Biology subjects

Vasemägi, A.

Publications and source records attributed to Vasemägi, A..

4 recordsLinked to original sources

bioRxiv2025

DNA extracted from boiled archival fish bones yields high quality whole genome sequencing data

Archival samples provide a unique source of DNA, offering the potential to extend the temporal scale of genetic studies by decades to centuries. Fish hard structures, such as otoliths and scales, serve as records for fish collected during fisheries monitoring across a large spatiotemporal scale. Operculum bones are a type of fish hard structure that, although less commonly collected, have been utilized in genetic studies. However, the usefulness of archived operculum bones to provide high quality whole genome sequence information has not been thoroughly evaluated. Here, we applied a commercially available extraction protocol, with minor adjustments, to isolate genomic DNA from operculum bones of Eurasian perch collected up to 47 years ago, followed by standard short-read whole genome sequencing. By comparing the metrics of DNA and whole genome sequencing data of bones with contemporary muscle samples, we demonstrate that the application of a simple extraction protocol on boiled archival fish operculum bones yields high quality genomic information that is comparable to fresh tissue, highlighting the role of archival operculum bones as an overlooked repository of valuable genomic information.

molecular biology↗

bioRxiv2024

Multi-decadal warming alters predator's effect on prey community composition

Predator responses to warming can occur via phenotypic plasticity and evolutionary adaptation, resulting in changes in their prey communities. However, we lack evidence of how warming-induced evolutionary changes in predators can influence the food web. Here, we ask whether fish subject to long-term warming across multiple generations differ in their impacts on prey communities compared to their nearby conspecifics experiencing a natural thermal regime. We carried out a common garden mesocosm experiment with larval perch (Perca fluviatilis), originating from one heated or one reference coastal environment, feeding on zooplankton communities under a gradient of experimental temperatures. We found that fish thermal origin influenced the zooplankton communities, and differently so depending on the experimental temperature. In presence of fish of heated origin, there were less zooplankton and also fewer individuals of large size, except for at intermediate experimental temperatures. Our findings show that differences between fish populations, potentially representing adaptation to local thermal environment, caused by multi-generational warming can cascade down via trophic interactions to also affect their zooplankton prey communities. Considering climate warming, our results suggest that rapid evolution in predators might have indirect cross-generational ecological consequences propagating through food webs.

ecology↗

bioRxiv2020

Population connectivity predicts vulnerability to white-nose syndrome in the Chilean myotis (Myotis chiloensis) - a genomics approach

Despite its peculiar distribution, the biology of the southernmost bat species in the world, the Chilean myotis (Myotis chiloensis), has garnered little attention so far. The species has a north-south distribution of c. 2800 km, mostly on the eastern side of the Andes mountain range. Use of extended torpor occurs in the southernmost portion of the range, putting the species at risk of bat white-nose syndrome (WNS), a fungal disease responsible for massive population declines in North American bats. Here, we examined how geographic distance and topology would be reflected in the population structure of M. chiloensis along the majority of its range using a double digestion RAD-tag method. We sampled 66 individuals across the species range and discovered pronounced isolation-by-distance. Furthermore, and surprisingly, we found higher degrees of heterozygosity in the southernmost populations compared to the north. A coalescence analysis revealed that our populations may still not have reached secondary contact after the Last Glacial Maximum. As for the potential spread of pathogens, such as the fungus causing WNS, connectivity among populations was noticeably low, especially between the southern hibernatory populations in the Magallanes and Tierra del Fuego, and more northerly populations. This suggests the probability of geographic spread of the disease from the north through bat-to-bat contact to susceptible populations is low. The study presents a rare case of defined population structure in a bat species and warrants further research on the underlying factors contributing to this.

evolutionary biology↗

bioRxiv2020

The strength and form of natural selection on transcript abundance in the wild

Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. We estimated selection on transcript abundance in cohort of a wild salmonid fish (Salmo trutta) affected by a myxozoan parasite through mark-recapture field sampling and the integration of RNA-seq with classical regression-based selection analysis. We show, based on fin transcriptomes of the host, that infection by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae) and subsequent host survival is linked to the upregulation of mitotic cell cycle genes. We also detect a widespread signal of disruptive selection; intermediate transcription levels were frequently associated with reduced host survival. Our results provide insights how selection can be measured at the transcriptome level to dissect the molecular mechanisms of contemporary natural selection driven by climate change and emerging anthropogenic threats.

evolutionary biology↗