After extinction in the wild in the beginning of the twentieth century, the European bison has been successfully recovered in two distinct genetic lines from only twelve and seven captive founders. We here aimed at characterizing the levels of realized inbreeding in these two restored lines to provide empirical insights into the genomic footprints left by population recovery from a small number of founders. To that end, we genotyped 183 European bison born over the last 40 years with the Illumina BovineHD beadchip that contained 22,602 informative autosomal SNPs after data filtering. We then identified homozygous-by-descent (HBD) segments and classified them into different age-related classes relying on a model-based approach. As expected, we observed that the strong and recent founder effect experienced by the two lines resulted in very high levels of recent inbreeding and in the presence of long HBD tracks (up to 120 Mb). These long HBD tracks were associated with ancestors living approximately from 4 to 32 generations in the past suggesting that inbreeding accumulated over multiple generations after the bottleneck. The contribution to inbreeding of the most recent groups of ancestors were however found to be decreasing in both lines. In addition, comparison of Lowland individuals born at different time periods showed that the levels of inbreeding tended to stabilize, HBD segments being shorter in animals born more recently which indicates efficient control of inbreeding. Monitoring HBD segment lengths over generations may thus be viewed as a valuable genomic diagnostic tool for populations in conservation or recovery programs.

中文翻译：

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欧洲野牛恢复的基因组足迹

在 20 世纪初在野外灭绝后，欧洲野牛已经成功地从仅 12 和 7 位圈养建立者的两个不同遗传系中恢复过来。我们在这里旨在表征这两个恢复品系中实现的近亲繁殖水平，以提供对少数创始人种群恢复所留下的基因组足迹的实证见解。为此，我们使用 Illumina BovineHD 珠芯片对过去 40 年出生的 183 头欧洲野牛进行基因分型，该芯片在数据过滤后包含 22,602 个信息丰富的常染色体 SNP。然后，我们确定了纯合子血统 (HBD) 段，并依靠基于模型的方法将它们分为不同的年龄相关类别。正如预期的那样，我们观察到，这两个品系所经历的强烈和最近的创始人效应导致近期近亲繁殖水平非常高，并且存在长 HBD 轨迹（高达 120 Mb）。这些长的 HBD 轨迹与过去大约生活 4 到 32 代的祖先有关，这表明近亲繁殖在瓶颈之后积累了多代。然而，发现最近的祖先群体对近亲繁殖的贡献在两个品系中都在下降。此外，在不同时期出生的低地个体的比较表明，近亲繁殖水平趋于稳定，最近出生的动物的 HBD 节段较短，这表明近亲繁殖得到了有效控制。