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

doi:10.1186/s13059-025-03555-0

IVPP-IR

	Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards
	Yang, Lin 1,2,3; Jin, Hong 1; Yang, Qien 4; Poyarkov, Andrey 5; Korablev, Miroslav 5; Rozhnov, Viatcheslav 5; Shao, Junjie 1,6; Fu, Qiaomei7 ; Hernandez-Blanco, Jose Antonio 5; Zhan, Xiangjiang 1,6; Yu, Li 8; Alexandrov, Dmitry 5; Dai, Qingyan 7; Munkhtsog, Bariushaa 9; Du, Xin 1,6; Munkhtsog, Bayaraa 10; Ma, Liqing 11,12; Chen, Wanlin 6; Malykh, Sergei 5; Jin, Yipeng 13; He, Shunfu 14; Zhang, Tongzuo 4; Wu, Guosheng 14; Shi, Yonghong 15; Wei, Fuwen 1,2,3; Hu, Yibo 1,6
	2025-04-14
发表期刊	GENOME BIOLOGY
ISSN	1474-760X
卷号	26 期号:1 页码:24
通讯作者	Wei, Fuwen(weifw@ioz.ac.cn) ; Hu, Yibo(ybhu@ioz.ac.cn)
摘要	BackgroundLong-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.ResultsWe 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.ConclusionsOur 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.
关键词	Snow leopards Population genomics Genetic structure Genomic diversity Deleterious variants EPAS1
DOI	10.1186/s13059-025-03555-0
关键词[WOS]	READ ALIGNMENT ; PREDICTION ; SEQUENCE ; TOOL ; GENERATION ; PROGRAM ; HISTORY ; FORMAT ; FINDER
收录类别	SCI
语种	英语
资助项目	The National Key Program of Research and Development of Ministry of Science and Technology
项目资助者	The National Key Program of Research and Development of Ministry of Science and Technology
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:001466492100002
出版者	BMC
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.205/handle/311034/24729
专题	中国科学院古脊椎动物与古人类研究所
通讯作者	Wei, Fuwen; Hu, Yibo
作者单位	1.Chinese Acad Sci, Inst Zool, CAS Key Lab Anim Ecol & Conservat Biol, Beijing, Peoples R China 2.Jiangxi Agr Univ, Coll Forestry, Jiangxi Key Lab Conservat Biol, Nanchang, Jiangxi, Peoples R China 3.Southern Marine Sci & Engn, Ctr Evolut & Conservat Biol, Guangdong Lab, Guangzhou, Peoples R China 4.Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining, Qinghai, Peoples R China 5.Russian Acad Sci, AN Severtsov Inst Ecol & Evolut, Moscow, Russia 6.Univ Chinese Acad Sci, Beijing, Peoples R China 7.Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing, Peoples R China 8.Yunnan Univ, State Key Lab Conservat & Utilizat Bioresource, Kunming 650091, Yunnan, Peoples R China 9.Irbis Mongolia Ctr, Ulaanbaatar, Mongolia 10.Mongolian Acad Sci, Inst Biol, Ulaanbaatar, Mongolia 11.Qinghai Univ, Qinghai Acad Anim Sci & Vet Med, Qinghai Prov Key Lab Pathogen Diag Anim Dis, Xining 810016, Qinghai, Peoples R China 12.Qinghai Univ, Green Techn Res Prevent & Control, Xining, Qinghai, Peoples R China 13.China Agr Univ, Coll Vet Med, Clin Dept, Beijing, Peoples R China 14.Xining Wildlife Zoo, Xining, Qinghai, Peoples R China 15.Golmud Forestry & Grassland Stn Qinghai Prov, Haixi 816000, Peoples R China
推荐引用方式 GB/T 7714	Yang, Lin,Jin, Hong,Yang, Qien,et al. Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards[J]. GENOME BIOLOGY,2025,26(1):24.
APA	Yang, Lin.,Jin, Hong.,Yang, Qien.,Poyarkov, Andrey.,Korablev, Miroslav.,...&Hu, Yibo.(2025).Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards.GENOME BIOLOGY,26(1),24.
MLA	Yang, Lin,et al."Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards".GENOME BIOLOGY 26.1(2025):24.