Extinct Hominin Admixture in South and South East Asians

[Bhapaji]

In the paper titled 'Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation' the authors show that populations from South and South East Asia harbor a small proportion of ancestry from an unknown extinct hominin, and this ancestry is absent from Europeans and East Asians.

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[okarinaofsteiner]

https://www.nature.com/articles/ng.3621- this paper is from 2016 btw. Can't see behind the paywall but I'm guessing the "Southeast Asian" populations they're referring to are the Negrito Orang Asli of Peninsular Malaysia/southernmost Thailand and the Aeta/Agta of the Philippines

Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation
Mayukh Mondal, Ferran Casals, Tina Xu, Giovanni M Dall'Olio, Marc Pybus, Mihai G Netea, David Comas, Hafid Laayouni, Qibin Li, Partha P Majumder & Jaume Bertranpetit
Nature Genetics volume 48, pages 1066–1070 (2016)
https://doi.org/10.1038/ng.3621

To shed light on the peopling of South Asia and the origins of the morphological adaptations found there, we analyzed whole-genome sequences from 10 Andamanese individuals and compared them with sequences for 60 individuals from mainland Indian populations with different ethnic histories and with publicly available data from other populations. We show that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves of migration1,2,3,4. We also show that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin, and this ancestry is absent from Europeans and East Asians. The footprints of adaptive selection in the genomes of the Andamanese show that the characteristic distinctive phenotypes of this population (including very short stature) do not reflect an ancient African origin but instead result from strong natural selection on genes related to human body size.

[Song]

^ There was an update to that study in 2018. Wonder if this includes southeast asia? 

'No evidence for unknown archaic ancestry in South Asia'
Pontus Skoglund,1,2, Swapan Mallick,1,2,3 Nick Patterson,2 and David Reich1,2,3
Published in final edited form as:Nat Genet. 2018 May
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6433599

Genomic studies have documented a contribution of archaic Neanderthals and Denisovans to non-African ancestry1,2. Recently Mondal et al.3 published a major dataset—the largest whole genome sequencing study of diverse South Asians to date—including 60 mainland groups and 10 indigenous Andamanese. They reported analyses claiming that nearly all South Asians harbor ancestry from an unknown archaic human population that is neither Neanderthal nor Denisovan. However, the statistics cited in support of this conclusion do not replicate in other data sets, and in fact contradict the conclusion.

[Song]

Another study.

This claims introgression in Southeast Asians, East Asians, South Asians and Oceania based on bayesian computation. 

Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania'
Mayukh Mondal,1 Jaume Bertranpetit,corresponding author2 and Oscar Laocorresponding author3,4 online 2019 Jan 16
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335398/

Introgression of Neanderthals and Denisovans left genomic signals in anatomically modern human after Out-of-Africa event. Here, the authors identify a third archaic introgression common to all Asian and Oceanian human populations by applying an approximate Bayesian computation with a Deep Learning framework.

[Song]

Another study I'm aware of.

Claims of trace introgression in southeast asians, east asians, south asians and oceanias.

Using hominin introgression to trace modern human dispersals'
João C. Teixeiraa,1 and Alan Coopera,1 2019 Jul 12

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6681743/

The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace’s Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.