Supplementary material from "Temporal genomics reveals widespread but unexpected consequences of a bottleneck in the Scandinavian brown bear"

After the last ice age, the brown bear (Ursus arctos) recolonised 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 ~130 individuals. After protective measures were taken, the population recovered and today it comprises ca. 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 was found when comparing the historical and modern subpopulations. However, analyses of population structure and admixture suggests 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.