Identification of African-Specific Admixture between Modern and Archaic Humans

Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evid...

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Published in:	American journal of human genetics Vol. 105; no. 6; pp. 1254 - 1261
Main Authors:	Wall, Jeffrey D., Ratan, Aakrosh, Stawiski, Eric, Kim, Hie Lim, Kim, Changhoon, Gupta, Ravi, Suryamohan, Kushal, Gusareva, Elena S., Purbojati, Rikky Wenang, Bhangale, Tushar, Stepanov, Vadim, Kharkov, Vladimir, Schrӧder, Markus S., Ramprasad, Vedam, Tom, Jennifer, Durinck, Steffen, Bei, Qixin, Li, Jiani, Guillory, Joseph, Phalke, Samir, Basu, Analabha, Stinson, Jeremy, Nair, Sandhya, Malaichamy, Sivasankar, Biswas, Nidhan K., Chambers, John C., Cheng, Keith C., George, Joyner T., Khor, Seik Soon, Kim, Jong-Il, Cho, Belong, Menon, Ramesh, Sattibabu, Thiramsetti, Bassi, Akshi, Deshmukh, Manjari, Verma, Anjali, Gopalan, Vivek, Shin, Jong-Yeon, Pratapneni, Mahesh, Santhosh, Sam, Tokunaga, Katsushi, Md-Zain, Badrul M., Chan, Kok Gan, Parani, Madasamy, Natarajan, Purushothaman, Hauser, Michael, Allingham, R. Rand, Santiago-Turla, Cecilia, Ghosh, Arkasubhra, Gadde, Santosh Gopi Krishna, Fuchsberger, Christian, Forer, Lukas, Shoenherr, Sebastian, Sudoyo, Herawati, Lansing, J. Stephen, Friedlaender, Jonathan, Koki, George, Cox, Murray P., Hammer, Michael, Karafet, Tatiana, Ang, Khai C., Mehdi, Syed Q., Radha, Venkatesan, Mohan, Viswanathan, Majumder, Partha P., Seshagiri, Sekar, Seo, Jeong-Sun, Schuster, Stephan, Peterson, Andrew S.
Format:	Journal Article
Language:	English
Published:	United States Elsevier Inc 05-12-2019 Elsevier
Subjects:	African Continental Ancestry Group - genetics Animals archaic humans Denisovan Fossils Gene Pool Genetics, Population Genome, Human GenomeAsia project ghost admixture Hominidae - genetics Humans Neanderthal Neanderthals - genetics Neanderthal ghost admixture archaic humans Denisovan GenomeAsia project
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Summary:	Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0002-9297 1537-6605
DOI:	10.1016/j.ajhg.2019.11.005