干旱区生态环境知识资源中心(Arid): Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0

Arid

DOI	10.1038/s41467-021-26503-5
	Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0
	Yuan, Kai; Ni, Xumin; Liu, Chang; Pan, Yuwen; Deng, Lian; Zhang, Rui; Gao, Yang; Ge, Xueling; Liu, Jiaojiao; Ma, Xixian; Lou, Haiyi; Wu, Taoyang; Xu, Shuhua
通讯作者	Xu, SH (corresponding author), Univ Chinese Acad Sci, Shanghai Inst Nutr & Hlth, Chinese Acad Sci, Key Lab Computat Biol, Shanghai 200031, Peoples R China. ; Xu, SH (corresponding author), Fudan Univ, Sch Life Sci, Collaborat Innovat Ctr Genet & Dev, Ctr Evolutionary Biol,State Key Lab Genet Engn, Shanghai 200433, Peoples R China. ; Xu, SH (corresponding author), ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China. ; Xu, SH (corresponding author), Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China. ; Xu, SH (corresponding author), Zhengzhou Univ, Henan Inst Med & Pharmaceut Sci, Zhengzhou 450052, Peoples R China. ; Xu, SH (corresponding author), Fudan Univ, Human Phenome Inst, Shanghai 201203, Peoples R China.
来源期刊	NATURE COMMUNICATIONS
EISSN	2041-1723
出版年	2021
卷号	12 期号:1
英文摘要	Existing methods to identify the presence of DNA from other hominin species can be limited in the ability to accurately estimate introgression waves, or can only be applied to specific populations. Here, the authors have developed a generalizable method to identify introgression in multi-wave situations. We developed a method, ArchaicSeeker 2.0, to identify introgressed hominin sequences and model multiple-wave admixture. The new method enabled us to discern two waves of introgression from both Denisovan-like and Neanderthal-like hominins in present-day Eurasian populations and an ancient Siberian individual. We estimated that an early Denisovan-like introgression occurred in Eurasia around 118.8-94.0 thousand years ago (kya). In contrast, we detected only one single episode of Denisovan-like admixture in indigenous peoples eastern to the Wallace-Line. Modeling ancient admixtures suggested an early dispersal of modern humans throughout Asia before the Toba volcanic super-eruption 74 kya, predating the initial peopling of Asia as proposed by the traditional Out-of-Africa model. Survived archaic sequences are involved in various phenotypes including immune and body mass (e.g., ZNF169), cardiovascular and lung function (e.g., HHAT), UV response and carbohydrate metabolism (e.g., HYAL1/HYAL2/HYAL3), while archaic deserts are enriched with genes associated with skin development and keratinization.
类型	Article
语种	英语
开放获取类型	Green Accepted, gold
收录类别	SCI-E
WOS记录号	WOS:000712910500019
WOS关键词	GENOME SEQUENCE ; NEANDERTHAL ANCESTRY ; ANCIENT ADMIXTURE ; GENETIC HISTORY ; STRATIGRAPHY ; CHRONOLOGY ; LANDSCAPE ; CAVE
WOS类目	Multidisciplinary Sciences
WOS研究方向	Science & Technology - Other Topics
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/368262
作者单位	[Yuan, Kai; Liu, Chang; Pan, Yuwen; Zhang, Rui; Gao, Yang; Ge, Xueling; Ma, Xixian; Xu, Shuhua] Univ Chinese Acad Sci, Shanghai Inst Nutr & Hlth, Chinese Acad Sci, Key Lab Computat Biol, Shanghai 200031, Peoples R China; [Ni, Xumin] Beijing Jiaotong Univ, Sch Sci, Dept Math, Beijing 100044, Peoples R China; [Deng, Lian; Liu, Jiaojiao; Lou, Haiyi; Xu, Shuhua] Fudan Univ, Sch Life Sci, Collaborat Innovat Ctr Genet & Dev, Ctr Evolutionary Biol,State Key Lab Genet Engn, Shanghai 200433, Peoples R China; [Gao, Yang; Xu, Shuhua] ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China; [Wu, Taoyang] Univ East Anglia, Sch Comp Sci, Norwich NR4 7TJ, Norfolk, England; [Xu, Shuhua] Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China; [Xu, Shuhua] Zhengzhou Univ, Henan Inst Med & Pharmaceut Sci, Zhengzhou 450052, Peoples R China; [Xu, Shuhua] Fudan Univ, Human Phenome Inst, Shanghai 201203, Peoples R China
推荐引用方式 GB/T 7714	Yuan, Kai,Ni, Xumin,Liu, Chang,et al. Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0[J],2021,12(1).
APA	Yuan, Kai.,Ni, Xumin.,Liu, Chang.,Pan, Yuwen.,Deng, Lian.,...&Xu, Shuhua.(2021).Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0.NATURE COMMUNICATIONS,12(1).
MLA	Yuan, Kai,et al."Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0".NATURE COMMUNICATIONS 12.1(2021).