Oral Presentation 40th Annual Lorne Genome Conference 2019

Multiple deeply divergent Denisovan ancestries in Papuans (#40)

Guy S Jacobs 1 , Georgi Hudjashov 2 3 , Lauri Saag 3 , Pradiptajati Kusuma 1 4 , Chelzie C Darusallam 4 , Daniel J Lawson 5 , Mayukh Mondal 3 , Luca Pagani 3 6 , François-Xavier Ricaut 7 , Mark Stoneking 8 , Mait Metspalu 3 , Herawati Sudoyo 4 9 10 , J. Stephen Lansing 1 11 12 , Murray P Cox 2
  1. Complexity Institute, Nanyang Technological University, Singapore 637723, Singapore
  2. Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
  3. Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
  4. Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
  5. Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS8 2BN, United Kingdom
  6. APE Lab, Department of Biology, University of Padova, Padova 35131, Italy
  7. CNRS, Université de Toulouse (Paul Sabatier), Toulouse 31073, France
  8. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
  9. Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta 10430, Indonesia
  10. Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
  11. Santa Fe Institute, Santa Fe, NM 87501, United States of America
  12. Stockholm Resilience Center, Kräftriket, 10405 Stockholm, Sweden

Genome sequences are known for two archaic hominins – Neanderthals and Denisovans – which interbred with anatomically modern humans as they dispersed out of Africa. By excavating archaic haplotypes from 161 new genomes spanning 14 island groups in Island Southeast Asia and Papua, we find large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from at least two deeply divergent Denisovan lineages, separated by over 350 thousand years. Geographical structure in these lineages implies introgression from Denisovans that must have lived east of the Wallace line and suggests considerable complexity in archaic contact among Papuan groups. A third Denisovan lineage occurs in modern Siberians, Native Americans and East Asians. This regional mosaic suggests that modern humans interbred with multiple Denisovan populations, which were geographically isolated from each other over deep evolutionary time.