Razib Khan One-stop-shopping for all of my content

June 29, 2018

Human genomics will uncover a lot of treasure in Southeast Asia

Filed under: Human Population Genetics,Negritos — Razib Khan @ 12:25 am

On this week’s podcast on “Isolated Populations” I mentioned offhand to Spencer that I believe it is a bit ridiculous to bracket a host of Southeast Asian populations as “Negritos,” as if they were an amorphous and homogeneous substratum over which the diversity of modern South and Southeast Asian agriculturalists were overlain.There was almost certainly a great deal of population structure which accrued over the Pleistocene. Another issue, which I didn’t mention, is that Southeast Asia is also very geographically expansive. Modern Indonesia alone spans the length of North America.

Of course, you could say the same for Europe, from the Urals to the Atlantic. And yet we know that European hunter-gatherers were relatively homogeneous (albeit, with some structure!) at the beginning of the Holocene. I think the difference though is that Europe was a landscape into which hunter-gatherers expanded during the Last Glacial Maximum, while Southeast Asia, like Africa, has long been a refuge for human populations even during the coldest and driest periods of the Pleistocene.

There are three major classes of “Negrito” peoples in South and Southeast Asia.  To the west, are the indigenous peoples of the Andaman Islands. These tribes probably arrived from what is today Myanmar during the Pleistocene, when sea levels were lower. In peninsular Malaysia you have groups such as the Semang. Though physically very different from their neighbors, these people speak the Aslian form of Austro-Asiatic languages. They are not linguistic isolates like the Andaman tribes.

This speaks to the reality that unlike the Andaman Islanders the Negritos of mainland Southeast Asia have long been interacting with local populations. The languages they speak reflect interactions with Austro-Asiatic rice farmers. Curiously though, the dominant people amongst whom they live no longer speak Austro-Asiatic languages. Rather, they speak Austronesian or Tai dialects. These two groups are later arrivals on the Southeast Asian scene, and both seem to have assimilated Austro-Asiatic groups culturally and genetically, except in Cambodia and Vietnam (and to a lesser extent in pockets of Thailand and Myanmar).

If you are curious about the relationship between the various modern Southeast Asian groups, then two ancient DNA papers, Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia and Ancient genomes document multiple waves of migration in Southeast Asian prehistory, should do the trick. Some of the migrations are historically or semi-historically attested. In particular, the intrusion of the Tai, the long occupation of what became Vietnam by the Chinese, and the settlement of Han officials amongst the local people, and the migrations of the ancestors of the Hmong into Laos.

Others processes are vaguer and poorly understood. It has long been clear that the Austronesian probably assimilated Austro-Asiatic rice farmers in much of maritime Southeast Asia. And yet unlike mainland Southeast Asia to my knowledge, there are no Austro-Asiatic populations in Indonesia. Additionally, it has been brought to my attention that the ~ 3,000-year-old sample from Myanmar has no clear Austro-Asiatic signature, despite the common sense suggestion that Austro-Asiatic languages must have entered India via that region (it has affinities to modern Tibeto-Burman individuals). And, importantly the Austro-Asiatic populations themselves seem to have been deeply mixed between a dominant element strongly related to the Han Chinese, and a minority component which was basal Southeast Asian, for lack of a better term. This means that the Munda populations within India have several distinct components of ancient South and Southeast Asian substratum.

Aeta family

But speaking of this substratum, probably the best paper recently focusing on these groups is from last year, Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture. In many ways, it just reinforced the results of Reich et al. 2011. All the Negrito groups are only distantly related to each other. The Negritos of the Andaman Islanders and those of peninsular Malaysia seem to be somewhat closer to each other than either is to those of the Philippines. And, the groups in the Phillippines seem to be somewhat closer to the peoples of Melanesia. To some extent, this is just geographically expected, but there are also interesting details.

The Negritos of the Philippines, in particular, those from the northern island of Luzon, have some of the highest fractions of Denisovan ancestry of any human populations outside of Melanesia. No one is clear whether the admixture is from the same event as the one that leads to the high fractions in Melanesians, or whether there were separate mixing events (not implausible). The western Negrito groups have far lower fractions of Denisovan.

Another surprising result is that the Negritos of the southern Philippines seem very distinct from those of the northern Philippines. This may be an artifact of particular admixture history, but I wouldn’t be surprised if these islands preserved a lot of diversity which has been homogenized elsewhere.

Like many people, I believe that human evolutionary genomics will have a lot to say about Africa in the next 10 years. But, outside of Africa Southeast Asia may be one of the most fertile regions in terms of exposing deep history. This was an area that was always amenable to habitation by modern-like Africans. It seems very likely now that the predominant modern human ancestry found in the Negrito substratum, and shared with all other non-Africans, is actually not the signal of the oldest modern humans to be present in Southeast Asia. Second, there seem to be many archaic human species which made their homes in Southeast Asia.

Humans arrived in Southeast Asia a long time ago. Our speciosity and census sizes were high. With more ancient DNA and better deep whole genome sequence analysis, we’ll uncover some surprising things. I guarantee.

July 21, 2011

Asian Negritos are not one population

Negrito, Philippines. Credit: Ken Ilio

In the post below I mentioned that the Malaysian and Philippine Negritos seem to be two very distinct populations. This was something I wanted to explore in more detail, so I naturally decided to poke around the Pan-Asian SNP data set. The aims are made somewhat more difficult by the fact that there are only ~56,000 markers in the data set (as opposed to ~600,000 in the HGDP and more than 1 million in the HapMap). Additionally, the intersection with other data sets is small. For example, only ~20,000 SNPs with the HGDP. With all that in mind I hazarded that something is better than nothing. Relatives and HapMap populations were removed from the data set (thanks Zack). Additionally, I beefed up the South Asian populations with the Gujaratis from the HapMap,which had an intersection of ~32,000 SNPs. After a few test runs I decided to remove the Mlabri. They always shook out very early as a separate population from many others nearby, and, their genetic distances were very high. This tribe is only numbered in the hundreds, ...

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