Quinn Liam, Garcia-Erill Genís, Santander Cindy, Brüniche-Olsen Anna, Liu Xiaodong, Sinding Mikkel-Holger S, Heaton Michael P, Smith Timothy P L, Pečnerová Patrícia, Bertola Laura D, Hanghøj Kristian, Rasmussen Malthe Sebro, de Jager Deon, Siegismund Hans R, Albrechtsen Anders, Heller Rasmus, Moltke Ida
Department of Biology, University of Copenhagen, Copenhagen, Denmark.
USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, New Brunswick, USA.
Mol Ecol. 2023 Apr;32(8):1860-1874. doi: 10.1111/mec.16851. Epub 2023 Feb 3.
The iconic Cape buffalo has experienced several documented population declines in recent history. These declines have been largely attributed to the late 19th century rinderpest pandemic. However, the effect of the rinderpest pandemic on their genetic diversity remains contentious, and other factors that have potentially affected this diversity include environmental changes during the Pleistocene, range expansions and recent human activity. Motivated by this, we present analyses of whole genome sequencing data from 59 individuals from across the Cape buffalo range to assess present-day levels of genome-wide genetic diversity and what factors have influenced these levels. We found that the Cape buffalo has high average heterozygosity overall (0.40%), with the two southernmost populations having significantly lower heterozygosity levels (0.33% and 0.29%) on par with that of the domesticated water buffalo (0.29%). Interestingly, we found that these lower levels are probably due to recent inbreeding (average fraction of runs of homozygosity 23.7% and 19.9%) rather than factors further back in time during the Pleistocene. Moreover, detailed investigations of recent demographic history show that events across the past three centuries were the main drivers of the exceptional loss of genetic diversity in the southernmost populations, coincident with the onset of colonialism in the southern extreme of the Cape buffalo range. Hence, our results add to the growing body of studies suggesting that multiple recent human-mediated impacts during the colonial period caused massive losses of large mammal abundance in southern Africa.
标志性的非洲水牛在近代经历了几次有记录的种群数量下降。这些下降主要归因于19世纪末的牛瘟大流行。然而，牛瘟大流行对其遗传多样性的影响仍存在争议，其他可能影响这种多样性的因素包括更新世期间的环境变化、范围扩张和近期的人类活动。受此启发，我们对来自非洲水牛分布范围内59个个体的全基因组测序数据进行了分析，以评估当今全基因组遗传多样性水平以及哪些因素影响了这些水平。我们发现，非洲水牛总体平均杂合度较高（0.40%），最南端的两个种群杂合度水平显著较低（0.33%和0.29%），与家养水牛的杂合度水平（0.29%）相当。有趣的是，我们发现这些较低的水平可能是由于近期的近亲繁殖（纯合子片段的平均比例为23.7%和19.9%），而不是更新世时期更早的因素。此外，对近期种群历史的详细调查表明，过去三个世纪的事件是最南端种群遗传多样性异常丧失的主要驱动因素，这与非洲水牛分布范围最南端殖民主义的开始相吻合。因此，我们的研究结果进一步丰富了越来越多的研究，表明殖民时期近期人类介导的多种影响导致了南部非洲大型哺乳动物数量的大量减少。
