{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T20:02:52Z","timestamp":1775160172725,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,1,23]],"date-time":"2024-01-23T00:00:00Z","timestamp":1705968000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFC2605400"],"award-info":[{"award-number":["2023YFC2605400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2023JBMC011"],"award-info":[{"award-number":["2023JBMC011"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32288101"],"award-info":[{"award-number":["32288101"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32030020"],"award-info":[{"award-number":["32030020"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31900418"],"award-info":[{"award-number":["31900418"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12271026"],"award-info":[{"award-number":["12271026"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Projects Development Fund"},{"name":"UK Royal Society-Newton Advanced Fellowship","award":["NAF\\R1\\191094"],"award-info":[{"award-number":["NAF\\R1\\191094"]}]},{"DOI":"10.13039\/501100004826","name":"Beijing Natural Science Foundation","doi-asserted-by":"publisher","award":["L222051"],"award-info":[{"award-number":["L222051"]}],"id":[{"id":"10.13039\/501100004826","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CFFF Computing Platform and the Human Phenome Data Center of Fudan University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Various methods have been proposed to reconstruct admixture histories by analyzing the length of ancestral chromosomal tracts, such as estimating the admixture time and number of admixture events. However, available methods do not explicitly consider the complex admixture structure, which characterizes the joining and mixing patterns of different ancestral populations during the admixture process, and instead assume a simplified one-by-one sequential admixture model. In this study, we proposed a novel approach that considers the non-sequential admixture structure to reconstruct admixture histories. Specifically, we introduced a hierarchical admixture model that incorporated four ancestral populations and developed a new method, called HierarchyMix, which uses the length of ancestral tracts and the number of ancestry switches along genomes to reconstruct the four-way admixture history. By automatically selecting the optimal admixture model using the Bayesian information criterion principles, HierarchyMix effectively estimates the corresponding admixture parameters. Simulation studies confirmed the effectiveness and robustness of HierarchyMix. We also applied HierarchyMix to Uyghurs and Kazakhs, enabling us to reconstruct the admixture histories of Central Asians. Our results highlight the importance of considering complex admixture structures and demonstrate that HierarchyMix is a useful tool for analyzing complex admixture events.<\/jats:p>","DOI":"10.1093\/bib\/bbad540","type":"journal-article","created":{"date-parts":[[2024,1,23]],"date-time":"2024-01-23T16:49:48Z","timestamp":1706028588000},"source":"Crossref","is-referenced-by-count":4,"title":["Reconstructing complex admixture history using a hierarchical model"],"prefix":"10.1093","volume":"25","author":[{"given":"Shi","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Mathematics and Statistics, Beijing Jiaotong University , Beijing, 100044 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Yuan","sequence":"additional","affiliation":[{"name":"Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lu","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Beijing Jiaotong University , Beijing, 100044 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chang","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuting","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Beijing Jiaotong University , Beijing, 100044 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xumin","family":"Ni","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Beijing Jiaotong University , Beijing, 100044 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1975-1002","authenticated-orcid":false,"given":"Shuhua","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering , Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, , Shanghai 200032 , China"},{"name":"Fudan University , Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, , Shanghai 200032 , China"},{"name":"Ministry of Education Key Laboratory of Contemporary Anthropology , Collaborative Innovation Center for Genetics and Development, , Shanghai 201203 , China"},{"name":"Fudan University , Collaborative Innovation Center for Genetics and Development, , Shanghai 201203 , China"},{"name":"School of Life Science and Technology, ShanghaiTech University , Shanghai 201210 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,1,22]]},"reference":[{"issue":"6172","key":"2024012316361188400_ref1","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1126\/science.1243518","article-title":"A genetic atlas of human admixture history","volume":"343","author":"Hellenthal","year":"2014","journal-title":"Science"},{"issue":"3","key":"2024012316361188400_ref2","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1534\/genetics.114.162362","article-title":"The lengths of admixture tracts","volume":"197","author":"Liang","year":"2014","journal-title":"Genetics"},{"issue":"2","key":"2024012316361188400_ref3","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1534\/genetics.112.139808","article-title":"Population genetics models of local ancestry","volume":"191","author":"Gravel","year":"2012","journal-title":"Genetics"},{"issue":"2","key":"2024012316361188400_ref4","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1534\/genetics.108.098095","article-title":"Inference of historical changes in migration rate from the lengths of migrant tracts","volume":"181","author":"Pool","year":"2009","journal-title":"Genetics"},{"issue":"2","key":"2024012316361188400_ref5","doi-asserted-by":"crossref","first-page":"R19","DOI":"10.1186\/gb-2011-12-2-r19","article-title":"Dating the age of admixture via wavelet transform analysis of genome-wide data","volume":"12","author":"Pugach","year":"2011","journal-title":"Genome Biol"},{"issue":"5","key":"2024012316361188400_ref6","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1016\/j.ajhg.2012.09.008","article-title":"Exploring population admixture dynamics via empirical and simulated genome-wide distribution of ancestral chromosomal segments","volume":"91","author":"Jin","year":"2012","journal-title":"Am J Human Genetics"},{"issue":"7","key":"2024012316361188400_ref7","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1038\/ejhg.2013.265","article-title":"Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping","volume":"22","author":"Jin","year":"2014","journal-title":"Eur J Hum Genet"},{"key":"2024012316361188400_ref8","doi-asserted-by":"crossref","first-page":"20048","DOI":"10.1038\/srep20048","article-title":"Length distribution of ancestral tracks under a general admixture model and its applications in population history inference","volume":"6","author":"Ni","year":"2016","journal-title":"Sci Rep"},{"issue":"1","key":"2024012316361188400_ref9","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1038\/s41437-017-0041-2","article-title":"Inference of multiple-wave admixtures by length distribution of ancestral tracks","volume":"121","author":"Ni","year":"2018","journal-title":"Heredity (Edinb)"},{"issue":"1","key":"2024012316361188400_ref10","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/s41431-018-0259-3","article-title":"MultiWaver 2.0: modeling discrete and continuous gene flow to reconstruct complex population admixtures","volume":"27","author":"Ni","year":"2019","journal-title":"Eur J Hum Genet"},{"issue":"1","key":"2024012316361188400_ref11","doi-asserted-by":"crossref","first-page":"6232","DOI":"10.1038\/s41467-021-26503-5","article-title":"Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0","volume":"12","author":"Yuan","year":"2021","journal-title":"Nat Commun"},{"key":"2024012316361188400_ref12","article-title":"MultiWaverX: modeling latent sex-biased admixture history","volume":"23","author":"Zhang","year":"2022","journal-title":"Brief Bioinform"},{"issue":"3","key":"2024012316361188400_ref13","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.ajhg.2020.02.002","article-title":"Population histories of the United States revealed through fine-scale migration and haplotype analysis","volume":"106","author":"Dai","year":"2020","journal-title":"The American Journal of Human Genetics"},{"issue":"14","key":"2024012316361188400_ref14","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abd6690","article-title":"Ancient Xinjiang mitogenomes reveal intense admixture with high genetic diversity","volume":"7","author":"Wang","year":"2021","journal-title":"Sci Adv"},{"issue":"10","key":"2024012316361188400_ref15","doi-asserted-by":"crossref","first-page":"2572","DOI":"10.1093\/molbev\/msx177","article-title":"Genetic history of Xinjiang's Uyghurs suggests bronze age multiple-way contacts in Eurasia","volume":"34","author":"Feng","year":"2017","journal-title":"Mol Biol Evol"},{"issue":"7481","key":"2024012316361188400_ref16","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nature12736","article-title":"Upper Palaeolithic Siberian genome reveals dual ancestry of native Americans","volume":"505","author":"Raghavan","year":"2014","journal-title":"Nature"},{"issue":"506","key":"2024012316361188400_ref17","first-page":"1","article-title":"AdmixSim 2: a forward-time simulator for modeling complex population admixture","volume":"22","author":"Zhang","year":"2021","journal-title":"BMC Bioinformatics"},{"issue":"7571","key":"2024012316361188400_ref18","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"Consortium","year":"2015","journal-title":"Nature"},{"issue":"7624","key":"2024012316361188400_ref19","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/nature19792","article-title":"Genomic analyses inform on migration events during the peopling of Eurasia","volume":"538","author":"Pagani","year":"2016","journal-title":"Nature"},{"issue":"2","key":"2024012316361188400_ref20","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.ajhg.2013.06.020","article-title":"RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference","volume":"93","author":"Maples","year":"2013","journal-title":"Am J Human Genetics"},{"issue":"4","key":"2024012316361188400_ref21","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004234","article-title":"A general approach for haplotype phasing across the full spectrum of relatedness","volume":"10","author":"O'Connell","year":"2014","journal-title":"PLoS Genet"},{"key":"2024012316361188400_ref22","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1741-7007-8-15","article-title":"Evidence that a west-east admixed population lived in the Tarim Basin as early as the early bronze age","volume":"8","author":"Li","year":"2010","journal-title":"BMC Biol"},{"key":"2024012316361188400_ref23","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1126\/science.abk1534","article-title":"Bronze and iron age population movements underlie Xinjiang population history","volume":"376","author":"Kumar","year":"2022","journal-title":"Science"},{"issue":"3","key":"2024012316361188400_ref24","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1534\/genetics.112.145037","article-title":"Ancient admixture in human history","volume":"192","author":"Patterson","year":"2012","journal-title":"Genetics"},{"issue":"4","key":"2024012316361188400_ref25","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1534\/genetics.112.147330","article-title":"Inferring admixture histories of human populations using linkage disequilibrium","volume":"193","author":"Loh","year":"2013","journal-title":"Genetics"},{"issue":"2","key":"2024012316361188400_ref26","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1002\/ajpa.20188","article-title":"Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies","volume":"128","author":"Fenner","year":"2005","journal-title":"Am J Phys Anthropol"},{"issue":"1542","key":"2024012316361188400_ref27","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1098\/rspb.2004.2698","article-title":"Unravelling migrations in the steppe: mitochondrial DNA sequences from ancient central Asians","volume":"271","author":"Lalueza-Fox","year":"2004","journal-title":"Proc Biol Sci"},{"key":"2024012316361188400_ref28","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/s12863-015-0237-5","article-title":"Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: insights into prehistoric population movements in the Tarim Basin, China","volume":"16","author":"Li","year":"2015","journal-title":"BMC Genet"},{"issue":"7518","key":"2024012316361188400_ref29","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/nature13673","article-title":"Ancient human genomes suggest three ancestral populations for present-day Europeans","volume":"513","author":"Lazaridis","year":"2014","journal-title":"Nature"},{"issue":"3","key":"2024012316361188400_ref30","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1016\/j.ajhg.2008.08.001","article-title":"A genome-wide analysis of admixture in Uyghurs and a high-density admixture map for disease-gene discovery","volume":"83","author":"Xu","year":"2008","journal-title":"Am J Human Genetics"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/2\/bbad540\/56325946\/bbad540.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/2\/bbad540\/56325946\/bbad540.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,23]],"date-time":"2024-01-23T16:50:22Z","timestamp":1706028622000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbad540\/7584785"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,22]]},"references-count":30,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,1,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbad540","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,3,1]]},"published":{"date-parts":[[2024,1,22]]},"article-number":"bbad540"}}