Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north-western Eurasia

Aim Using sequences of complete mitochondrial genomes, our aims were: (1) to investigate the matrilineal phylogeographical structure, migration patterns and lineage coalescence times in a large, continuous population of brown bears (Ursus arctos); and (2) to develop a novel spatial genetic method to identify migration corridors and barriers. Location North-western Eurasia: from eastern European Russia to the Baltic Sea. Methods We sequenced the complete mitochondrial genomes of 95 brown bears. The phylogeographical resolution of complete genomes was compared to that derived from subsets of the genome, including the most commonly used shorter sequences. We conducted network and Bayesian phylogeographical analyses and developed a novel, spatially explicit, individual-based approach (called DResD) for identifying migration corridors and barriers. Results Analysis of mitogenome sequences revealed five haplogroups, specific to particular geographical areas, exhibiting far greater resolving power than shorter sequences. Estimated coalescence times for the haplogroups ranged from 7.7 to 15.2ka, suggesting that their divergence took place after the last glaciation. We found several migration trends, including a large westward migration from eastern European Russia towards Finland. We also found evidence of a potential barrier and a migration corridor in the south-west of the study area. Main conclusions The use of complete mitochondrial genomes from a brown bear population in north-western Eurasia allowed us to identify phylogeographical structure, signatures of demographic history and spatial processes that had not previously been detected using shorter sequences. These findings have implications for studies on other species and populations, especially those exhibiting low mtDNA diversity. The relatively recent divergence estimates for haplogroups highlight the significance not only of the last glaciation but also of climatic fluctuations during the post-glacial period for the divergence of mammal populations in Europe. Our spatial genetic method represents a new tool for the analysis of genetic data in a geographical context and is applicable to any data that yield genetic distance matrices, including microsatellites, amplified fragment length polymorphisms (AFLPs) and single-nucleotide polymorphisms (SNPs).