Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations
Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations
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DOI：
10.1093/gbe/evaa065
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发表时间：
2020-03
影响因子：
3.3
通讯作者：
Kohta Yoshida;M. Ravinet;T. Makino;A. Toyoda;T. Kokita;Seiichi Mori;J. Kitano
中科院分区：
文献类型：
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作者：
Kohta Yoshida;M. Ravinet;T. Makino;A. Toyoda;T. Kokita;Seiichi Mori;J. Kitano
摘要新栖息地的殖民化往往会减少种群规模，并可能导致遗传漂变造成有害突变的积累。与适应新环境的基因组基础相比，对孤立种群中有害突变的全基因组分析仍然有限。在本研究中，我们调查了在日本大陆中部的五个濒危淡水种群的三棘鱼（Gasterosteus aculeatus）的有害突变的积累。利用全基因组重测序数据，我们首先进行了基因组分析，并确认了至少两个独立的淡水殖民事件在大陆中部的祖先海洋生态型。其次，单核苷酸多态性分析表明，与海洋种群相比，淡水种群的杂合性大幅减少。杂合性的减少在每条染色体的中心比周边和X染色体上比常染色体上更明显。第三，有害突变的生物信息学分析表明，内陆淡水种群与海洋种群相比，有害突变的积累增加。对于大多数的人口检查，有害突变的频率较高的X染色体比常染色体。种群间比较表明，大多数有害突变可能是独立积累的。因此，濒危种群的全基因组重测序可以帮助估计有害突变的积累，并告诉我们哪些种群是最严重的濒危。此外，分析染色体之间的变异可以了解任何特定的染色体是否可能积累有害的突变。
Abstract Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared with the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole-genome resequencing data, we first conducted phylogenomic analysis and confirmed at least two independent freshwater colonization events in the central mainland from ancestral marine ecotypes. Next, analyses of single nucleotide polymorphisms showed a substantial reduction of heterozygosity in freshwater populations compared with marine populations. Reduction in heterozygosity was more apparent at the center of each chromosome than the peripheries and on X chromosomes compared with autosomes. Third, bioinformatic analysis of deleterious mutations showed increased accumulation of putatively deleterious mutations in the landlocked freshwater populations compared with marine populations. For the majority of populations examined, the frequencies of putatively deleterious mutations were higher on X chromosomes than on autosomes. The interpopulation comparison indicated that the majority of putatively deleterious mutations may have accumulated independently. Thus, whole-genome resequencing of endangered populations can help to estimate the accumulation of deleterious mutations and inform us of which populations are the most severely endangered. Furthermore, analysis of variation among chromosomes can give insights into whether any particular chromosomes are likely to accumulate deleterious mutations.