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

Heino, M. T.; Nyman, T.; Palo, J. U.; Harmoinen, J.; Valtonen, M.; Pilot, M.; Översti, S.; Salmela, E.; Kunnasranta, M.; Hoelzel, A. R.; Ruokonen, M.; Aspi, J.

doi:10.1101/2022.05.19.492422

bioRxiv · 10.1101/2022.05.19.492422

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

Heino, M. T.·Nyman, T.·Palo, J. U.·Harmoinen, J.·Valtonen, M.·Pilot, M.·Översti, S.·Salmela, E.·Kunnasranta, M.·Hoelzel, A. R.·Ruokonen, M.·Aspi, J.

View original source ↗Export metadata ↓

Abstract

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.

Source connections

Published article ↗

Explore related subjects

evolutionary biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Heino, M. T., Nyman, T., Palo, J. U., Harmoinen, J., Valtonen, M., Pilot, M., Översti, S., Salmela, E., Kunnasranta, M., Hoelzel, A. R., Ruokonen, M., Aspi, J.. 2022-05-20. Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections. https://doi.org/10.1101/2022.05.19.492422

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Both genetic and social inheritance influence female aggressive and submissive behavior in a wild primate

Agonistic interactions are important determinants of resource access in wild animals, but their genetic basis remains poorly understood. Here we use a quantitative genetics approach to estimate the heritability of aggressive and submissive behavior of wild female baboons, considering relative rates of both individual and dyadic aggression and submission. To control for the social inheritance that creates kin-based dominance hierarchies, we implemented a multi-matrix model that included a social status similarity matrix alongside the additive genetic matrix. Despite a substantial contribution of social inheritance, especially for submissive behavior, we found heritable components for both aggressive and submissive behavior (h2=0.21 and h2=0.09-0.11, respectively). In dyadic models, aggressive behavior was primarily influenced by the aggressor's genotype (a direct genetic effect), while submissive behavior was primarily affected by the social partner's genotype (an indirect genetic effect). Finally, we found evidence for a negative genetic (but not phenotypic) correlation between aggressive and submissive behavior within dyads, and a negative genetic correlation between submissive behavior and eliciting submissive behavior. Together, our results highlight how direct genetic, indirect genetic, and social inheritance effects combine to influence primate social behavior.

evolutionary biology↗

bioRxiv2026

Genomic signatures of local adaptation in marram grass highlight the importance of provenance in dune restoration

Coastal sand dunes provide critical natural flood defences and key habitats for a range of threatened species. These systems are formed when shifting sands are stabilised by specialised coastal grasses. In Europe, marram grass (Calamagrostis arenaria) is the main dune building species. However, despite its ecological importance and its widespread use in dune restoration, little is known about the genomic innovations that facilitated the colonisation of the coast, the extent of local adaptation in current populations, or the genetic consequences of restoration practices. Using a chromosome-scale reference genome we generate here, we show that C. arenaria has significant expansions in several gene families relevant to coastal adaptation, including those associated with salinity, drought, and nutrient limitation. Using ddRAD-Seq data for over 200 individuals from 10 European populations, we identified strong genetic differentiation between northern and southern populations which corresponds to recognised subspecies. Within the northern european populations, the genetic structure is largely driven by isolation-by-distance. Although, we detected evidence of non-local planting in a restored Swedish dune system, where introduced plants were genetically distinct from the native population and both groups exhibited reduced genetic diversity. Genome-wide scans for local adaptation within the northern European marram grass individuals identified outlying genomic regions that were enriched for genes with functions associated with nutrient deficiency, drought, pathogen defence, and other environmental stressors characteristic of coastal dunes, potentially indicating local adaptation. Outlying regions also include genes associated with lignin biosynthesis and culm mechanical strength, potentially reflecting selection on the structural properties required to withstand different burial and wind exposure regimes. Overall, these findings show widespread local adaptation in C. arenaria, and support the use of local provenance in dune restoration and conservation.

evolutionary biology↗

bioRxiv2026

Parallel Trajectories in the Evolution of C-class MADS-box Genes in Flowering Plants and Conifers

Gene duplication events frequently underpin phenotypic diversity due to the increase in genetic material that can be shaped by evolution. AGAMOUS (AG) genes are members of the MADS-box gene family that show conserved function in specifying reproductive organ identity in seed plants. While the function, expression, and evolution of these genes have been extensively studied in flowering plants, they remain understudied in gymnosperms. Consequently, little is known about how AG has contributed to reproductive diversity and evolution outside of the flowering plants. Here, we report that AG genes underwent two duplication events within conifers prior to the split between Cupressaceae and its sister family, Taxaceae. Further, we characterize the in situ expression pattern for each resulting paralog (AG1, AG2, and AG3) in seed cones of three Cupressaceae species, Metasequoia glyptostroboides, Taxodium distichum, and Juniperus virginiana. We discover gene expression patterns consistent with subfunctionalization: AG1 specialized in seed and sporangial development, AG2 in seed cone and seed coat development, and AG3 in ovuliferous scale development. This study provides an evolutionary mechanism for the development of unique seed cone reproductive traits in Cupressaceae. More broadly, our results uncover convergent patterns in the evolution of AG gene lineages across conifers and angiosperms.

evolutionary biology↗