Resequencing of reindeer genomes provides clues to their docile habits

Abstract

Reindeer have long been served as vital subsistence resources for inhabitants of Arctic and subarctic regions owing to their domestication. However, the evolutionary relationships and divergence times among different reindeer populations, genetic traits that distinguish domesticated reindeer, and factors that contribute to their relative docility compared with that of other Cervidae specie, remain unclear. In this study, we sequenced the genomes of 32 individuals from wild and domestic reindeer populations that inhabit Arctic and subarctic regions. We found that reindeer experienced 2 or more independent domestication events characterized by weak artificial selection pressure and limited significant differences in genomic parameters between wild and domestic populations. Alterations in conserved noncoding elements in the reindeer genomes, particularly those associated with nervous system development, may have contributed to their domestication by rendering the nervous system less responsive. Together, our results suggest that inherent species-specific traits, rather than intense artificial selection, may have played a significant role in the relatively docile behavior of reindeer and offer valuable insights into the domestication process of these animals.

Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies

“…The broad spectrum of Y HTs in domestic reindeer are in concordance with Wu et al. ( 2024 ), who detected comparable levels of genetic diversity and linkage disequilibrium in wild and domestic reindeer populations.…”

“…In our dataset, we had 27 domesticated EuroBeringian reindeer and those formed five Y HGs (Figure 3 ). These HGs were distributed over the EuroBeringian clade suggesting that several wild lineages underwent domestication, which is in line with the proposed two or more independent domestication events in a recent study based on autosomal data (Wu et al., 2024 ). In Fennoscandian domesticates, two Y HGs, DF1 and DN1, were identified.…”

“…The hierarchic single locus Y tree, based on 55 samples from five subspecies, revealed that woodland caribou and EuroBeringian reindeer are clearly differentiated as evidenced by their deep splits in both phylogenies. The Y topology is therefore in agreement with established knowledge of two lineages based on mtDNA (Flagstad & Røed, 2003;Hold et al, 2024;Taylor et al, 2021) and autosomal (Dussex et al, 2023;Wu et al, 2024;Yannic et al, 2014Yannic et al, , 2018 data.…”

“…The pronounced Y-chromosomal sequence diversity in domesticated reindeer can be either interpreted as reindeer domestication is still in its early stages (Baskin, 2000), or it may reflect the unique breeding strategies applied by herders based on the unique biology and needs of the animals and humans in a specific natural and cultural environment (Beach & Stammler, 2006;Stammler & Takakura, 2010). The broad spectrum of Y HTs in domestic reindeer are in concordance with Wu et al (2024), who detected comparable levels of genetic diversity and linkage disequilibrium in wild and domestic reindeer populations.…”

“…Hence, the Y confirmed the hypothesis of their isolation by the Laurentide ice sheet (Hewitt, 1996 ; Yannic et al., 2014 ). However, the split time of the two Y clades was estimated around 40 ± 6.1 kya which is substantially younger than the 110 kya split time calculated from autosomal (Wu et al., 2024 ) and the 70kya calculated for the split of mtDNA clades (Hold et al., 2024 ). It is important to keep in mind that we used the last possible contact between EuroBeringian lineages over the continents (Figure 2b ) to calibrate the Y phylogeny.…”