Multiple Deeply Divergent Denisovan Ancestries in Papuans

Genome sequences are known for two archaic hominins—Neanderthals and Denisovans—which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and f...

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Bibliographic Details
Published in:	Cell 2019-05, Vol.177 (4), p.1010-1021.e32
Main Authors:	Jacobs, Guy S., Hudjashov, Georgi, Saag, Lauri, Kusuma, Pradiptajati, Darusallam, Chelzie C., Lawson, Daniel J., Mondal, Mayukh, Pagani, Luca, Ricaut, François-Xavier, Stoneking, Mark, Metspalu, Mait, Sudoyo, Herawati, Lansing, J. Stephen, Cox, Murray P.
Format:	Article
Language:	eng
Subjects:	Animals archaic ancestry Asian Continental Ancestry Group - genetics Biological anthropology Biological Evolution Denisovan Gene Flow Genetic Introgression - genetics Genetic Variation - genetics Genome, Human - genetics Haplotypes - genetics Hominidae - genetics Humanities and Social Sciences Humans Indonesia Island Southeast Asia Neanderthal Neanderthals - genetics New Guinea Oceania
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Summary:	Genome sequences are known for two archaic hominins—Neanderthals and Denisovans—which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time. [Display omitted] •A new dataset of 161 genomes covering the understudied Indonesia-New Guinea region•Introgressing Denisovans comprise at least three genetically divergent groups•Papuans carry haplotypes from two Denisovan groups, with one unique to Oceania•Some Denisovan introgression was recent and likely occurred in New Guinea or Wallacea Genome sequences from Island Southeast Asia suggest two independent Denisovan lineages, distinct from the Altai Denisovan, that have contributed to modern Papuan genomes, with one group potentially present east of the Wallace Line and thus capable of crossing geographical barriers.
ISSN:	0092-8674 1097-4172 1097-4172