Category Archives: Melanesia

Synthesis of the early colonization of Asia and Australasia by Homo sapiens (haploid genetics)

Continuing with the joint series in Spanish language with David Sánchez at his blog Noticias de Prehistoria, I have just written an article on the early expansion of Homo sapiens in Asia and Australasia after the “out of Africa” migration. 
I have in the past explored this matter on this blog and its predecessor but there has been some time since I did it the last time. Therefore it may be interesting to share a synthesis of this updated review with the readers of For what they were…
As usual the review is built upon geographic reconstructions and an overly simple “molecular clock”, in the case of mtDNA only (which is the base of the interpretation), that merely counts coding region mutations from the most recent common ancestor (the L3 node), using the latest version of PhyloTree (build 15).
The result for mtDNA are the following five maps:
Map 1: the expansion of L3 sublineages from Africa to South Asia. Molecular time: L3+0 to L3+3. 
The big M star indicates the large M star-like explosion upon arrival to South Asia.
Map 2 represents the molecular time L3+4 (=M+1). There is an evident expansion in South Asia but also into SE Asia. 
The presence of M29’Q in Papua must be taken with some caution, as always that a single lineage is involved, what has low statistical significance.
Map 3 represents the molecular time L3+5, which corresponds to the coalescence of haplogroup N, as well as many M sublineages. There is a slowing down in the number of nodes sprouting at this “time”, so I would estimate it to correspond with Toba supervolcano (c. 74 Ka BP).
Map 4 represents the molecular time L3+6, which corresponds with the coalescence of R. The rhythm of expansion recovers and the colonization of Australasia seems by now quite statistically significant.
Map 5 represents the molecular time L3+7, which shows the first indications of expansion to NE Asia and Western Eurasia (the Neanderlands), while expansion in South Asia continues very strong (this dynamism of South Asian M lineages may explain why N and R had a limited impact in the subcontinent). 
I stopped here because I did not want to stretch too much the potential of my simplified molecular clock method, surely more likely to err as we move away from the reference point (L3 node) but the tendencies outlined in map 5 clearly continue and even increase at later “moments”. 
I also made a rough age estimate of the various maps, assuming map 2 to correspond to Jwalapuram (since c. 80 Ka BP) and map 5 to the earliest Aurignacoid cultures (Emirian, since c. 55 Ka BP or maybe a bit earlier). The result is:
  1. Arrival to South Asia: c. 93-83 Ka BP
  2. First expansion: c. 85-75 Ka BP
  3. Slowing down of the expansion (Toba) and N node: c. 77-67 Ka BP
  4. Reactivation of the expansion and clear arrival to Australasia: c. 69-59 Ka BP
  5. Expansion to less hospitable areas (NE Asia, the Neanderlands): c. 61-51 Ka BP
It is in any case a rough (yet quite coherent) estimate: there is no genetic equivalent of radiocarbon or other physical methods of age calculation.
I did not even try to make any time approximation for Y-DNA, whose expansion I just split in two phases. First what could well be the overall process of expansion from Africa into Tropical Asia (roughly comparable to mtDNA maps 1, 2 and 3):

And then the later expansions, divided in two maps for clarity (they should be roughly simultaneous processes):

General expansion of macro-haplogroups C and D (Y-DNA)
General expansion of macro-haplogroup F and its major descendant MNOPS (highlighted in a lighter, fuchsia shade).

The continuous arrows in these two maps should correspond in essence to mtDNA maps 4 and 5 and even later in time. The dotted arrows merely indicate some important but late processes since at least 30 Ka BP up to the Late Neolithic.
In all maps there is some uncertainty about the exact coalescing location of each clade or node but overall they should be at least approximate. Particularly uncertain are the original locations of mtDNA N and Y-DNA C and MNOPS but should all have coalesced somewhere between Varanasi and Guangzhou, so to say. 

Hawaiian genetic study shows 2-1 Asian-Melanesian admixture in Polynesians

Queen Liliuokalani of Hawaii in her youth

Native Hawaiians still make up some 38% of the population of Hawaii but most of them have mixed ancestry nowadays. This new study may help to understand them better and also includes some interesting findings about the overall origins of Polynesians, whose Melanesian ancestry is revealed as very significant.

Sung K. Kim et al., Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047881]


The population genetic structure of Native Hawaiians has yet to be comprehensively studied, and the ancestral origins of Polynesians remain in question. In this study, we utilized high-resolution genome-wide SNP data and mitochondrial genomes of 148 and 160 Native Hawaiians, respectively, to characterize their population structure of the nuclear and mitochondrial genomes, ancestral origins, and population expansion. Native Hawaiians, who self-reported full Native Hawaiian heritage, demonstrated 78% Native Hawaiian, 11.5% European, and 7.8% Asian ancestry with 99% belonging to the B4 mitochondrial haplogroup. The estimated proportions of Native Hawaiian ancestry for those who reported mixed ancestry (i.e. 75% and 50% Native Hawaiian heritage) were found to be consistent with their self-reported heritage. A significant proportion of Melanesian ancestry (mean = 32%) was estimated in 100% self-reported Native Hawaiians in an ADMIXTURE analysis of Asian, Melanesian, and Native Hawaiian populations of K = 2, where K denotes the number of ancestral populations. This notable proportion of Melanesian admixture supports the “Slow-Boat” model of migration of ancestral Polynesian populations from East Asia to the Pacific Islands. In addition, approximately 1,300 years ago a single, strong expansion of the Native Hawaiian population was estimated. By providing important insight into the underlying population structure of Native Hawaiians, this study lays the foundation for future genetic association studies of this U.S. minority population.

In my understanding, the most interesting elements from this study are the ADMIXTURE analyses:

Figure 1. ADMIXTURE clustering of Native Hawaiians for K = 5 (A) and K = 6 (B). Figures 1A and 1B illustrate the clustering of Native Hawaiians and HGDP samples based on GWAS data.

As the general Admixture analysis was not really conclusive about the Melanesian and Asian affinities of Native Hawaiians, the authors also performed a supervised K=2 analysis:

Figure 4. Supervised ADMIXTURE results for K = 2…
This appears to show rather unmistakably that Hawaiians (and by extension surely also other Polynesians, very close in genetics and history across the Pacific Ocean) have an important amount of Melanesian genetics, consistent with the “Slow Boat” model and the relevance of Melanesian Y-DNA haplogroup C2a among all Polynesian populations.

Review of Tropical Neolithic flows

Michael Petraglia at Ancient Indian Ocean Corridors blog draws our attention to a quite interesting review on the Neolithic of the various regions surrounding the Indian Ocean, all them of rather tropical climate:
I strongly recommend full reading as I can only dedicate some space here and the study, while not really long, covers many diverse aspects of plant and animal domestication and translocation around the Indian Ocean. 
South Asia and Africa
First the authors deal with the issue of how the most important tropical crops of South Asia, which are mostly of African origin, arrived there. They conclude that the transfer took place at the very end of the Harappa (IVC) period, rather than earlier, even if it is confirmed that Harappa and the Persian Gulf (but not yet East Africa apparently) kept trading relations since much earlier. These African crops (millet and sorghum specially) were critical, as we know, in enabling the expansion of farming towards Southern India.

In return India gave Africa the zebuine species of cow, which, after hybridization, fueled the expansion of East African pastoralists into Equatorial areas.
This route between East Africa and South Asia is declared to be the precursor of the spice trade of later days:

The first hint of this spice trade comes from the findings of valued black peppercorns that were used to fragrance the nostrils of the deceased Pharaoh Ramses II (c. 1200 BC) (Plu 1985). This spice is endemic only to the wet forests of southern India (Asouti & Fuller 2008: 47), and in all likelihood was supplied by hunter-gatherer groups to coastal groups (Morrison 2002).

Tropical Asian crops
Another section deals with the transfer of diverse crops between South and SE Asia (and even as far as New Guinea).
Indian pulses migrated to the East, while a number of other crops (areca nut, sandalwood, betle leaf and maybe banana) did in the opposite direction. The origin of mangos and lemons is also discussed and seems distributed between both regions. 
Many of these flows may have been from approximately the same time as the African-Indian connection, in the late 2nd millennium BCE.
The Malagasy connection
Finally a third layer of agricultural flows appear to connect SE Asia with Africa, the most notable being the banana, but also yams, taro and chickens. 
This one seems most likely related to Austronesian (Malay) flows in westward direction, leading to the formation of the Malagasy people and the colonization of Madagascar. 
In their journey westwards, the proto-Malagasy appear to have left some maritime vocabulary in Sri Lanka, SW India and the Maldives, where they also left their outrigger technology. A variant of this one, with two outriggers, is also widespread through East Africa, from Somalia to Mozambique and, of course, Madagascar. 
The Austronesians would have spread these crops and the chicken to Africa, bringing also possibly some commensals like the rat, the mouse and the Asian shrew, as well as a weed. Some of these may however been introduced in several episodes.

Blond hair in Melanesia genetically distinct from that of Europeans calls my attention today to this paper:

Naturally blond hair is rare in humans and found almost exclusively in Europe and Oceania. Here, we identify an arginine-to-cysteine change at a highly conserved residue in tyrosinase-related protein 1 (TYRP1) as a major determinant of blond hair in Solomon Islanders. This missense mutation is predicted to affect catalytic activity of TYRP1 and causes blond hair through a recessive mode of inheritance. The mutation is at a frequency of 26% in the Solomon Islands, is absent outside of Oceania, represents a strong common genetic effect on a complex human phenotype, and highlights the importance of examining genetic associations worldwide. 

Actually natural blond hair is also found in West and Central Asia and North Africa, and red hair even in the Horn of Africa now and then. But I guess that’s what the authors mean by “Europe”, duh! It’s also found occasionally among South Asians, specially the young, and among SE Asians regardless of age.
Whatever the case with the authors ethno-geographic misconceptions, the results are still most interesting: the gene causing blond hair among Melanesians (and some relatives like Fijians) is not the same as those involved in blond hair in Europe. Mind you that it is not clear yet which are these European genes of blondism but it is clear that the Melanesian allele is not it either. 
There is also an article at New Scientist.
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Posted by on May 4, 2012 in human genetics, Melanesia, pigmentation


Extremely ancient introgression in Papuans

Neanderfollia mentions today[cat] new genetic research that has found unusual diversity in gene OAS1 among Papuans. They contend that this is caused by extremely old introgression that they estimate in more than three million years (more than the age of the genus Homo).


Recent analysis of DNA extracted from two Eurasian forms of archaic human show that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. While these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene, OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We re-sequenced a 7 kb region encompassing the OAS1 gene in 88 individuals from 6 Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5′ region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 million years, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.

This is what I have been arguing since December 2010: “denisovan” admixture in Australasian and SE Asian aborigines stems from Homo erectus (diverged from our line at least 1.8 Ma ago) or even maybe a most distant cousin (maybe H. floresiensis, argued by some to be more archaic than H. erectus in key elements like the wrist or toes). 
Yet I am a bit skeptic of the age estimate, because, unless the H. floresiensis australopithecine hypothesis could be confirmed, the date is out of bounds for Humankind proper and creates many conceptual challenges, which are admittedly hard to swallow. While the “australopithecine hobbit” hypothesis would fit this scenario, it remains hard to swallow that the two genus would still be inter-fertile just a few dozen millennia ago and then again, why would archaic admixture come from this remote relative and not the much closer H. erectus, which we know lived in East Asia until rather recently. 
Finally I am in general very skeptic of age estimates as such and their ability to be able to inform more than they confuse. Normally I find them too recent but the opposite (too ancient) can also happen, I imagine. They are in any case just estimates: educated guesses and nothing else.


Got a copy of the paper (thanks again) and I would say that these two figures are of special interest:

Fig. 2 – Median joining network of OAS 1 haplotypes

Fig. 3 Geographic distribution of the deep lineage in A) Old World populations and B)
South East Asians and Oceanians.

I find particularly notable that the haplotype has been found at very low frequencies in South Asia and nowhere else West of Wallace Line. It can be backflow but may also be indicator about the possible location of the admixture event.

Certainly nothing seems to suggests in these or other maps (1, 2) of “Denisovan” admixture that the episode could have happened in Altai or nearby areas as some readers, stubborn proponents of obsolete migration models, have insisted on. Instead all the evidence suggests that the admixture episode happened in SE or otherwise Tropical Asia, whether deep in Indonesia or more towards the mainland is debatable indeed.

See also: