Episodes of diversification and isolation in Island Southeast Asian and Near Oceanian male lineages

Karmin, Monika, Flores, Rodrigo, Saag, Lauri, Hudjashov, Georgi, Brucato, Nicolas, Crenna-Darusallam, Chelzie, Larena, Maximilian, Endicott, Phillip L., Jakobsson, Mattias, Lansing, J. Stephen, Sudoyo, Herawati, Leavesley, Matthew, Metspalu, Mait, Ricaut, François-xavier, and Cox, Murray P. (2022) Episodes of diversification and isolation in Island Southeast Asian and Near Oceanian male lineages. Molecular Biology and Evolution, 39 (3). msac045.

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Island Southeast Asia and Oceania host one of the world’s richest assemblages of human phenotypic, linguistic and cultural diversity. Despite this, the region’s male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this dataset allows us to fully resolve and date the regional Y chromosome phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region’s initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40-25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in Island Southeast Asia, New Guinea and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the Last Glacial Maximum. This improved Y chromosome topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and Island Southeast Asia, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the Y chromosome presented here thus enables a detailed exploration of past isolation, interaction and change in one of the world’s least understood regions.

Item ID: 72756
Item Type: Article (Research - C1)
ISSN: 1537-1719
Keywords: Y chromosome, human population genetics, Island Southeast Asia, phylogeography, migration
Copyright Information: © The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Date Deposited: 29 Mar 2022 00:11
FoR Codes: 45 INDIGENOUS STUDIES > 4513 Pacific Peoples culture, language and history > 451301 Archaeology of New Guinea and Pacific Islands (excl. New Zealand) @ 30%
43 HISTORY, HERITAGE AND ARCHAEOLOGY > 4301 Archaeology > 430101 Archaeological science @ 70%
SEO Codes: 13 CULTURE AND SOCIETY > 1307 Understanding past societies > 130703 Understanding Australia’s past @ 50%
13 CULTURE AND SOCIETY > 1307 Understanding past societies > 130799 Understanding past societies not elsewhere classified @ 50%
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