[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-detail-41111-en":3,"doc-seo-41111-105":30,"detail-sidebar-cat-0-en-105":91},{"code":4,"msg":5,"data":6},0,"success",{"doc_id":7,"user_id":8,"nickname":9,"user_avatar":10,"doc_module":4,"category_id":11,"category_name":12,"doc_title":13,"doc_description":14,"doc_content":15,"file_id":16,"file_url":17,"file_type":18,"file_size":19,"view_count":20,"is_deleted":4,"is_public":21,"is_downloadable":21,"audit_status":21,"page_count":22,"language":23,"language_code":24,"site_id":25,"html_lang":24,"table_of_contents":26,"faqs":27,"seo_title":13,"seo_description":14,"update_tm":28,"read_time":29},41111,7971461741311,"Ophelia","https://ap-avatar.wpscdn.com/avatar/74000253aff267980c6?x-image-process=image/resize,m_fixed,w_180,h_180&k=1779345379180704826",8,"Research & Report","Human population history revealed by a supertree approach","Employing the matrix representation with parsimony (MRP) method, the study constructs a composite phylogeny (supertree) for modern human populations by integrating 257 published genetic/genomic and linguistic phylogenetic trees together with 44 admixture plots from 200 studies (1990–2014). The inferred topology places South African Khoisan as most basal, followed by Central African Pygmies and a paraphyletic grouping of other sub-Saharan peoples. A largely robust, genetically dominated structure highlights key unstable regions and “wildcard taxa,” and shows weaker agreement with linguistic classification.","[www. nature.com/scientificreports](www. nature.com/scientificreports)  \nOPEN  \nReceived: 16 March 2016  \nAccepted: 23 June 2016  \nPublished: 19 July 2016  \nHuman population history revealed by a supertree approach  \nPavel Duda1,2 & Jan Zrzavý1  \nOver the past two decades numerous new trees of modern human populations have been published extensively but little attention has been paid to formal phylogenetic synthesis. We utilized the“matrix representation with parsimony”(MRP) method to infer a composite phylogeny (supertree) of modern human populations, based on 257 genetic/genomic, as well as linguistic, phylogenetic trees and 44 admixture plots from 200 published studies (1990–2014). The resulting supertree topology includes the most basal position ofS African Khoisan followed by C African Pygmies, and the paraphyletic section of all other sub-Saharan peoples. The sub-Saharan African section is basaltothe monophyletic clade consisting of the N African–W Eurasian assemblage and the consistently monophyletic Eastern superclade (Sahul–Oceanian, E Asian, and Beringian–American peoples). This topology, dominated by genetic data, is well-resolved and robust to parameter set changes, with a few unstable areas (e.g., West Eurasia, Sahul–Melanesia) reflecting the existing phylogenetic controversies. A few populations were identified as highly unstable“wildcard taxa”(e.g. Andamanese, Malagasy). The linguistic classification fits rather poorly on the supertree topology, supporting a view that direct coevolution between genes and languages is far from universal.  \nEvolutionary history of modern human populations is an extensively studied topic of great complexity. Human population history is certainly not purely phylogenetic, or tree-like1, as genetic admixture, mediated by processes such as migrations, expansions, intermarriage, trade, or slavery, have played an important role in shaping human history2. There is, however, a strong hierarchical signal that can be hypothesized as phylogeny in both genetic3,4 and cultural (especially linguistic) data5,6. It is worth noting that even using such terms as “genetic admixture” and“horizontal gene flow” implies an assumption of an underlying tree-like model7. Recently developed phylogenetic methods applied to both genetic8,9 and linguistic data10 allow us to visualize evolutionary history of populations using a bifurcating tree with horizontal links (“admixture edges”), accounting for both population splits and mixtures.  \nToday, no unified picture of modern human evolution based on genetic data is available, as studies that infer human population history have used different types of genetic markers, from “classical polymorphisms”(such as AB0 blood groups and protein allomorphisms) and uniparental markers (the mitochondrial DNA and the non-recombining portion of the Y chromosome) to genome-wide allele frequency data and data based on whole-genome sequencing11. Moreover, individual studies only partially overlap taxonomically. Even the largest published tree (267 populations) based on genome-wide data12 lacks several population groups important for a comprehensive description of human population history on a global scale (e.g., populations of N Africa, Anatolia, Balkans, E Europe, Indonesia, N Asia, Beringia, and N America) . A recent meta-analysis of human genomic diversity projects13 has also pointed to the lack of several key population groups (e.g., Hadza, Sandawe, Fulani, Chadic speakers, Australian Aboriginals, populations of Indonesia, Polynesia, and Northern America) .  \nThe language phylogenies published to date include up to 542 language varieties14 but usually cover just one language family each (mostly Bantu, Indo-European, or Austronesian). Formal attempts to reconstruct genealogical relationships between languages beyond the level of the families have been rare so far15,16, and nearly all of the proposed linguistic macrofamilies such as Eurasiatic/Nostratic17–19, Indo-Pacific20, and","cbCailTZPaAucVBT","https://ap.wps.com/l/cbCailTZPaAucVBT","pdf",1892896,3,1,10,"English","en",105,"# Introduction\n## Phylogenetic synthesis challenges\n## Data heterogeneity across genetics and language\n# Methods and data integration\n## Matrix representation with parsimony (MRP)\n# Results and interpretation\n## Supertree topology\n## Robustness and unstable regions\n## Comparison with linguistic classifications","[{\"question\":\"What method is used to build the human population supertree?\",\"answer\":\"The study uses the matrix representation with parsimony (MRP) method to infer a composite phylogeny (supertree).\"},{\"question\":\"How many sources of evidence are integrated in the analysis?\",\"answer\":\"The supertree is based on 257 genetic/genomic and linguistic phylogenetic trees and 44 admixture plots collected from 200 published studies covering 1990–2014.\"},{\"question\":\"How well do linguistic classifications match the genetic-dominated supertree?\",\"answer\":\"Linguistic classifications fit rather poorly on the supertree topology, indicating that direct coevolution between genes and languages is far from 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method is used to build the human population supertree?","Question",{"text":75,"@type":76},"The study uses the matrix representation with parsimony (MRP) method to infer a composite phylogeny (supertree).","Answer",{"name":78,"@type":73,"acceptedAnswer":79},"How many sources of evidence are integrated in the analysis?",{"text":80,"@type":76},"The supertree is based on 257 genetic/genomic and linguistic phylogenetic trees and 44 admixture plots collected from 200 published studies covering 1990–2014.",{"name":82,"@type":73,"acceptedAnswer":83},"How well do linguistic classifications match the genetic-dominated supertree?",{"text":84,"@type":76},"Linguistic classifications fit rather poorly on the supertree topology, indicating that direct coevolution between genes and languages is far from 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