalsrud, H. T.

Publications and source records attributed to Baalsrud, H. T..

7 recordsLinked to original sources

bioRxiv2026

Recent effective population size of the snowy owl (Bubo scandiacus) tracks historical climate variation

Arctic ecosystems are undergoing rapid climate warming, providing an opportunity to examine molecular evolution under environmental stress. Here, we used whole-genome resequencing to assess population structure, genetic diversity, and recent demographic history in the snowy owl (Bubo scandiacus), a highly mobile Arctic apex predator classified as Vulnerable by the IUCN. We analysed genome-wide data from individuals sampled across the species' circumpolar range using a chromosome-level reference genome. Population genomic analyses revealed an absence of detectable population structure, indicating extensive gene flow and near-panmixia across continents. Genome-wide nucleotide diversity was low ({pi}= 2.47 x 10^(-4)), while runs of homozygosity were dominated by short tracts, indicating limited standing genetic variation despite little evidence for recent close inbreeding. Our demographic inference revealed a sustained decline in effective population size over the past ~1,600 years, a pronounced reduction coinciding with the Medieval Warm Period followed by a partial recovery during the subsequent cooler interval. This direct, measurable effect of past climate warming on effective population size raises concerns for the long-term survival of the snowy owl. Our results demonstrate that high connectivity and low levels of recent inbreeding have not necessarily buffered this species against climate-driven demographic erosion of genetic diversity. This study highlights the value of using whole-genome population genomics to inform genomic monitoring and conservation decision-making in rapidly changing environments.

genetics↗

bioRxiv2025

Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758)

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 little 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 8 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 (LTR) 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.

genomics↗

bioRxiv2025

Calcium starvation leads to strain-specific gene regulation of lipid and carotenoid production in Mucor Circinelloides

AO_SCPLOWBSTRACTC_SCPLOWFungi 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 it 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 have 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, i.e. the lipidome. Several pathways show divergent regulation between strains, which explains the phenotypic divergence between VI04473 and FRR5020. The complex gene family evolution of several lipidome genes probably also affected specialization of these strains to calcium stress. 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. This research advances our knowledge on complexity of fungal lipid metabolism and the role of calcium in regulating metabolic pathways.

genomics↗

bioRxiv2025

Chromosomal inversions mediated by tandem insertions of transposable elements

Chromosomal inversions play a crucial role in evolution by influencing phenotypes through the linkage of co-adapted alleles. While inversions have been found across a large number of taxa, mapping and characterizing inversion breakpoint regions remains challenging, often due to the presence of complex tandem repeats and transposable elements (TEs). Here, we identify and quantify TEs 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 TE orders and superfamilies with terminal inverted repeats (TIRs) within the inversion breakpoints of chromosomes 1, 7 and 12. Notably, we discovered a tandem accumulation of miniature inverted-repeat transposable elements (MITEs) 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 TEs in breakpoint regions suggests that they have driven the appearance of inversions through ectopic recombination, further supporting the potential of TEs in facilitating chromosomal reorganizations with large evolutionary implications.

evolutionary biology↗

bioRxiv2024

Evolutionary new centromeres in the snowy owl genome putatively seeded from a transposable element

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 centromeric satellite DNA, which appears to have originated from an endogenous retrovirus (ERV1). Using gene collinearity analyses we show that the position of these evolutionary new centromeres (ECNs) 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 transposable element-driven evolution of lineage-specific centromeres, which could have played a role in reproductive isolation and speciation of the snowy owl.

genomics↗

bioRxiv2021

Origin and fate of supergenes in Atlantic cod

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 that chromosomal inversions underlie all four supergenes, and show that they originated at different times between 0.40 and 1.66 million years ago. While we found no evidence for a role of introgression in the origin of the four supergenes, we reveal gene flux between supergene haplotypes with derived and ancestral arrangements, occurring both through gene conversion and double crossover. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the purging of introduced genetic variation.

evolutionary biology↗

bioRxiv2018

Long-read sequence capture elucidates the evolution of the hemoglobin gene clusters in codfishes

Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the hemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100kb) and MN (~200kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genetic organization and synteny of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.

genomics↗