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Link to original content: https://pubmed.ncbi.nlm.nih.gov/28854687
Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture - PubMed Skip to main page content
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. 2017 Aug 1;9(8):2013-2022.
doi: 10.1093/gbe/evx118.

Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture

Timothy A Jinam  1 , Maude E Phipps  2 , Farhang Aghakhanian  2 , Partha P Majumder  3 , Francisco Datar  4 , Mark Stoneking  5 , Hiromi Sawai  6 , Nao Nishida  6   7 , Katsushi Tokunaga  6 , Shoji Kawamura  8 , Keiichi Omoto  9 , Naruya Saitou  1
Affiliations

Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture

Timothy A Jinam et al. Genome Biol Evol. .

Abstract

Human presence in Southeast Asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the "First Sundaland People." To understand the relationship between these Negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the Philippine Negritos and compared them with existing data from other populations. Phylogenetic tree analyses show that Negritos are basal to other East and Southeast Asians, and that they diverged from West Eurasians at least 38,000 years ago. We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facial morphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People.

Keywords: Denisovan; Negritos; Southeast Asia; admixture; population genetics.

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Figures

<sc>Fig</sc>. 1.
Fig. 1.
—Principal component analysis plot of (A) Andamanese (Jarawa and Onge), Malaysian Negritos (Batek, Jehai, and Kintak), and Philippine Negritos (Aeta, Agta, Mamanwa, and Batak) with non-Negrito Southeast Asians; (B) Malaysian and Philippine populations. Mly-NN, Malaysian non-Negritos (Temuan and Bidayuh); Phil-NN, Philippine non-Negritos (Tagalog and Visayan; Manobo was treated separately).
<sc>Fig</sc>. 2.
Fig. 2.
—Results of ADMIXTURE assuming k = 2 to k = 7. Each vertical line represents an individual and the different colors represent various ancestry components. Negrito group labels are indicated in red text.
<sc>Fig</sc>. 3.
Fig. 3.
—(A) Neighbor-joining tree constructed from Nei’s standard genetic distance. (B) Maximum-likelihood tree generated using Treemix, assuming five geneflow events, with only three shown for clarity. Numbers in red and blue text represent average migration weights and bootstrap supports for branches out of 1,000 bootstrap replicates, respectively. Only bootstrap values >50% are shown.
<sc>Fig</sc>. 4.
Fig. 4.
—Estimation of Denisovan ancestry in Southeast Asians using the f4 ratio test. Proportion of Denisovan ancestry is represented by colored circles. Phil-NN, Philippine non-Negritos (Tagalog, Visayan, and Manobo).
<sc>Fig</sc>. 5.
Fig. 5.
—(A) Distribution of Denisovan allele-sharing in Papuan, Australian Aborigine, and Aeta (Philippine Negrito) published genome sequences, calculated in 1,000 SNP blocks and (B) Example of Denisovan allele-sharing patterns in chromosome 3 for Papuan and Aeta.
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