Following glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears’ mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears.

After the last ice age, the brown bear (Ursus arctos) recolonized Scandinavia, likely from two different source populations, resulting in two subpopulations with distinct mitochondrial haplogroups. In the early 1900s, human persecution led to a severe bottleneck that reduced the overall population size from around 5000 to approximately 130 individuals. After protective measures were taken, the population recovered and today it comprises roughly 3000 individuals. Such bottlenecks can lead to loss of genetic variation, which can have long-lasting effects on population viability and population recovery. In this study, we generated whole-genome data of seven historical and 21 contemporary Scandinavian brown bears to estimate heterozygosity, inbreeding and mutational load, as well as population structure in the pre- and post-bottleneck subpopulations. Surprisingly, no significant decrease in heterozygosity and no significant increase in inbreeding and mutational load were found when comparing the historical and modern subpopulations. However, analyses of population structure and admixture suggest that the southern subpopulation has lost most of its genetic uniqueness, except in the mitochondrial genome. Our results indicate that the bottleneck led to an increase in male-driven gene flow from the north to the south, which maintained the subpopulation’s genome-wide diversity and may have contributed to its successful recovery.

BACKGROUND: The Norwegian lemming (Lemmus lemmus) is a small rodent endemic to the Fennoscandian alpine and arctic tundra. The species is known for cyclic population outbreaks and mass movements during peak years. Previous research based on microsatellites revealed high genetic variation but a weak population structure in the Norwegian lemming. RESULTS: In this study, we revisit the population structure of the species using genome-wide data. To do this, we generated a high-quality de novo reference genome for Lemmus lemmus, and resequenced genomes to 2.5-5 × coverage, from 86 lemmings sampled across the species' entire geographic distribution. Our results reveal that the population is geographically structured into distinct subpopulations, with an overall pattern characterised by isolation-by-distance among subpopulations. Furthermore, our results are consistent with earlier work suggesting that the species survived the last ice age within a northern refugium. CONCLUSIONS: Together, these findings provide a genome-wide perspective on today's population structure of the Norwegian lemming. In addition, we provide a de novo reference genome, which we believe will be a valuable resource to the research community.