Mitochondrial Genome Variability and Demographic History of Domesticated and Wild Reindeer (Rangifer tarandus)

On the basis of whole-genome sequencing of mitochondrial DNA and comparative analysis of sequences from domesticated and wild reindeer, the highest level of nucleotide diversity was detected in wild populations. In total, 1551 polymorphic sites were identified, of which 405 were informative. The most conserved regions included the 12S and 16S rRNA genes (π < 0.002) as well as the segment between ND2 and COI containing tRNA genes (π < 0.001). The most variable regions were ND1 (π = 0.001–0.003), ND2 (π = 0.001–0.003), and ND5 (π > 0.003 except in wild reindeer from Amur oblast), which correlate with adaptation to cold environments. Differences in genetic diversity levels between domesticated and wild reindeer populations reflect both demographic processes and possible selective pressure acting on specific regions of the mitochondrial genome. Reconstruction of demographic history revealed distinct effective population size dynamics among reindeer breeds. The Nenets breed exhibited a pronounced population expansion about 3000 years ago. No comparable effective size increase was observed in the Chukotka and Evenk breeds. Fu and Li’s D test showed contrasting patterns between domesticated and wild samples: domesticated reindeer displayed localized signals of deviation, consistent with artificial selection and restricted herd sizes, whereas wild populations demonstrated more extended and pronounced patterns indicative of demographic processes and natural selection. Modern reindeer mitogenomes retain ancient haplotypes, and several regions appear to have undergone selection, particularly ND5, Cytb, and ATP6. The Nenets, Evenk, and Chukotka breeds do not form distinct clades, contrary to expectations, considering their geographically distant ranges; instead, they comprise extensive mixed branches sharing similar or closely related haplotypes.