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Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia

View ORCID ProfileJoão C. Teixeira, View ORCID ProfileGuy S. Jacobs, Chris Stringer, View ORCID ProfileJonathan Tuke, View ORCID ProfileGeorgi Hudjashov, View ORCID ProfileGludhug A. Purnomo, Herawati Sudoyo, View ORCID ProfileMurray P. Cox, View ORCID ProfileRay Tobler, View ORCID ProfileChris S.M. Turney, Alan Cooper, View ORCID ProfileKristofer M. Helgen
doi: https://doi.org/10.1101/2020.07.24.219048
João C. Teixeira
1Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, SA 5005, Australia
2ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), The University of Adelaide, SA 5005, Australia
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  • For correspondence: joao.teixeira@adelaide.edu.au
Guy S. Jacobs
3Complexity Institute, Nanyang Technological University, Singapore 637723, Singapore
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Chris Stringer
4Centre for Human Evolution Research, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
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Jonathan Tuke
5School of Mathematical Sciences, The University of Adelaide, SA 5005, Australia
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Georgi Hudjashov
6Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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Gludhug A. Purnomo
1Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, SA 5005, Australia
7Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
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Herawati Sudoyo
7Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
8Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta 10430, Indonesia
9Sydney Medical School, University of Sydney, NSW 2006, Australia
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Murray P. Cox
6Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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Ray Tobler
1Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, SA 5005, Australia
2ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), The University of Adelaide, SA 5005, Australia
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Chris S.M. Turney
10Chronos 14Carbon-Cycle Facility, Palaeontology, Geobiology and Earth Archives Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, NSW 2052, Australia
11ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of New South Wales, NSW 2052, Australia
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Alan Cooper
12South Australian Museum, Adelaide, SA 5000, Australia
13BlueSky Genetics, PO Box 287, SA 5137, Australia
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Kristofer M. Helgen
11ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of New South Wales, NSW 2052, Australia
14Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW 2010, Australia
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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 (AMH) arrived in the region >50,000 years ago. Contemporary human populations carry signals consistent with interbreeding events with Denisovans in ISEA – a species that is thought to be more closely related to AMH than the super-archaic endemic ISEA hominins. To query this disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes. Our results corroborate widespread Denisovan ancestry in ISEA populations but fail to detect any super-archaic admixture signals. By highlighting local megafaunal survival east of the Wallace Line as a potential signature of deep, pre-H. sapiens hominin-faunal interaction, we propose that this understudied region may hold the key to unlocking significant chapters in Denisovan prehistory.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 24, 2020.
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Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia
João C. Teixeira, Guy S. Jacobs, Chris Stringer, Jonathan Tuke, Georgi Hudjashov, Gludhug A. Purnomo, Herawati Sudoyo, Murray P. Cox, Ray Tobler, Chris S.M. Turney, Alan Cooper, Kristofer M. Helgen
bioRxiv 2020.07.24.219048; doi: https://doi.org/10.1101/2020.07.24.219048
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Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia
João C. Teixeira, Guy S. Jacobs, Chris Stringer, Jonathan Tuke, Georgi Hudjashov, Gludhug A. Purnomo, Herawati Sudoyo, Murray P. Cox, Ray Tobler, Chris S.M. Turney, Alan Cooper, Kristofer M. Helgen
bioRxiv 2020.07.24.219048; doi: https://doi.org/10.1101/2020.07.24.219048

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