Tag: Southeast Asia

Where the oldest of the old are no more, and are

By Razib Khan | July 20, 2013 7:35 pm

Malaysian “Negritos,” presumably the indigenous people of the Malay peninsula

A few days ago Dienekes pointed to a paper which reports on the presence of anatomically modern humans in China 80-100,000 years before the present. I say “anatomically modern” because there is a presumable distinction between populations which resemble moderns in their gross morphology, which first emerged in southern and eastern Africa 100 to 200 thousand years ago (and were dominant all across the world after 40,000 years before the present), and “behaviorally modern” societies, which exhibit all the hallmarks of protean symbolic cultural expression that are the hallmarks of humanity. The paper reporting on such old specimens is not particularly revolutionary. Rather, it’s part of a growing corpus which contributes to a “counter-narrative” to the dominant model, whereby behaviorally modern humans swept across Eurasia (and Australia) ~50,000 years B.P. after the “Out of Africa” event. Obviously the problem here is that if there were anatomically modern humans in China tens of thousands years before this expansion, were they replaced? Or is the chronology wrong? (e.g. the mutation rate controversy, though please note that the dominant model has many physical anthropologists who support it as well). On Twitter I pointed out to Aylwyn Scally that we do have evidence of substantial population replacement across East and Southeast Asia.

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CATEGORIZED UNDER: Genetics, Human Genetics

The Indonesian cline

By Razib Khan | March 11, 2012 2:34 pm

Dienekes has touched upon it in detail, so I don’t have much to add. Except for two points:

1) The ancestry cline here is not due to isolation-by-distance, but the expansion of the Austronesian population rather precipitously ~4,000 years ago. As Dienekes observed this was rather clear by non-genetic means; this is just icing on the cake.

2) There is evidence of an Austro-Asiatic substrate across maritime Southeast Asia. For whatever reason it seems that Austro-Asiatic speaking agriculturalists ceased their push east at the Wallace Line.

MORE ABOUT: Southeast Asia

Southeast Asian migrations, Indians and Tai

By Razib Khan | July 23, 2011 3:30 pm

If you have not read my post “To the antipode of Asia”, this might be a good time to do so if you are unfamiliar with the history, prehistory, and ethnography of mainland Southeast Asia. In this post I will focus on mainland Southeast Asia, and how it relates implicitly to India and China genetically, and what inferences we can make about demography and history. Though I will touch upon the Malay peninsula in the preliminary results, I have removed the Indonesian and Philippine samples from the data set in totality. This means that in this post I will not touch upon spread of the Austronesians.

I present before you two tentative questions:

- What was the relationship of the spread of Indic culture to Indic genes in mainland Southeast Asia before 1000 A.D.?

- What was the relationship of the spread of Tai culture to Tai genes in mainland Southeast Asia after 1000 A.D.?

The two maps above show the distribution of Austro-Asiatic and Tai languages in mainland Southeast Asia. Observe that when you join the two together in a union they cover much of the eastern 2/3 of mainland Southeast Asia. The fragmented nature of Austro-Asiatic languages in the northern region, edging into the People’s Republic of China, implies to us immediately that it is likely that in the past there was a continuous zone of Austro-Asiatic speech in this region. From the histories and mythologies of the Tai people we know that this group migrated from the southern fringes of China around ~1000 A.D. This is obvious when we note that there are still Tai people in southern China, and the expansion of the Tai across what is today Thailand is to some extent historically attested. Between 1000 and 1500 there was a wholesale ethnic reorganization of the Chao Phray river basin. Was that a matter of demographic replacement, or cultural assimilation, or some of both?

Second, what was the impact of Indians upon mainland Southeast Asia? One of the easiest ways to ascertain Indian influence is script. Burmese, Thai and Cambodian scripts all derive from Grantha, an archaic Tamil script (non-Islamic scripts in island Southeast Asia, such as Javanese and Balinese, are also derive from South Indian precursors). The Indian religious influences also are more southern than northern, manifesting in the southern forms of Shaivite Hinduism and Sri Lankan Theravada Buddhism.

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CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics, History

Asian Negritos are not one population

By Razib Khan | July 21, 2011 8:39 pm


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, and I wouldn’t be surprised if they’ve been subjected to a lot of population bottlenecks, resulting in some very distinctive allele frequencies.

But before I move to the results, let’s back up for a moment. Who are the “Negritos”? As suggested by the term Negrito refers to a range of populations which are characterized by small size and African-like features (very dark skin and frizzy hair). In general their distribution is limited to Southeast Asia (there are suggestions that a Negrito population may only recently have gone extinct in Australia’s rainforests, but that’s speculative. On a more antique scale there are records which may be interpreted to suggest the existence of Negritos in Taiwan as late as 1900, and in southern China within the past 1,000 years). So you can bracket their distribution from the Andaman Islands to the Philippines, with isolated groups in the Malay peninsula. Negritos are presumed to be the original inhabitants of Southeast Asia before the arrival of rice farmers from the north. Like the Pygmies of Africa most of the Negritos speak languages whic hare known in other populations. Those of the Philippines speak Austronesian dialects. Interestingly those of Malaysia speak an Austro-Asiatic language, and so have affinities with many groups to their north linguistically, being surrounded by Austronesian speakers. Only the Andaman Islanders have a distinctive language, which makes sense seeing as how they have been relatively isolated from mainland Asian influences.

I ran ADMIXTURE from K = 4 to K = 12. K = 8 seemed the most informative to me (at higher K’s the major dynamic is that the Philippine Negritos start fragmenting into many distinct clusters). I’ve made a few cosmetic changes. With this East and Southeast Asia heavy data set there’s almost no difference between all the various Indian groups, so I amalgamated them together. I also did the same for related populations geographically adjacent which exhibited no genetic difference (e.g., Central and East Javanese).

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Bacteria tell the tale of human intercourse

By Razib Khan | July 20, 2011 1:39 am

The Pith: the genetic relationships between bacteria in our stomach can tell us a lot about the relationships between various groups of people. Additionally, the distribution of different strains of bacteria may have significant public health implications.

The above image is from a paper which was pushed online yesterday in PLoS ONE: Evolutionary History of Helicobacter pylori Sequences Reflect Past Human Migrations in Southeast Asia. It’s a paper which caught my attention for several reasons. First, I’ve exhibited some curiosity about the history and prehistory of Southeast Asia of late. Elucidating this region’s historical dynamics may bear upon more general questions of human evolutionary and cultural process. Second, H. pylori is a fascinating organism whose connection to specific human populations is tight enough that it can shed light on past interactions of different groups. In short, just like humans H. pylori exhibits regional specificity and local history. But additionally, H. pylori is also subject to natural selection after introduction into a new population, and so can serve as a window upon cultural contacts which might otherwise leave a light demographic footprint. In other words, the spread of H. pylori across human populations may be compared to the spread of Buddhism. This religion came to China and Japan with some Buddhists of South and Central Asian origin, but by and large its spread was memetic rather than through natural increase of a Buddhist population.

First, let’s hit the abstract:

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CATEGORIZED UNDER: Anthroplogy, Genetics, Medicine

To the antipode of Asia

By Razib Khan | July 18, 2011 1:57 am

Markers show populations sampled by HUGO Pan-Asian SNP Consortium


The Pith: Southeast Asia was settled by a series of distinct peoples. The pattern of settlement can be discerned in part by examination of patterns of genetic variation. It seems likely that Austro-Asiatic populations were dominant across the western half of Indonesia before the arrival of Austronesians.

About a year and a half ago I reviewed a paper in Science which did a first pass through some of the findings suggested by the HUGO Pan-Asian SNP Consortium data set, which pooled a wide range of Asian populations. You can see the locations on the map above (alas, the labels are too small to read the codes). The important issue in relation to this data set is that it has a thick coverage of Southeast Asia, which is not well represented in the HGDP. Unfortunately there are only ~50,000 markers, which is not optimal for really fine-grained intra-regional analysis in my opinion. But better than nothing, and definitely sufficient for coarser scale analysis.

A few things have changed since I first reviewed this paper. First, I pulled down a copy of the Pan-Asian SNP data set. I’m going to play with it myself soon. Second, after reading Strange Parallels, volume 1 and 2, I know a lot more about Southeast Asian history. Finally, the possibility of archaic admixture amongst Near Oceanians makes the genetics of the regions which were once Sundaland and Sahul of particular interest.

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Language, genes, & peoples of Southeast Asia

By Razib Khan | June 15, 2011 5:44 pm

As I am currently reading Victor Lieberman’s magisterial Strange Parallels: Volume 2. So I was very interested in a new paper from BMC Genetics, Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand, pointed to by Dienekes today. Here are the results and conclusions:

A large fraction of genetic variation is observed within populations (about 80% and 90 % for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2 %) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern.

The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them.

There are many occasions when it has taken a synthetic scholar to point out to me the overall structure of a constellation of facts which I was conscious of prior. So it is with Lieberman’s work. I had known that the eruption of the Thai peoples into Southeast Asia occurred with the last 1,000 years, before which the peninsula was divided between Tibeto-Burman populations to the west and Austro-Asiatic languages to the east (the latter divided between the Khmer and Vietnamese). Additionally, it is presumed that the Tibeto-Burman languages themselves displaced Austro-Asiatic in the western zone (as evident by the persistence of Mon in modern Burma). What was noted in volume 1 of Strange Parallels though is that the three geographical regions engaged with and assimilated the Thai invasions different. In the center the Thai succeeded in dominating the previous groups and imposing their identity upon the region. It is often asserted that modern Cambodia’s existence as an independent state is a function of the protection conferred upon it by the French from the expansive ambitions of the Empire of Siam. But in the east the Vietnamese state was barely impacted by the Thai folk wandering. As in China the Thai in Vietnam are marginalized “mountain tribes.” Finally, in the west, in the zone which became Burma, the Thai did not take over the cultural commanding heights. But neither were they absolutely marginalized as in the east. Rather, the Shan people became part of the of the Burmese landscape, integrated into the Theravada Buddhist culture, but also a significant secondary ethnos to the Burman majority (along with Karens, Mons, etc.).

What does this have to do with genetics? Possibly everything and nothing, and all answers in between.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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