Phylogeography of ancient and modern brown bears from eastern Eurasia

Abstract

The brown bear (Ursus arctos) is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5–40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.

Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear (Ursus arctos) Population during the Holocene

“…Moreover, the Northeast Eurasian brown bears (modern and Holocene one) are genetically close to the U16 Kol (4.2-3.6 kya) brown bear specimen from the foothills of the Altai Mountains (South Siberia) and have a common ancestor with modern U. arctos populations from Estonia and the European part of Russia (Figure 2B). Interestingly, the previously published Pleistocene brown bear specimen from South Siberia (U2 Chu, ~40 kya) [6] is genetically close to the Pleistocene specimens from Northeast Eurasia (F-2374, 25.9 kya and F-2296, 41.1 kya) [3] (Figure 2B).…”

“…Over 60% of the modern distribution range of brown bears falls within Russia; however palaeoecological and palaeobiological data from the region remain rare [ 1 , 2 , 3 ]. Genetic data, including complete modern Eurasian brown bear mitogenomes, are abundant in the literature, but Pleistocene brown bear mitochondrial genomes are scarce [ 3 , 4 , 5 , 6 , 7 ].…”

“…The mitochondrial DNA haplotypes of modern brown bears are significantly correlated with the origin of the specimens, indicating probable maternal philopatry across the modern distribution of this species in the Holarctic [ 3 , 4 , 5 , 6 ].…”

Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence

“…Only on closer inspection an indistinct geographical division appears to exist between variants of this haplotype (Fig. 2b ) 20 , 31 .…”

“…Brown bears have a broad Palaearctic distribution 5 and exhibit extensive morphological, ecological, and behavioural variability across a large spatial scale [6][7][8][9][10] . While numerous nuclear DNA (nDNA) studies have elucidated the evolutionary relationship between brown bears and polar bears (Ursus maritimus) [11][12][13][14][15][16][17] , brown bear phylogeography still relies mostly, with few exceptions [17][18][19] , on analyses of mtDNA data [20][21][22][23][24][25][26][27][28][29][30][31] . These analyses revealed dissimilarity across contiguous populations and haplotype sharing across populations separated in time and space 23 , resulting in strikingly disjunct distributions of mtDNA haplotypes.…”