Multiple Deeply Divergent Denisovan Ancestries in Papuans

Guy S Jacobs; Georgi Hudjashov; Lauri Saag; Pradiptajati Kusuma; Chelzie C Darusallam; Daniel J Lawson; Mayukh Mondal; Luca Pagani; François-Xavier Ricaut; Mark Stoneking; Mait Metspalu; Herawati Sudoyo; J Stephen Lansing; Murray P Cox

doi:10.1016/j.cell.2019.02.035

Multiple Deeply Divergent Denisovan Ancestries in Papuans

Cell. 2019 May 2;177(4):1010-1021.e32. doi: 10.1016/j.cell.2019.02.035. Epub 2019 Apr 11.

Authors

Affiliations

¹ Complexity Institute, Nanyang Technological University, Singapore 637723, Singapore.
² Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand; Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia. Electronic address: g.hudjashov@massey.ac.nz.
³ Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia.
⁴ Complexity Institute, Nanyang Technological University, Singapore 637723, Singapore; Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia.
⁵ Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia.
⁶ Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS8 2BN, UK.
⁷ Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia; APE Lab, Department of Biology, University of Padova, Padova 35131, Italy.
⁸ Department of Evolution and Biological Diversity (UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 31062 Toulouse, France.
⁹ Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
¹⁰ Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia; Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta 10430, Indonesia; Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia.
¹¹ Asian School of the Environment, Nanyang Technological University, Singapore 637723, Singapore; Santa Fe Institute, Santa Fe, NM 87501, USA; Stockholm Resilience Center, Kräftriket, 10405 Stockholm, Sweden.
¹² Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand. Electronic address: m.p.cox@massey.ac.nz.

PMID: 30981557
DOI: 10.1016/j.cell.2019.02.035

Abstract

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.

Keywords: Denisovan; Indonesia; Island Southeast Asia; Neanderthal; New Guinea; archaic ancestry.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Asian People / genetics
Biological Evolution
Gene Flow
Genetic Introgression / genetics*
Genetic Variation / genetics
Genome, Human / genetics
Haplotypes / genetics*
Hominidae / genetics*
Humans
Indonesia
Neanderthals / genetics
Oceania