Paasivaara, A. | Search bioRxiv

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↗

bioRxiv2023

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

Semi-domestic reindeer (Rangifer tarandus tarandus) play a vital role in the culture and livelihoods of indigenous people across the 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 utilization. Here we have generated a new genome assembly for the Fennoscandian semi-domestic reindeer with high contiguity, making it the most complete reference genome for reindeer to date. The new genome assembly was utilized 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 gene clusters, with the Finnish wild forest reindeer standing out as a unique sub-species. Divergence time estimates suggested a separation of [~]52,000 years ago between Northern-European Rangifer tarandus fennicus and Rangifer tarandus tarandus. Our study identified three main genetic clusters: Fennoscandian, the eastern/northern Russian and Alaskan group, and the Finnish forest reindeer. Furthermore, two independent reindeer domestication events were inferred suggesting separate origins for the semi-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.

genomics↗