Increasing human disturbance and climate change have a major impact on habitat integrity and size, with far‐reaching consequences for wild fauna and flora. Specifically, population decline and habitat fragmentation result in small, isolated populations. To what extend different endangered species can cope with small population size is still largely unknown. Studies on the genomic landscape of these species can shed light on past demographic dynamics and current genetic load, thereby also providing guidance for conservation programs. The pygmy hog (Porcula salvania) is the smallest and rarest wild pig in the world, with current estimation of only a few hundred living in the wild. Here, we analyzed whole‐genome sequencing data of six pygmy hogs, three from the wild and three from a captive population, along with 30 pigs representing six other Suidae. First, we show that the pygmy hog had a very small population size with low genetic diversity over the course of the past ~1 million years. One indication of historical small effective population size is the absence of mitochondrial variation in the six sequenced individuals. Second, we evaluated the impact of historical demography. Runs of homozygosity (ROH) analysis suggests that the pygmy hog population has gone through past but not recent inbreeding. Also, the long‐term, extremely small population size may have led to the accumulation of harmful mutations suggesting that the accumulation of deleterious mutations is exceeding purifying selection in this species. Thus, care has to be taken in the conservation program to avoid or minimize the potential for further inbreeding depression, and guard against environmental changes in the future.

中文翻译：

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极度濒危侏儒猪长期有效种群规模较小的遗传后果


日益增加的人类干扰和气候变化对栖息地的完整性和规模产生重大影响，对野生动植物产生深远的影响。具体而言，人口减少和栖息地破碎化导致种群规模小而孤立。不同的濒危物种能够在多大程度上应对较小的种群规模仍然很大程度上未知。对这些物种的基因组景观的研究可以揭示过去的人口动态和当前的遗传负荷，从而也为保护计划提供指导。侏儒猪（ Porcula salvania ）是世界上最小、最稀有的野猪，目前估计野外仅有几百头。在这里，我们分析了六头侏儒猪（三头来自野生，三头来自圈养种群）以及代表其他六种猪科动物的 30 头猪的全基因组测序数据。首先，我们表明，在过去约 100 万年的时间里，侏儒猪的种群规模非常小，遗传多样性也很低。历史上有效种群规模较小的一个迹象是，六个已测序个体不存在线粒体变异。其次，我们评估了历史人口统计的影响。纯合性（ROH）分析表明，侏儒猪种群过去曾经历过近亲繁殖，但近期并未经历过近亲繁殖。此外，长期的、极小的种群规模可能导致有害突变的积累，这表明有害突变的积累超过了该物种的纯化选择。因此，在保护计划中必须小心谨慎，以避免或尽量减少进一步近交衰退的可能性，并防范未来的环境变化。