Biology subjects

Niemi, M.

Publications and source records attributed to Niemi, M..

6 recordsLinked to original sources

bioRxiv2026

Chromosome-level reference genome assembly of the Saimaa ringed seal (Pusa saimensis) - an ancient glacial relict landlocked pinniped

We present a high-quality chromosome-level reference genome for the Saimaa ringed seal (Pusa saimensis), an endangered freshwater pinniped endemic to Lake Saimaa, Finland. The assembly spans 2.353 Gb and comprises 15 autosomes together with the X and Y sex chromosomes. Using Oxford Nanopore Technologies (ONT) long-read sequencing and Hi-C scaffolding, we achieved a telomere-to-telomere assembly for all chromosomes, except the Y chromosome. Genome annotation identified approximately 21,800 protein-coding genes, consistent with other mammalian genomes. Assembly completeness was high, with BUSCO analysis recovering 99.6% of expected complete single-copy genes (98.2% single-copy and 1.3% duplicated). Comparative analyses revealed a highly conserved chromosomal architecture, with only minor syntenic differences relative to other pinniped chromosome-level assemblies. Previously described cytogenetic fusion events in Phocidae were confirmed (chromosomes 2 and 7). A translocation between chromosomes 6 and 7 distinguishes phocids from the otariids. In general, more distantly related taxa exhibit an increasing degree of intrachromosomal rearrangements. Notably, we identified a large intrachromosomal rearrangement on chromosome 2 that appears specific to the Saimaa ringed seal. Phylogenomic analysis based on 9,226 single-copy orthologues placed the Saimaa ringed seal as a sister lineage to the Baltic ringed seal (Pusa hispida botnica), while confirming also other established evolutionary relationships among pinnipeds. Comparative gene family analysis between the Saimaa ringed seal and the closely related grey seal (Halichoerus grypus) revealed lineage-specific differences driven by a limited number of gene families. In the Saimaa ringed seal, expansions were observed in ion transport, cytoskeleton, and regulatory genes, potentially reflecting adaptation to freshwater conditions. In contrast, the grey seal showed expansions in olfaction, immune-and spermatogenesis-associated gene families, including MAGE/MIA genes, consistent with differences in ecology and mating systems. This reference genome provides an important resource for studies of pinniped genome evolution, as well as conservation and population genomics of the Saimaa ringed seal, facilitating future work on genetic diversity, inbreeding, mutational load and adaptive potential in this highly endangered species.

genomics↗

bioRxiv2026

Boreal and subarctic freshwaters harbour a diversity of jumbophages

Bacteriophages (phages) are major drivers of microbial evolution and ecology, yet their diversity and functional roles remain poorly characterised in many natural environments, such as in freshwater systems. In boreal and subarctic freshwater habitats, where bacteria are typically slow-growing and nutrient-limited, phages are predicted to have a critical role in host regulation and horizontal gene exchange. However, only a few isolates have been obtained from such environments, leaving the genetic and functional diversity of these phages largely unexplored. Here, we present a collection of 40 bacteriophages isolated from boreal lakes and rivers using a set of diverse freshwater bacterial hosts. Despite using conventional isolation methods, eight of the isolates possess genomes larger than 200 kilobases and are classified as jumbophages. All jumbophages exhibited myovirus morphology and comparatively slow infection dynamics. These jumbophages include the first known representatives infecting members of Janthinobacterium and Herbaspirillum. Comparative genomic and phylogenetic analyses show that nearly all genomes are distinct from previously described phages, indicating substantial novelty. Diverse auxiliary metabolic and anti-defence systems were identified, including putative NAD+ salvage and acyl carrier protein modules, along with predicted Anti-Thoeris and Anti-CBASS elements. The Pseudomonas-infecting jumbophage Ahti encoded homologues of all 21 core genes that define the nucleus-forming family Chimalliviridae. Additionally, Ahti displayed compartmentalisation of DNA during infection, establishing it as the first freshwater nucleus-forming phage. These findings expand our understanding of the ecological, genomic, and functional diversity of phages in boreal environments, and highlight the role of freshwater ecosystems as significant reservoirs of novel viral lineages. ImportanceBacteriophages are viruses that infect bacteria and play important roles in shaping microbial communities and nutrient cycling in natural waters. However, much of what is known about their diversity comes from sequencing data alone, without environmental isolates that allow direct studies on their biology. In this study, we described 40 bacteriophages from boreal and subarctic lakes and rivers using freshwater bacterial hosts, including species of Flavobacterium, Pseudomonas, Janthinobacterium and other lesser-known phage hosts. Eight of these viruses had exceptionally large genomes, categorising them as jumbophages. These isolates included the first known jumbophages infecting Janthinobacterium and Herbaspirillum, as well as the first freshwater jumbophage shown to form a nucleus-like structure during infection. Together, these findings reveal boreal freshwaters as an important source of previously unknown virus diversity and provide new model systems for exploring phage biology in environmentally relevant contexts.

microbiology↗

bioRxiv2024

Linking ringed seal foraging behaviour to environmental variability

BackgroundForaging rates directly influence animals energetic intake and expenditure and are thus linked to body condition and the ability to survive and reproduce. Further, understanding the underlying processes driving a species behaviour and habitat use is important as changes in behaviour could result from changes in environmental conditions. MethodsIn this study, the dives of Saimaa ringed seals (Pusa hispida saimensis) were classified for the first time using hidden Markov models and telemetry data collected on individual dives, and the behavioural states of the diving seals were estimated. In addition, we used generalized additive mixed models on the foraging probability of the seals to identify environmental and temporal drivers of foraging behaviour. ResultsWe inferred three (in winter) or four (in summer) different dive types: sleeping/resting dives, shallow inactive dives, transiting dives and foraging dives, based on differences in dive metrics logged by or derived from data from telemetry tags. Long and relatively deep sleeping/resting dives were missing entirely in the winter, compensated by an increased proportion of time used for haul-out. We found profound differences in the behaviour of Saimaa ringed seals during the summer open water season compared to the ice-covered winter, with the greatest proportion of time allocated to foraging during the summer months (36%) and the lowest proportion in the winter (21%). The seals foraging probability peaked in summer (July) and was highest during the daytime during both summer and winter months. Moreover, foraging probability was highest at depths of 7-30 m in the winter and at depths >15 m in the summer. We also found some evidence of sex-specific foraging strategies that are adapted seasonally, with females preferring more sheltered water areas during winter. ConclusionsWe suggest that the foraging behaviour of Saimaa ringed seals is largely influenced by diel vertical movements and availability of fish, and that the seals optimize their energy acquisition while conserving energy, especially during the cold winter months. Further, the seals display some flexibility in foraging strategies, a feature that may help this endangered subspecies to cope with ongoing anthropogenic climate change.

ecology↗

bioRxiv2024

Ungulate substrate selection in fauna passages

Fauna passages are increasingly constructed at major roads and railways to mitigate the negative effects of infrastructure and traffic on wildlife. The function of such passages depends on design, including the construction materials, soil and vegetation. Providing "naturalness" in fauna passages may entail significant costs, yet its benefits are unclear. By using camera trap data, we examined ungulate substrate use in seven passages serving both fauna and local roads (overpasses) and fauna and watercourses (underpasses) in boreal Sweden and Finland. While all substrates were used, during snow-free periods, ungulates used smoother surfaces (fine-grained topsoil, grass, artificial fiber mat, and dirt road) more than expected based on their availability. Coarser surface (stony/rocky ground), shrub, and water were used less than expected. The results for road and water were, however, inconsistent between passages; in one overpass road was instead used less than expected, and in one underpass the water section was used particularly during winter but also by moose wading or swimming through in summer and autumn. General patterns of use largely remained when analysed byspecies, although sample sizes were limited. Despite limitations, our study offers valuable insights for planning and constructing fauna passages. To our knowledge, this study was the first of its kind describing how ungulates use different substrates in fauna passages. We suggest to conduct further research on this issue, for example by more detailed study of animal trajectories through passages and by experimental modification of substrates.

animal behavior and cognition↗

bioRxiv2023

Pure wild forest reindeer (Rangifer tarandus fennicus) or hybrids? A whole-genome sequencing approach to solve the taxonomical status

In Finland, the geographic distribution of semi-domestic reindeer (Rangifer tarandus tarandus) and wild forest reindeer (Rangifer tarandus fennicus) partly overlap in the vicinity of the southern border of the reindeer herding area. Hybridisation of these two subspecies is one of the major threats for the wild forest reindeer population, and the implemented conservation program targets preventing the crossbreeding of these reindeer. In this paper, we resequenced genomes of four Rangifer tarandus individuals with unknown taxonomical status and investigated their ancestries by comparing the genomic data with the existing resequenced data of the Finnish semi-domestic reindeer and Finnish wild forest reindeer. The genetic relationship investigations suggest that the four individuals were pure forest reindeer animals. Our study provides critical knowledge for practical conservation actions of wild forest reindeer in the reintroduction project, for which it is essential to recognise each individuals origin. In the future, it will also offer novel insights into the spread of native wild forest reindeer to new geographic regions in Finland. For subsequent studies, additional resequenced genomic data of Rangifer individuals will be needed to develop an ancestry information marker panel of single nucleotide polymorphisms for rapid and cost-effective identification of hybrid individuals of semi-domestic reindeer and wild forest reindeer.

genomics↗

bioRxiv2017

Autosomal recessive coding variants explain only a small proportion of undiagnosed developmental disorders in the British Isles

Large exome-sequencing datasets offer an unprecedented opportunity to understand the genetic architecture of rare diseases, informing clinical genetics counseling and optimal study designs for disease gene identification. We analyzed 7,448 exome-sequenced families from the Deciphering Developmental Disorders study, and, for the first time, estimated the causal contribution of recessive coding variation exome-wide. We found that the proportion of cases attributable to recessive coding variants is surprisingly low in patients of European ancestry, at only 3.6%, versus 50% of cases explained by de novo coding mutations. Surprisingly, we found that, even in European probands with affected siblings, recessive coding variants are only likely to explain ~12% of cases. In contrast, they account for 31% of probands with Pakistani ancestry due to elevated autozygosity. We tested every gene for an excess of damaging homozygous or compound heterozygous genotypes and found three genes that passed stringent Bonferroni correction: EIF3F, KDM5B, and THOC6. EIF3F is a novel disease gene, and KDM5B has previously been reported as a dominant disease gene. KDM5B appears to follow a complex mode of inheritance, in which heterozygous loss-of-function variants (LoFs) show incomplete penetrance and biallelic LoFs are fully penetrant. Our results suggest that a large proportion of undiagnosed developmental disorders remain to be explained by other factors, such as noncoding variants and polygenic risk.

genetics↗