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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. 
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The human colonization of Australia and Near Melanesia

Continuing with the joint series of articles on the expansion of Homo sapiens, David Sánchez published last week an interesting piece[es] on the original colonization of Australia and Papua at Noticias de Prehistoria – Prehistoria al Día, which I’ll try to synthesize here.

Earliest evidences of human occupation of Australia and Near Melanesia (all before 30 Ka BP)

Maybe the most interesting detail is that Lake Mungo 3 has dates that clearly establish a colonization of the continent at least 60,000 years ago:

81.000 +- 21.000 U (Uranium series)
62.000 +- 6.000 ESR/U (Electron spin resonance/Uranium)
61.000 +- 2.000 OSL (Optical Stimulated luminiscence)
40.000 +- 2.000 OSL (Optical Stimulated luminiscence)

The sites of Nauwalbila I and Malakunanja II have provided similar dates: 60-50 Ka BP (OSL) and 61,000 BP +9,000/-13,000 (TL) respectively. So we can safely discard the conservative approach that only allowed for at most 50 Ka as earliest colonization boundary for the Oceanian continental landmass. 
The depiction of a Genyornis, giant duck-like bird extinct before 40 Ka, in Australian rock art ago also supports a very early date for the settlement of Australia. In Highland Papua human presence is also confirmed to at least 49 Ka ago, as I reported in 2010.
Naturally the settlers must have arrived by sea, the most commonly accepted candidate for such a vessel is a humble raft still used by some Papuan populations and which has parallels in Southern Asia (also still in use in some places):

Such a journey was attempted with a similar but larger raft, equipped with a simple sail named Nale Tasih 2. This craft had no trouble in reaching the continental platform of Australia from Timor in just six days and they actually managed to reach the modern Australian coast, although they desisted of beaching by night in the middle of a storm in an area infested by the largest crocodiles on Earth, being evacuated by the coastguard instead (the barge was later recovered in perfect state).
 

Australian Burrup Peninsula’s rock art is 30,000 years old

The open air engravings have managed to survive thanks to the extremely low erosion rates produced by the hardness of the rock combined with the local climate. 

The petroglyphs have been dated using the isotope beryllium-10. Based on current evidence, the archaeologists say, the occupation of the peninsula cannot be dated to before c. 42,000 years ago. 

Source: Australian Geographic.

 
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Posted by on April 22, 2013 in Australia, Oceania, rock art, Upper Paleolithic

 

Questioning the India-Australia link and timeline

Darshi Arachige recently made me aware of a study of his authorship, which is broadly coincident with the criticisms I made to Pugach 2013:
Darshi Arachige, Do the Estimated Admixture Times Confirm the Proposed Holocene Gene Flow from India to Australia? Social Science Research Network 2013 → LINK

Abstract


This paper argues that the current estimates for the time of influx of Indian genes into some sections of Australian Aboriginal population during Holocene bear large uncertainties which make elimination of the probability of a more recent gene flow less likely. It also highlights that indications for the plausibility of a later gene flow exist and can also be placed in a likely archaeological perspective.

My own very brief synthesis of the criticisms (all very legitimate) is as follows:
  • Excessive conclusions come from subjective interpretation the PC (eigenvector) analysis. 
  • Too large, diverse dataset: Pugach et al. use an excessively broad dataset, what tends to hide important information unless you look at great depths, which they do not.
  • Confidence intervals were hugely underestimated (a way too common academic malpractice).
  • The arbitrarily wrong interpretation of the Holocene techno-cultural changes in Australia, which in no way are related to India but to SE Asia.
  • Ignoring Kumar 2009, whose estimates for the South Asia – Australia gene flow is of 60-50 Ka BP. 

Intriguingly however, Arachige mentions the Aboriginal legends about the Bajini, which he considers as possible Dravidian migrants, with all cautions. 

Conclusion


In the preceding discussion, it was shown that the possibility of a Holocene gene flow between Indian people and Australian Aboriginal people is real. However, the external evidence quoted to support the thesis of such genomic fusion around four thousand years ago is inadequate and does not enjoy the support of many experts in the field. Given the errors associated with the estimated times of a localised admixture between these populations, it is not impossible to find a more recent time for an encounter between South Indian migrants to South East Asia and Aboriginal people from northern parts of Australia. Such an encounter is far more plausible from the archaeological evidence available in the neighbouring islands. Even though it is not possible to link the Baijini gypsies with the Dravidians due to flimsiness of the available information about the former, it is a possibility worth pursuing.

 

Very skeptic on claim of Neolithic flow from India to Australia

I feel quite skeptic about the claims held by this paper but in any case it is worth mentioning.
Irina Pugach et al., Genome-wide data substantiate Holocene gene flow from India to Australia. PNAS 2013. Pay per view (6-month embargo, then freely accessible) → LINK [10.1073/pnas.1211927110 ]

Abstract

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India. 

The evidence for this claim is all derived exclusively by statistical inference on autosomal DNA. Suspiciously enough, even if the authors claim admixture levels of as much as 11% and as recent as a mere 4000 years ago, no patrilineage (Y-DNA) nor matrilineage (mtDNA) [correction: see update below] has been ever detected that could be associated with this purported migration. 
Additionally c. 4000 years ago Southern India, the alleged origin of the genetic flow, was already immersed in a flourishing agricultural economy and it looks very strange that the migrants, people who were exchanging crops with Africa for example, would not carry a single element of this new economy to the island continent. Of course this inconsistency could easily be fixed by merely arguing that the molecular clock estimates used tick too quickly, which is a general problem anyhow and therefore no real surprise.
If the hypothesized migration happened earlier, in the Epipaleolithic or Late Upper Paleolithic, then it would also be easier to explain that, with smaller populations, genetic drift could have caused the extinction of whatever Indian uniparental markers that the migrants carried with them initially. It still causes my eyebrows to rise instinctively. 
Even then, if this was the case, we should be able to identify some sort of techno-cultural elements that the migrants may have carried with them, like microlithic stone technologies or whatever. As far as I know nothing of the like exists. 
The only techno-cultural burden that the migrants might have brought with them to Australia would therefore have been the dingo, but this dog has lots of relatives in Island SE Asia, where the authors could not detect any significant Indian admixture.
So the hypothesis looks weak to me. Let’s see the evidence they present:

Above we can see the ADMIXTURE K=4 result, probably not the optimal one (which would probably produce an Australian-specific cluster (mostly but not fully masked as Papuan) and surely two different Indian ones, partly masked as European and Onge affinity) but the one the authors decided to show us as evidence for their hypothesis.
Not only this is surely not the optimal clustering level but also Australian Aborigines are comparatively undersampled, while Indian weight is overwhelming. This is a clear example of how NOT to design a scientifically useful sampling strategy for ADMIXTURE-like comparisons like this (because oversampled populations tend to overshadow the rest just by the weight of numbers). 
As it is, this graph proves nothing but rather suggests that some Indian affinity is part of Australian Aborigine ancestral or founder specificity, when compared with Papuans. This may have many explanations first of which is a mere artifact by reason of a poor sampling and depth design of the experiment. ADMIXTURE is a powerful neutral tool, just a like a test tube or the Geneva particle accelerator, but what we do with it may well not be neutral, either by reason of mischievous manipulation or mere error.
In this case I find the test very poorly designed and executed. If I have some time later in the weekend, I may try to perform an alternative test according to my humble possibilities – I promise nothing however.
A complementary test that the authors perform used Tree Mix. As I have discussed elsewhere, TreeMix often produces very strange results and I do not consider it a reliable tool at all, but for whatever is worth here it is what they got:

While the purported migrations generated by the Tree Mix algorithm appear to suggest a secondary genetic flow from India to Australia (orange arrow at C) the data on which such result is based (D) only gives the most tenuous level (green) of extra genetic affinity between Southern Indians (DRA) and Australian Aborigines (AUA). Meanwhile the highly questionable algorithm identifies Dravidians and North Chinese (CHB) as being genetically very close (blue), when they are not in fact.
So what do I get from this paper? TreeMix’ usual senseless noise and apparent mismanagement of ADMIXTURE, a powerful tool when used properly.
Less than inconclusive, I’d say. But your take of course.

Update: G Horvat (see comments) points me to Kumar 2009 (so far unchallenged at PhyloTree)  for a shared mitochondrial lineage between Australia and India, known as M42. This haplogroup has the following structure (each → indicates a coding region mutation according to PhyloTree, Kumar originally listed a few more):
    • → M42’74 
      • → M42 
        • →→→→ M42a (Australian Aborigines)
        • → M42b (India)
      • →→ M74 (South China, Vietnam, India)
This allows for a potential mtDNA backing of this purported connection, however it is a very small lineage and Kumar claimed that M42 coalesced long ago, in the context of the first colonization of Asia and Australasia by Homo sapiens:

The divergence of the Indian and Australian M42 coding-region sequences suggests an early colonization of Australia, ~60 to 50 kyBP, quite in agreement with archaeological evidences. 

Yet the relatively long stem leading to M42a does allow for a later time-frame of arrival to Australia. Neolithic anyhow looks still most unlikely to me.

Update (Jan 18): Dingo DNA:

An important element to consider here are the origins of the dingo as the Australian wild dog is known. This dog variant suffered a strong founder effect upon arrival to Australia described mainly by two variants of the haplotype A29. This lineage only links to East Asia however, having arrived almost without doubt, via Indonesia from mainland East Asia (either Indochina or China or both).

It is clearly not related to Austronesian expansion and could have arrived either within the early Neolithic of ISEA (arguably Austroasiatic in language) or even earlier. At least one of the papers I checked rather supports a pre-Neolithic introduction and certainly before the archaeologically supported age of c. 3000 years ago.

The Y-DNA of dingos also shows a strong founder effect (only two haplotypes, with overlapping but distinct distributions) and again the most obvious connections seem to be in SE Asia.

See (freely accessible):

Update (Jan 18): It is probably interesting also to mention that Australian Aborigines show no difference with Papuans in their overall amount of Denisovan ancestry. This also appears as contradictory with the idea of significant external admixture, which should have diluted at least minimally that Denisovan component (Indians have none).

Update (Apr 7): A new “working paper” has been published on this matter, sharing my critical stand towards the sloppiness of Puhach’s team but still considering plausible a Holocene gene flow from India. I have commented in a new entry.

     
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    Posted by on January 17, 2013 in Australia, autosomal DNA, India, South Asia

     

    "Megadrought" may have affected NW Australia some 5500 years ago

    Depictions of the Wondjina rain spirits
    (CC by Whinging Pom)
    Researchers have detected an apparent “megadrought” affecting at least the region of Kimberley (NW Australia), which hosts some of the most important collections of Aboriginal rock art and may have been one of the first inhabited regions of the island-continent.
    The drought may explain a change in artistic style between the Gwion (or Bradshaw) style and the Wondjina one, more modern. Memory of the drought persists in the legends from the Dream Time of the Aboriginal peoples of Australia.
    Hamish McGowan et al., Evidence of ENSO* mega-drought triggered collapse of prehistory Aboriginal society in northwest Australia. GEOPHYSICAL RESEARCH LETTERS, VOL. 39, 2012. Pay per viewLINK [doi:10.1029/2012GL053916]
    Abstract
    The Kimberley region of northwest Australia contains one of the World’s largest collections of rock art characterised by two distinct art forms; the fine featured anthropomorphic figures of the Gwion Gwion or Bradshaw paintings, and broad stroke Wandjina figures. Luminescence dating of mud wasp nests overlying Gwion Gwion paintings has confirmed an age of at least 17,000 yrs B.P. with the most recent dates for these paintings from around the mid-Holocene (5000 to 7000 yrs B.P.). Radiocarbon dating indicates that the Wandjina rock art then emerged around 3800 to 4000 yrs B.P. following a hiatus of at least 1200 yrs. Here we show that a mid-Holocene ENSO forced collapse of the Australian summer monsoon and ensuing mega-drought spanning approximately 1500 yrs was the likely catalyst of this change in rock art. The severity of the drought we believe was enhanced through positive feedbacks triggered by change in land surface condition and increased aerosol loading of the atmosphere leading to a weakening or failure of monsoon rains. This confirms that pre-historic aboriginal cultures experienced catastrophic upheaval due to rapid natural climate variability and that current abundant seasonal water supplies may fail again if significant change in ENSO occurs. 
    See also article at Past Horizons (h/t Pileta). 
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    Posted by on December 13, 2012 in Australia, climate, Epipaleolithic, rock art

     

    Australian rock art gets oldest radiocarbon dating: 28,000 years

    In relation with the previous entry, where I mentioned again, among many other things, that Australia probably hosts the oldest rock art of all Earth because of the depiction of the giant duck Genyornis, which went extinct c. 40,000 years ago, now it has been known that an Australian rock art site has produced the oldest radiocarbon date on Earth for such kind of material. 
    The site, in Arnhem Land (Northern Territory), is known as Nawarla Gabarnmang.
    The 28,000 years old site of Nawarla Gabarnmang
    Notice that radiocarbon can only be measured on charcoal or other organic materials, and therefore it has some practical limitations: only drawings in black (usually made with charcoal dust) can be measured and there are limitations of persistence of the materials, which tend to degrade because of their very organic nature. 
    That’s why radiocarbon dating of rock art can’t give many answers. Still worth mentioning in the context of the heating debate about the earliest rock art (Iberia, Australia? Neanderthal, Sapiens?) and dating methods. 
    Source and some more details (in English): Pileta (originally from an Australian PPV newspaper).
     
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    Posted by on June 18, 2012 in Australia, Eurasian colonization, rock art