Data from: Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear

The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution.

约100年前，因高强度狩猎，斯堪的纳维亚棕熊（Scandinavian brown bear）的种群规模曾大幅缩减。在得到保护后，该种群随后得以恢复，如今种群数量已达数千只。学界已对当代种群的遗传多样性开展了较为深入的研究，结果显示该种群包含多个亚种群，各亚种群均具备较高水平的遗传变异。不过，既往研究均未能明确此次种群瓶颈（demographic bottleneck）对当代遗传结构与遗传多样性的影响程度。本研究借助瓶颈事件前后的斯堪的纳维亚棕熊样本的线粒体DNA（mitochondrial DNA）与微卫星DNA（microsatellite DNA）分子标记，探究了此次瓶颈事件的影响。模拟分析与多变量分析结果显示，历史样本与现代样本的遗传结构一致，二者均可划分为斯堪的纳维亚南部、中部与北部的三个亚种群。但南部亚种群的等位基因频率似乎发生了显著改变。对整个种群的线粒体DNA多样性进行比对后发现，瓶颈事件导致单倍型（haplotype）数量大幅减少。不过，常染色体遗传多样性的丢失则相对缓和，尽管南部亚种群的等位基因丰富度（allelic richness）出现了显著下降。近似贝叶斯计算（approximate Bayesian computations）结果明确证实，南部与北部亚种群在瓶颈事件期间均出现了有效种群大小（effective population size）的缩减。这些研究结果对斯堪的纳维亚棕熊的未来管理具有指导意义：它们既揭示了近期发生的遗传多样性丢失现象，也表明当前的遗传结构或由历史生态过程塑造，而非近期的人为迫害所致。