Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture

João C Teixeira; Guy S Jacobs; Chris Stringer; Jonathan Tuke; Georgi Hudjashov; Gludhug A Purnomo; Herawati Sudoyo; Murray P Cox; Raymond Tobler; Chris S M Turney; Alan Cooper; Kristofer M Helgen

doi:10.1038/s41559-021-01408-0

Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture

Nat Ecol Evol. 2021 May;5(5):616-624. doi: 10.1038/s41559-021-01408-0. Epub 2021 Mar 22.

Authors

João C Teixeira^{1

2}, Guy S Jacobs^{3

4}, Chris Stringer⁵, Jonathan Tuke⁶, Georgi Hudjashov⁷, Gludhug A Purnomo^{8

9}, Herawati Sudoyo^{9

10

11}, Murray P Cox⁷, Raymond Tobler^#^{8

12}, Chris S M Turney^#^{13

14}, Alan Cooper^#^{15

16}, Kristofer M Helgen^#^{14

17}

Affiliations

¹ Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia. joao.teixeira@adelaide.edu.au.
² ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), The University of Adelaide, Adelaide, South Australia, Australia. joao.teixeira@adelaide.edu.au.
³ Complexity Institute, Nanyang Technological University, Singapore, Singapore.
⁴ Department of Archaeology, University of Cambridge, Cambridge, UK.
⁵ Centre for Human Evolution Research, Department of Earth Sciences, Natural History Museum, London, UK.
⁶ School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
⁷ Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
⁸ Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
⁹ Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
¹⁰ Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.
¹¹ Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.
¹² ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), The University of Adelaide, Adelaide, South Australia, Australia.
¹³ Chronos 14Carbon-Cycle Facility, Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
¹⁴ ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of New South Wales, Sydney, New South Wales, Australia.
¹⁵ South Australian Museum, Adelaide, South Australia, Australia.
¹⁶ BlueSky Genetics, Ashton, South Australia, Australia.
¹⁷ Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.

^# Contributed equally.

PMID: 33753899
DOI: 10.1038/s41559-021-01408-0

Abstract

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.

Publication types

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

MeSH terms

Animals
Asia, Southeastern
Fossils
Hominidae* / genetics
Humans
Islands
Neanderthals*