Abstract
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.
Highlights
During the last glacial maximum, the ranges of most temperate species shifted and shrunk as temperatures decreased (Davis &Shaw, 2001)
In extremely small populations, genetic drift tends to prevail over natural selection, limiting the potential for purifying selection against deleterious variation, and even allowing deleterious variants to increase in frequency
We investigated the historical changes of effective population size within pygmy hogs and compared them with other Suidae species
Summary
During the last glacial maximum, the ranges of most temperate species shifted and shrunk as temperatures decreased The lack of apparent phenotypical defects suggests that deleterious variants were purged from the island fox population in parallel with further adaptation to the local environment (Robinson et al, 2016, 2018) It is, important to understand demographic history as well as temporal changes in mutational load in small, fragmented populations in order to predict the impact of inbreeding and increase the chances of long-term population persistence. It is still largely unknown whether the small population has experienced purifying selection of harmful mutations and whether current inbreeding leads to inbreeding depression in this population To infer their demographic history, and eventual inbreeding concerns, we studied whole-genome data of six pygmy hogs: three from the wild and three from the breeding program. These results provide a strong foundation in evaluating the conservation status of the pygmy hog and highlighting the importance of genomic monitoring in population management of pygmy hogs and other endangered species, both in situ and ex situ
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