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 (SNP) 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.Timothy A. Jinam, et al., "Discerning the origins of the Negritos, First Sundaland Peoples: deep divergence and archaic admixture" Genome Biol Evol evx118. (July 11, 2017)
PNAS also has a new paper out on the population genetics of Madagascar but it is currently closed access.
"Human presence in Southeast Asia dates back to at least 40,000 years ago"
The presence has to be much older than that if 'Humans Were Present In Australia 65,000 Years Ago'.
"This is in contrast to the study based on whole genome sequences that suggested Australian Aboriginal/Papuan first split from European/East Asians 60 kya"
In spite of the authors' findings that date must be correct if the new paper is correct.
"It may be possible that East Asians and Negritos appear close in the phylogenetic tree as a result of a long-term admixture".
That would be my guess, because: "studies that have shown links among all the three Negrito groups are few". And the authors do mention the possibility.
"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’".
Technically only Peninsular Malaysia is part of Sundaland. If these Negritos are intimately connected genetically to Australian Aborigines and Papuans these two groups would also have been part of the First Sundaland People.
"The distribution of those blocks shows that the highest allele
sharing with Denisovans was in the Australian Aborigine, followed by Papuan and Aeta"
Which tends to indicate that the Australian Aborigines may have brought the Denisovan element to SE Asia. It subsequently became mixed with the Aeta and the people who became Papuans. The different patterns could easily be the result of drift.
It would have been interesting to see Australian Aborigines and Papuans indicated separately in the diagrams and tables.
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