Whole‑genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia

Kisun Pokrahel, Melak Weldenegodguad, Stephan Dudeck, Mervi Honkatukia, Heli Lindeberg, Nuccio Mazzullo, Antti Paasivaara, Jaana Peippo, Päivi Soppela, Florian Stammler, Juha Kantanen

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Abstract

Domestic reindeer (Rangifer tarandus) play a vital role in the culture and livelihoods of indigenous people across northern Eurasia. These animals are well adapted to harsh environmental conditions, such as extreme cold, limited feed availability and long migration distances. Therefore, understanding the genomics of reindeer is crucial for improving their management, conservation and utilisation. In this study, we have generated a new genome assembly for the Fennoscandian domestic reindeer with high contiguity, making it the most complete reference genome for reindeer to date. The new genome assembly was utilised to explore genetic diversity, population structure and selective sweeps in Eurasian Rangifer tarandus populations which was based on the largest population genomic dataset for reindeer, encompassing 58 individuals from diverse populations. Phylogenetic analyses revealed distinct genetic clusters, with the Finnish wild forest reindeer (Rangifer tarandus fennicus) standing out as a unique subspecies. Divergence time estimates suggested a separation of ~ 52 thousand years ago (Kya) between the northern European Rangifer tarandus fennicus and Rangifer tarandus tarandus. Our study identified four main genetic clusters: Fennoscandian, the eastern/northern Russian and Alaskan group, the Finnish forest reindeer, and the Svalbard reindeer. Furthermore, two independent reindeer domestication processes were inferred, suggesting separate origins for the domestic Fennoscandian and eastern/northern Russian reindeer. Notably, shared genes under selection, including retroviral genes, point towards molecular domestication processes that aided adaptation of this species to diverse environments.
Original languageEnglish
Article number23019
Number of pages16
JournalScientific Reports
Volume13
DOIs
Publication statusPublished - 2023
MoEC publication typeA1 Journal article-refereed

Field of science

  • Social and economic geography
  • Ecology, evolutionary biology
  • Genetics, developmental biology, physiology

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