Category Archives: SE Asia

Mitochondrial lineages from Myanmar

Myanmar, also known as Burma, has been one of those blind spots in the mapping of human genetics. Finally now we get to know something about the peoples of this SE Asian multiethnic state, although there are limitations because the sampling was performed among refugees in Thailand.
Monica Summerer et al., Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar. BMC Evolutionary Biology 2014. Open accessLINK [doi:10.1186/1471-2148-14-17]



Myanmar is the largest country in mainland Southeast Asia with a population of 55 million people subdivided into more than 100 ethnic groups. Ruled by changing kingdoms and dynasties and lying on the trade route between India and China, Myanmar was influenced by numerous cultures. Since its independence from British occupation, tensions between the ruling Bamar and ethnic minorities increased.


Our aim was to search for genetic footprints of Myanmar’s geographic, historic and sociocultural characteristics and to contribute to the picture of human colonization by describing and dating of new mitochondrial DNA (mtDNA) haplogroups. Therefore, we sequenced the mtDNA control region of 327 unrelated donors and the complete mitochondrial genome of 44 selected individuals according to highest quality standards.


Phylogenetic analyses of the entire mtDNA genomes uncovered eight new haplogroups and three unclassified basal M-lineages. The multi-ethnic population and the complex history of Myanmar were reflected in its mtDNA heterogeneity. Population genetic analyses of Burmese control region sequences combined with population data from neighboring countries revealed that the Myanmar haplogroup distribution showed a typical Southeast Asian pattern, but also Northeast Asian and Indian influences. The population structure of the extraordinarily diverse Bamar differed from that of the Karen people who displayed signs of genetic isolation. Migration analyses indicated a considerable genetic exchange with an overall positive migration balance from Myanmar to neighboring countries. Age estimates of the newly described haplogroups point to the existence of evolutionary windows where climatic and cultural changes gave rise to mitochondrial haplogroup diversification in Asia.

The main sampled ethnic group are the Karen, who live at the border with Thailand, but the Bamar or Burmans, the largest ethnic group, were also sampled in big numbers. 
Fig. 2.- Origin of samples and mitochondrial haplogroup distribution of Southeast Asian populations. Although most of the study participants originated from Karen State (red), a broad
sample spectrum from nearly all divisions and states of Myanmar (a) was included in this study. b shows the haplogroup distributions of populations from Myanmar and four other Southeast
Asian regions. In the white insert box the haplogroup heterogeneity of two ethnic
groups of Myanmar is illustrated. The hatched area in the map surrounding the border
between Myanmar and Thailand shows the main population area of the Karen people. The
Bamar represent the largest ethnic group (68%) in Myanmar. The size of the pie diagrams
corresponds to sample size.
The smaller samples are only detailed in the supplementary data for what I have seen, so I will not discuss them right now (maybe in an update?). 
Overall all SE Asians including the Southern Han from Hong-Kong appear similar in broad terms. Excepted Laos, this relative similitude is quite apparent in figure 3:
Fig. 3.- Multi-dimensional scaling plot of pairwise Fst-values and haplogroup distribution
of populations from Myanmar and 12 other Asian regions.
A distinct geographic pattern appeared in the multi-dimensional scaling plot (Stress = 0.086;
R2 = 0.970) of pairwise Fst-values: The Myanmar sample fitted very well within the Southeast
Asian cluster, the Central Asian populations formed a second cluster, the Korean sample
represented East Asia, the Afghanistan population was representative for South Asia
and Russia symbolized Western Eurasia. The main haplogroup distributions are displayed
as pie charts. The size of the pie diagrams corresponds to sample size. The proportion
of N-lineages (without A,B and R9’F) increases from very low percentages in Southeast
and East Asia over 50% in Central Asia to more than 75% in Afghanistan and 100% in
the sample of Russian origin. The proportion of the American founding haplogroups
A,B,C and D displayed an interesting pattern: from inexistent in Russians it increased
to more than 50% in East Asian Korea.
Looking at the particular differences in haplogroup frequencies, I’d say that the Thai are quite unremarkable, while the other populations show some peculiarities:
  • Karen: higher frequencies of R9/F, A, C and G
  • Bamar: much higher M* (and extremely diverse)
  • Laotian: higher frequencies of B and M7
  • Vietnamese: more B and N*
  • South Han (Hong-Kong): more D
It is very notable the high diversity of paragroup M* among the Bamar. The authors notice that not more than three individuals shared each different subhaplogroup, what points to a very high diversity within haplogroup M. I don’t have time right now to ponder the various lineages, some of which are newly described, but I probably will in the future, because, together with the high diversity in NE India, they have the potential of shifting the paradigm of Asian colonization by H. sapiens a bit towards the East.
The various M* and other novel haplogroups described in Myanmar is shown in fig. 4. Haplogroups M90 and M91 are new basal M sublineages, along with three other unnamed private lineages, which also appear as basal. Also M20a, M49a and G2b1a are new sublineages further downstream. Within N/R, another newly described lineage is B6a1.
The Bamar are extremely diverse not just within M*:

… the haplogroup composition of Bamar
was exceptionally diverse with 80 different haplogroups and a maximum of 6 samples
in the same haplogroup (Figure 4).

On the other hand, the Karen show the signs of genetic isolation instead, with large concentrations in the same haplogroups.
Interestingly, the authors think that rather than being a receiver, Myanmar was a major source of population to its neighbors:

Migration analyses of Myanmar and four Southeast Asian regions displayed a vivid exchange
of genetic material between the countries and demonstrated a strong outwards migration
of Myanmar to all analyzed neighboring regions (for details see Additional file 4: Table S4).

This influence is most intense to Laos, Thailand and South China, while things are more balanced regarding Vietnam instead.

Sago trees were important in Neolithic Guangxi

What did SE Asians eat before the spread of rice farming?
Xiaoyan Yang et al., Sago-Type Palms Were an Important Plant Food Prior to Rice in Southern Subtropical China. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0063148]

Poor preservation of plant macroremains in the acid soils of southern subtropical China has hampered understanding of prehistoric diets in the region and of the spread of domesticated rice southwards from the Yangtze River region. According to records in ancient books and archaeological discoveries from historical sites, it is presumed that roots and tubers were the staple plant foods in this region before rice agriculture was widely practiced. But no direct evidences provided to test the hypothesis. Here we present evidence from starch and phytolith analyses of samples obtained during systematic excavations at the site of Xincun on the southern coast of China, demonstrating that during 3,350–2,470 aBC humans exploited sago palms, bananas, freshwater roots and tubers, fern roots, acorns, Job’s-tears as well as wild rice. A dominance of starches and phytoliths from palms suggest that the sago-type palms were an important plant food prior to the rice in south subtropical China. We also believe that because of their reliance on a wide range of starch-rich plant foods, the transition towards labour intensive rice agriculture was a slow process.

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Posted by on June 8, 2013 in China, Neolithic, SE Asia


Another SE Asian genetic adaption to Malaria

Malaria has been one of the greatest challenges to human survival in the tropics and subtropical areas, which make up the bulk of our early distribution as species. In response we have developed a number of genetic-biological strategies of which the best known is the allele that causes the sickle cell disease in homozygotes but protects heterozygotes against the deadly infection in a clear example of balancing selection. This is not however the only adaption against malaria.
A new study explores a SE Asian (including Southern Chinese) adaption that also seems to be a way to fight against the disease, which is a variant of Alpha-Thalassemia:
Qin-Wei Qiu et al., Evidence of recent natural selection on the Southeast Asian deletion (–SEA) causing alpha-thalassemia in South China. BMC Evolutionary Biology 2013. Open access → LINK [doi:10.1186/1471-2148-13-63]

Abstract (provisional)


The Southeast Asian deletion (–SEA) is the most commonly observed mutation among diverse alpha-thalassemia alleles in Southeast Asia and South China. It is generally argued that mutation –SEA, like other variants causing hemoglobin disorders, is associated with protection against malaria that is endemic in these regions. However, little evidence has been provided to support this claim.


We first examined the genetic imprint of recent positive selection on the –SEA allele and flanking sequences in the human alpha-globin cluster, covering a genomic region spanning ~410 kb, by genotyping 28 SNPs in a Chinese population consisting of 76 –SEA heterozygotes and 138 normal individuals. The pattern of linkage disequilibrium (LD) and the long-range haplotype test revealed a signature of positive selection. The network of inferred haplotypes suggested a single origin of the –SEA allele.


Thus, our data support the hypothesis that the –SEA allele has been subjected to recent balancing selection, triggered by malaria.
See also:

The genetic and phenotype complexity of the Oceanic language area

In this entry, rather than discussing Polynesians alone, which seem to be just the tip of the Eastern Austronesian iceberg, I’ll try to understand here the complexity of speakers of Oceanic languages, the main native language family of Island Oceania. 
Oceanic is a branch of Austronesian but for the purposes of this entry we will only mention other Austronesian peoples/languages tangentially. The focus is Oceanic because we can’t understand the parts without the whole here most probably. 


Oceanic languages are scattered as follows:

  Admiralties and Yapese
  St Matthias
  Western Oceanic and Meso-Melanesian (two distinct sub-families)
  Southeast Solomons
  Southern Oceanic
Black enclosed zones are pockets of languages from other families.
(CC by kwami)

It is certainly interesting that Micronesian and Fijian-Polynesian seem to be particularly related among them. Instead the Western Oceanic and Admiralty subfamilies (both from the islands near Papua) seem to have separated early on or diverged farther for whatever other reasons (stronger substrate influence for example).


Lapita pot from Tonga (source)
As I cited recently, Polynesians seem to have spread from Society Islands in the 1190-1290 CE window. The genesis of the Micronesian family is not well understood… but the overall genesis of Oceanic languages seems to be at the Lapita culture, which spread through Island Melanesia (excluding Papua) and some nearby islands (notably Tonga and Samoa also Marquesas c. 300 CE(ref)).
Early Lapita culture is dated to c. 1350-750 BCE, while a Late phase is dated to c. 250 BCE, spreading to the Solomon Islands, which show no indications of the earlier period (Ricaut 2010, fig. 2).
So a simplified chronology for Oceanic expansion would be
  1. Lapita culture from near Melanesia to Vanuatu and Kanaky (New Caledonia), then to:
    1. Fiji, Samoa and Tonga since c. 900 BCE
    2. Solomon Is. c. 250 BCE
  2. Arrival to Society Islands (Tahiti, etc.) c. 300-800 CE from maybe Samoa.
  3. Main Polynesian expansion to the farthest islands (Hawaii, Rapa Nui, Aotearoa-NZ) c. 1200 CE from Society Is.

Phenotype (‘race’)

A classical and unavoidable element in the ethnographic division of the region is phenotype, appearance (i.e. ‘race’). Since the first European arrival to the area the division between black Melanesians and white Polynesians (very relative as we will see now) has been part of all our conceptualizations of the region. 
Conscious of that and wanting to get a better impression I collected from the Internet what I estimate may be representative faces from the Oceanic linguistic zone and nearby areas (other Austronesians and Melanesians) and put them on a map:

Click to expand

A relatively homogeneous Polynesian phenotype can be identified and one can imagine that it stems from the area of Samoa-Tonga, considering the previous prehistorical review. But otherwise the diversity, gradations and abundance of local uniqueness seems quite impressive.
Based on other cases, one would imagine also that phenotype differences would be coincidental with genetic ones. However this is not too easy to discern, partly because Polynesians have strong founder effects that blur the matter, partly because there is no obvious strict dividing line between the various phenotypes and partly because of the insistence of some in considering Lapita as a Polynesian phenomenon, when it is obviously an Oceanic one, including and emphasizing the Melanesian side of the diverse Oceanic landscape, of which the Polynesian-Micronesian branch is just one element (famous and extended but not the core). 
The main Y-DNA lineage among Polynesians is C2a1 (P33), not found outside Polynesia senso stricto but reaching there frequencies of 63-90% (excepted Tonga where it’s only 33%). This is a clear founder effect in this population.

C subclades in SE Asia and Oceania
(from Karafet 2010, annotated with ISOGG nomenclature)
C2a1 is clearly derived from a Melanesian superset C2a (M208) still found as C2a(xC2a1) at low frequencies in Samoa (8%) and Tahiti (4%) but also in Vanuatu (2%) and coastal Papua (13%). C2a establishes a probably genetic link of Polynesians with Lapita culture and Melanesian peoples in general.
An earlier pylogenetic stage is C2 (M38), which is probably in the region since the very first colonization process some 50 thousand years ago (or maybe even earlier). C2(xC2a) is most common in Wallacea (East Indonesia, East Timor), where it reaches maybe figures of 33% on average. It is however also found in highland Papua (13%) and Vanuatu (20%) but as it is most doubtful that C2a evolved as recently as Lapita times, we should really focus on C2a as such rather than the wider C2, which only seems to confuse the matter.
The lack of C2(xC2a) in most of the Oceanic languages’ area clearly indicates that the expansion (and subsequent founder effects) did not begin in Wallacea but in  Melanesia, at least in what regards to C sublineages.
The other major Polynesian haplogroup is O3a2 (P201), which would seem to have originated in Philippines and maybe arrived there via Micronesia:

O3 subclades in SE Asia and Oceania
(from Karafet 2010, annotated with ISOGG nomenclature)

Melanesian populations also sport some lineages that are not common among other Oceanic-speaker peoples, notably K, M and S. However they are irregularly shared with Wallacea (Eastern Indonesia, East Timor). Like C2 these lineages coalesced in the region soon after colonization by Homo sapiens.
In the motherly side of things genetic, the absolutely dominant mtDNA lineage among Polynesians (the so-called Polynesian motif) is B4a1a1, which ultimately stems from East or rather SE Asia. However it probably arrived to the region (again) via Melanesia, albeit maybe somewhat tangentially.

From Friedlander 2007 (fig. 4)

Spatial frequency distribution of haplogroup B4a* and B4a1a1 in Island Southeast Asia and the western Pacific, created using the Kriging algorithm of the Surfer package of haplogroups. Figure 4b presents the detailed distribution for Northern Island Melanesia. Data details are provided in table S3.

The matrilineal Polynesian motif does offer a possible pattern of settlement, maybe related specifically to Late Lapita, that could allow us to understand the possible origin of the phenotype differences between Melanesians and Polynesians, as could do the Y-DNA lineage O3a2. However there are lots of remnants of quite strictly Melanesian Early Lapita, as is evident by the (Y-DNA) C2a lineages retained so strongly among Polynesians within their own founder effects, whose importance we cannot afford to dismiss.

Other mtDNA lineages like Q1 or M27 are of relevance in Melanesian populations. Q1 did make its way into some Polynesian populations but as minority lineage only.

Update (Oct 31):

Terry in the comments sections grunts a lot but now and then provides useful complementary data, for example this Y-DNA map of the region from Kayser 2006:

Kayser 2006 – fig. 1
Frequency distribution of (A, B) NRY and (C, D) mtDNA haplogroups found in Polynesia with a genetic origin in (A, C) Asia or (B, D) Melanesia.

As is apparent since Kayser’s publication (if not before), the Melanesian patrilineages are much more common (actually dominant) among Polynesians than the matrilineages from the same origin, what is attributable to a founder effect related to the Lapita culture.
Another interesting reference is this Y-DNA map of Papua (New Guinea) and some nearby islands (from Mona 2007):

Mona 2007 FIG. 2.—Y-chromosome haplogroups and their frequencies in populations from the Bird’s Head region and elsewhere in New Guinea. Data from other populations of New Guinea were used from previous studies (Kayser et al. 2003, 2006). Size of the pie charts is according to sample size of the groups. Abbreviations are as in supplementary table S1, Supplementary Material online.

Both maps and/or the data in the relevant papers provide key information on possible origins for the C2a-M208 patrilineal founder effect, so important in general in the Oceanic peoples and specially the Polynesian branch. The exact origin cannot be pinpointed without further research (or maybe not at all) but it’s clear that C2a-M208 only exists from Papua (New Guinea) to the East, so it must have a Melanesian origin be it Papuan or from the nearby islands.


  • François-Xavier Ricaut et al., Ancient Solomon Islands mtDNA: assessing Holocene settlement and the impact of European contact. Journal of Archaeological Science, 2010 ··> LINK (PDF).
  • Jonathan S. Friedlaender et al., Melanesian mtDNA Complexity. PLoS ONE, 2007 ··> LINK (open access).
  • Tatiana Karafet et al., Major East-West Division Underlies Y Chromosome Stratification Across Indonesia. MBE 2010 ··> LINK (free access).
  • Michael Knapp et al., Complete mitochondrial DNA genome sequences from the first New Zealanders. PNAS 2012 ··> LINK (open access).
  • Manfred Kayser et al., Melanesian and Asian Origins of Polynesians: mtDNA and Y Chromosome Gradients Across the Pacific. MBE 2006 ··> LINK (free access).
  • Stephano Mona et al., Patterns of Y-Chromosome Diversity Intersect with the Trans-New Guinea Hypothesis. MBE 2007 ··> LINK (free access).

Note: updates after first posted version in maroon color.


IL-4 genetic combo protects Indian hunter-gatherers from Malaria

Or, more precisely, protects many of those who have it in diverse populations but it is most concentrated among hunter-gatherers of the so-called Ancestral Tribal Populations (ATP).
Aditya Nath Jha et al., IL-4 Haplotype -590T, -34T and Intron-3 VNTR R2 Is Associated with Reduced Malaria Risk among Ancestral Indian Tribal Populations. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0048136]



Interleukin 4 (IL-4) is an anti-inflammatory cytokine, which regulates balance between TH1 and TH2 immune response, immunoglobulin class switching and humoral immunity. Polymorphisms in this gene have been reported to affect the risk of infectious and autoimmune diseases.


We have analyzed three regulatory IL-4 polymorphisms; -590C>T, -34C>T and 70 bp intron-3 VNTR, in 4216 individuals; including: (1) 430 ethnically matched case-control groups (173 severe malaria, 101 mild malaria and 156 asymptomatic); (2) 3452 individuals from 76 linguistically and geographically distinct endogamous populations of India, and (3) 334 individuals with different ancestry from outside India (84 Brazilian, 104 Syrian, and 146 Vietnamese).


The 590T, 34T and intron-3 VNTR R2 alleles were found to be associated with reduced malaria risk (P<0.001 for 590C>T and 34C>T, and P = 0.003 for VNTR). These three alleles were in strong LD (r2>0.75) and the TTR2 (590T, 34T and intron-3 VNTR R2) haplotype appeared to be a susceptibility factor for malaria (P = 0.009, OR = 0.552, 95% CI = 0.356 –0.854). Allele and genotype frequencies differ significantly between caste, nomadic, tribe and ancestral tribal populations (ATP). The distribution of protective haplotype TTR2 was found to be significant (χ23 = 182.95, p-value <0.001), which is highest in ATP (40.5%); intermediate in tribes (33%); and lowest in caste (17.8%) and nomadic (21.6%).


Our study suggests that the IL-4 polymorphisms regulate host susceptibility to malaria and disease progression. TTR2 haplotype, which gives protection against malaria, is high among ATPs. Since they inhabited in isolation and mainly practice hunter-gatherer lifestyles and exposed to various parasites, IL-4 TTR2 haplotype might be under positive selection.

The protection is not absolute but it holds very strong statistical significance for the R2-R3 heterozygous combo, as shown in fig. 1:
Figure 1. Distribution of IL-4 intron-3 VNTR polymorphism.
and B: genotype and allelic distribution between malaria case control
groups, respectively; C and D: genotype and allelic distribution among
caste, nomadic, tribe and ancestral tribe, respectively.

Combo that is most common (near-optimal distribution) among the ATPs. The correlation holds for the four linguistic families with variations being more a matter of individual ATP tribes: from 35% among the AoNaga (TB, Nagaland) to 67% among the Baiga (IE, Madhya Pradesh) or 63% among the Onge (Jarawa-Onge, Andaman Is.)
See also:


Neolithic ‘calendar’ found in Vietnam

The artifact, marked with ordered dots and strips that may well represent the lunar cycle, was found in Nguom Hau Cave (Na Hang District, Tuyên Quang province, Northern Vietnam). 

A similar artifact was discovered in 1985 not far away: Na Cooc Cave (Thái Nguyên province). 

The calendar has been estimated to be from c. 4000 years ago. 

The stone tool was found in a tomb marked with 14 large stones laid at a length of 1.6m. Bones were found under the stones but no skull was found, with Chung guessing that the skull may have decayed due to the humidity in the cave.

A number of other stone tools were buried with the corpse.

The dig also produced much other information from the Iron Age (3.0-3.5 Ka BP), Late Neolithic (4.0-4.3 Ka BP) and a deeper and very thick Early Neolithic layer consisting of many polished stone axes and other tools.
Together with other findings, the evidence mounts for inhabitation from at least 8000 years ago in this area. 

Source: Viêt Nam News (via Pileta).


Posted by on September 27, 2012 in archaeoastronomy, archaeology, East Asia, Neolithic, SE Asia, Vietnam


Beautiful polished axe from Arunachal Pradesh

From the Archaeology Network:

A prehistoric tool of Neolithic period has been found in Taksing under Upper Subansiri district, bordering China.

The Neolithic axe-head found at Taksing [Credit: Arunachal Front]
Tade Ebo, Taksing  CCR evangelist and one Talin Rigia handed over the axe-shaped Neolithic tool to research director Dr. Tage Tada on September 12, which is now on display in the Itafort Archaeological Museum here.

The tool is of rectangular in shaped and made out of diorite black stone. Both the surfaces are fully grounded and finely polished but a few sears are seen in the lateral margin of the tool. The cutting edge very sharp, convex and bifacially beveled. The shape, size and workmanship of the tool indicate that it was used as axe by the people in the Neolithic age, most probably for the purpose of agriculture and farming.

Tada informed that this was the first finding from the remote Indo-China (Tibet) border. “The possession of the tool will provide opportunity to the students of archaeology of the state for its further investigation and add definite information on the prehistoric period of the area”, he added.

The Director further said that in Arunachal Pradesh, local people believe such prehistoric tools possess certain sprits. Some believe that such object comes from sky while other believes that such tools are used by the malevolent sprit. “In Taksing the local Nah and Tagin people believe that this has fallen from sky used by malevolent sprits, thus they are very scared of touching the artifact.”

Source: Arunachal Front [September 16, 2012]


Geographical and anthropological note: Arunachal Pradesh is effectively administrated by India as state but also claimed by China (via its annexation of Tibet). For what I care it belongs to its own peoples, a diverse array of mostly Tibeto-Burman ethnicities. From an anthropological viewpoint the whole region so-called NE India (between Bangla Desh and Burma is transitional between South Asia and SE Asia.
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Posted by on September 20, 2012 in India, Neolithic, SE Asia, South Asia