Biology subjects

Kunnasranta, M.

Publications and source records attributed to Kunnasranta, M..

7 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

Contemporary hybridization and localized genomic differentiation between grey seal subspecies

Grey seals are divided into two subspecies, Halichoerus grypus grypus in the Baltic Sea and H. grypus atlantica in the North Atlantic Ocean. Historically, intense hunting caused local extinctions of grey seals across their range and promoted geographical isolation of the subspecies. However, recent population recovery and recolonization have renewed their overlap in a contact zone in Danish and Swedish waters. Here, using whole-genome sequencing data from 119 individuals, we investigate the demographic history of grey seals, the divergence of the subspecies, and genomic signatures of local adaptation and potential hybridization in the contact zone. We estimate that divergence began approximately 10,000 years ago, with gene flow ceasing 2000 years ago. We detect peaks of high genetic differentiation near genes with putative functions in osmo- and thermoregulation, consistent with salinity and temperature differences between the Baltic Sea and the North Atlantic. As evidence of the geographic isolation breaking up, we report a hybrid individual in the southwest Baltic contact zone, with Baltic maternal and Atlantic paternal ancestry, and identify a migrant of Baltic origin in the North Sea. Our study illustrates how local environmental variation and long-term hunting pressure have contributed to divergence between mammal subspecies over a short evolutionary timescale, with recent population recovery, recolonization and hybridization reshaping gene flow dynamics. Broadly, our work emphasizes the importance of studying evolutionary processes amid anthropogenic influences, including both disturbances and conservation successes, where demographic fluctuations, range shifts, altered gene flow, and adaptation to changing environments interact in complex, potentially consequential ways.

evolutionary biology↗

bioRxiv2025

Deep origins and distinct adaptations indicated for a glacial relict seal

Isolated populations of postglacial relicts are known from many regions and are typically found on mountains for terrestrial species and in lakes for aquatic species. Among the few aquatic mammalian relicts, the Saimaa ringed seal (Pusa hispida saimensis) has been landlocked in Lake Saimaa, Finland, for the last 10,000 years. Saimaa ringed seals show genetic, behavioral, and morphological differences to the other ringed seal subspecies, but the extent these differences stem from the end of the last glacial period remains unclear. Here, we demonstrate with comprehensive sampling and state-of-the-art genomic methods that the Saimaa ringed seals are much older than the lake they inhabit, having formed a separate evolutionary branch for at least 60,000 years. This deep evolutionary origin of the Saimaa ringed seals is further underscored by our ecomorphological analyses revealing adaptively distinct features in their dentition and tongue. Overall, glacial relicts, many threatened by extinction, may harbor a richer selection of evolutionary history than might be expected from their recent isolation history alone.

zoology↗

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

Automatic parameter estimation and detection of Saimaa ringed seal knocking vocalizations

Passive acoustic monitoring (PAM) offers a non-invasive method for monitoring elusive pinnipeds, but manual analysis of large recording datasets limits its scalability. For the endangered Saimaa ringed seal ( Pusa saimensis ), PAM provides a rare opportunity to study breeding-season behavior beneath seasonal ice cover. We evaluated automated methods for detecting and characterizing the species' distinctive knocking vocalizations using recordings from Lake Saimaa. Annotated data ( n = 12 565 calls) were used to develop pulse repetition rate (PRR) estimation and call-detection systems. The best-performing PRR estimator matched manual measurements with a mean absolute error of 1.50 Hz, while a spectrogram-based convolutional neural network detected knocking calls with a mean F1-score of up to 99.28%. These results show close agreement with manual approaches, indicating that automated detection and characterization are achievable at a standard that could substantially reduce PAM analysis effort. This represents an important step toward scalable, long-term acoustic monitoring of this endangered seal.

ecology↗

bioRxiv2022

Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections

AimThe Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to post-glacial bedrock rebound around 9,000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. Our main aim was to evaluate the role of the 20th century bottleneck in the erosion of genetic diversity in the Saimaa seal population. We also evaluated connections with other ringed seals from the Baltic Sea, Lake Ladoga, North America, Svalbard and the White Sea. LocationLake Saimaa, Finland, together with the Baltic Sea and the Arctic Ocean. MethodsWe sequenced sections of the mitochondrial control region from 60 up to 125 years old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies, and how it is phylogenetically related to other ringed seal populations. ResultsWe observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation shows also affinities to North American ringed seals. Main conclusionsOur results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seals do not represent well the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.

evolutionary biology↗

bioRxiv2020

Patterns of microbiome variation among infrapopulations of permanent bloodsucking parasites

While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.

ecology↗