Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages

Abstract Island Southeast Asia (ISEA) 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 (chrY) sequenc...

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Bibliographic Details
Published in:	Molecular biology and evolution Vol. 39; no. 3
Main Authors:	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, Cox, Murray P
Format:	Journal Article
Language:	English
Published:	United States Oxford University Press 02-03-2022 Oxford University Press (OUP)
Subjects:	Asia, Southeastern Asian People Biological anthropology Discoveries DNA, Mitochondrial - genetics Genetics Human genetics human population genetics Humanities and Social Sciences Humans Island Southeast Asia Life Sciences Male migration Mitochondria - genetics Mitochondrial DNA Multiculturalism Phylogeny phylogeography Population genetics Populations and Evolution Y chromosome Asia, Southeastern Southeast Asia Papua New Guinea Pacific Islands Philippines Taiwan East Asia France Australia Indonesia Oceania migration human population genetics Island Southeast Asia Y chromosome phylogeography
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Summary:	Abstract Island Southeast Asia (ISEA) 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 (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY 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 ISEA, 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 chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, 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 chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world’s least understood regions.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0737-4038 1537-1719 1537-1719
DOI:	10.1093/molbev/msac045