Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Lin Yang, Hong Jin, Qien Yang, Andrey Poyarkov, Miroslav Korablev, Viatcheslav Rozhnov, Junjie Shao, Qiaomei Fu, Jose Antonio Hernandez-Blanco, Xiangjiang Zhan, Li Yu, Dmitry Alexandrov, Qingyan Dai, Bariushaa Munkhtsog, Xin Du, Bayaraa Munkhtsog, Liqing Ma, Wanlin Chen, Sergei Malykh, Yipeng Jin, Shunfu He, Tongzuo Zhang, Guosheng Wu, Yonghong Shi, Fuwen Wei, Yibo Hu
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引用次数: 0

Abstract

Long-term persistence of species with low genetic diversity is the focus of widespread attention in conservation biology. The snow leopard, Panthera uncia, is a big cat from high-alpine regions of Asia. However, its subspecies taxonomy, evolutionary history, evolutionary potential, and survival strategy remain unclear, which greatly hampers their conservation. We sequence a high-quality chromosome-level genome of the snow leopard and the genomes of 52 wild snow leopards. Population genomics reveal the existence of two large genetic lineages in global snow leopards, the northern and southern lineages, supported by the biogeography. The Last Glacial Maximum drove the divergence of two lineages. Microclimate differences and large rivers between the western and central Himalayas likely maintain the differentiation of two lineages. EPAS1 is positively selected in the southern lineage with almost fixed amino acid substitutions and shows an increased allele frequency with elevation. Compared to the southern lineage, the northern lineage exhibits a lower level of genomic diversity and higher levels of inbreeding and genetic load, consistent with its recent population decline. We find that snow leopards have extremely low genomic diversity and higher inbreeding than other Carnivora species; however, strong deleterious mutations have been effectively purged in snow leopards by historical population bottlenecks and inbreeding, which may be a vital genetic mechanism for their population survival and viability. Our findings reveal the survival strategy of a species with low genetic diversity and highlight the importance of unveiling both genetic diversity and genetic burden for the conservation of threatened species.
基因组证据表明,雪豹的遗传多样性低,但清除了强烈的有害变异
低遗传多样性物种的长期存在是保护生物学广泛关注的焦点。雪豹,学名Panthera uncia,是一种生活在亚洲高高山地区的大型猫科动物。然而,其亚种分类、进化历史、进化潜力和生存策略等方面的研究仍不清楚,这极大地阻碍了其保护。我们测序了高质量的雪豹染色体水平基因组和52只野生雪豹的基因组。种群基因组学揭示了全球雪豹存在北方和南方两大遗传谱系,并得到了生物地理学的支持。末次盛冰期推动了两个谱系的分化。喜马拉雅山脉西部和中部的小气候差异和大河可能维持了两个谱系的分化。EPAS1在几乎固定的氨基酸替换的南方谱系中是正选择的,并且等位基因频率随着海拔的升高而增加。与南方世系相比,北方世系表现出较低的基因组多样性水平和较高的近交和遗传负荷水平,这与其近期种群数量下降相一致。研究发现,雪豹的基因组多样性极低,近亲繁殖率高于其他食肉动物;然而,历史种群瓶颈和近亲繁殖有效地清除了雪豹种群中强烈的有害突变,这可能是雪豹种群生存和活力的重要遗传机制。我们的研究结果揭示了低遗传多样性物种的生存策略,并强调了揭示遗传多样性和遗传负担对濒危物种保护的重要性。
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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