.2021 May;5(5):616-624.

doi: 10.1038/s41559-021-01408-0. Epub 2021 Mar 22.

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

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

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

João C Teixeira et al. Nat Ecol Evol.2021 May.

.2021 May;5(5):616-624.

doi: 10.1038/s41559-021-01408-0. Epub 2021 Mar 22.

Authors

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.

PubMed Disclaimer

Cited by

Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects.
Taufik L, Teixeira JC, Llamas B, Sudoyo H, Tobler R, Purnomo GA.Taufik L, et al.Genes (Basel). 2022 Dec 16;13(12):2373. doi: 10.3390/genes13122373.Genes (Basel). 2022.PMID:36553640Free PMC article.Review.
Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture.
Ahlquist KD, Bañuelos MM, Funk A, Lai J, Rong S, Villanea FA, Witt KE.Ahlquist KD, et al.Genome Biol Evol. 2021 Jul 6;13(7):evab115. doi: 10.1093/gbe/evab115.Genome Biol Evol. 2021.PMID:34028527Free PMC article.Review.
Fossils, fish and tropical forests: prehistoric human adaptations on the island frontiers of Oceania.
Roberts P, Douka K, Tromp M, Bedford S, Hawkins S, Bouffandeau L, Ilgner J, Lucas M, Marzo S, Hamilton R, Ambrose W, Bulbeck D, Luu S, Shing R, Gosden C, Summerhayes G, Spriggs M.Roberts P, et al.Philos Trans R Soc Lond B Biol Sci. 2022 Apr 25;377(1849):20200495. doi: 10.1098/rstb.2020.0495. Epub 2022 Mar 7.Philos Trans R Soc Lond B Biol Sci. 2022.PMID:35249390Free PMC article.
Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact.
Purnomo GA, Mitchell KJ, O'Connor S, Kealy S, Taufik L, Schiller S, Rohrlach A, Cooper A, Llamas B, Sudoyo H, Teixeira JC, Tobler R.Purnomo GA, et al.Genes (Basel). 2021 Jun 24;12(7):965. doi: 10.3390/genes12070965.Genes (Basel). 2021.PMID:34202821Free PMC article.
Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations.
Koller D, Wendt FR, Pathak GA, De Lillo A, De Angelis F, Cabrera-Mendoza B, Tucci S, Polimanti R.Koller D, et al.BMC Biol. 2022 Nov 7;20(1):249. doi: 10.1186/s12915-022-01449-2.BMC Biol. 2022.PMID:36344982Free PMC article.

See all "Cited by" articles

References

1. Kaifu, Y. Archaic hominin populations in Asia before the arrival of modern humans: their phylogeny and implications for the ‘southern Denisovans’. Curr. Anthropol. 58, S418–S433 (2017). - DOI
1. Morwood, M. J., O’Sullivan, P., Susanto, E. E. & Aziz, F. Revised age for Mojokerto 1, an early Homo erectus cranium from east Java, Indonesia. Aust. Archaeol. 57, 1–4 (2003). - DOI
1. Rizal, Y. et al. Last appearance of Homo erectus at Ngandong, Java, 117,000–108,000 years ago. Nature 577, 381–385 (2020). - PubMed - DOI
1. Matsu’ura, S. et al. Age control of the first appearance datum for Javanese in the Sangiran area. Science 367, 210–214 (2020). - PubMed - DOI
1. Westaway, K. E. et al. An early modern human presence in Sumatra 73,000–63,000 years ago. Nature 548, 322–325 (2017). - PubMed - DOI

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions

Related information

MedGen

LinkOut - more resources

Full Text Sources
- Nature Publishing Group
Other Literature Sources
- scite Smart Citations

Movatterモバイル変換

Account

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Full text links

Actions

Share

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

Affiliations

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

Authors

Affiliations

Abstract

Similar articles

Cited by

References

Publication types

MeSH terms

Related information

LinkOut - more resources

Full Text Sources

Other Literature Sources