April 17, 2014

mtDNA history of Oceania (Duggan et al. 2014)

AJHG doi:10.1016/j.ajhg.2014.03.014

Maternal History of Oceania from Complete mtDNA Genomes: Contrasting Ancient Diversity with Recent Homogenization Due to the Austronesian Expansion

Ana T. Duggan et al.

Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario.

Link

11 comments:

MOCKBA said...

Santa Cruz islanders are unusual linguistically too, and until recently they were thought to speak Papuan languages. Presently it's recognized that despite extreme phonetic shifts and wide-ranging vocabulary replacements, they nevertheless possess core features of Austronesian languages.
It must be said that Santa Cruz islands are not *very* remote in Remote Oceania. They are a part of Solomon Islands, although on the side of the archipelago which is the fathest from the shores of Papua.

Fionn said...

I agree with MOCKBA. Santa Cruz is only 250 miles South East of the main Solomon islands. Not very remote and therefor no much of an anomaly.

MOCKBA said...

Southern Vanuatu, considerably further to the SE, is also a notable linguistic anomaly. Until recently, linguists tended to assume that Vanuatu languages are pidgin / creolized languages which emerged from mixing of indigenous (and presently extinct) Papuan languages and later Austronesian settlers (reviewed e.g. by Donohue 2008). But the increasing body of archaeological data makes the contemporary researches conclude that there was no habitation of Remote Oceania before the Lapita culture. And Lapita pottery technology is supposed to be linguistically Austronesian.

Which brings forward a familiar paradigm: did technologies expand with peoples, or did peoples adopt technologies? Donohue hypothesizes that the earliest Lapita peoples may have been of Papuan or mixed stock. More recently, Pawley makes a different suggestion, that the early radiating Lapita settlers may have been predominantly Austronesian but that their boats also included varying, and substantial, numbers of Papuan wives and/or slaves.

BTW did the AJHG mtDNA paper sample Vanuatus? Especially in the South where the languages are the most Papuan-infuenced?

terryt said...

"It must be said that Santa Cruz islands are not *very* remote in Remote Oceania".

Remote enough to be culturally connected more to Vanuatu rather than to the Solomons. Distances of 250 miles seem to have been too great for boating technology available before the Austronesian expansion. It is interesting that 'simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario'. It has long been assumed they were settled early in the Austronesian expansion but largely bypassed from then on. Unfortunately I can't access the article.

terryt said...

"Until recently, linguists tended to assume that Vanuatu languages are pidgin / creolized languages which emerged from mixing of indigenous (and presently extinct) Papuan languages and later Austronesian settlers (reviewed e.g. by Donohue 2008)".

Thanks for the link. I hadn't seen it before. What I found most interesting in the paper is the apparently pivotal roloe of mainland northern New Guinea in the expansion. Until now I had assumed the expansion was mainly via the Admiralty/New Britain/New Ireland groups.

"Donohue hypothesizes that the earliest Lapita peoples may have been of Papuan or mixed stock".

Mixed, certainly, but Papuan? Unlikely. I don't think the article come close to disproving the idea that languages in Vanuatu 'emerged from mixing of indigenous ... Papuan languages and ... Austronesian settlers'. Where they perhaps go wrong is in assuming a Papuan substrate in Vanuatu whereas it is much more likely the 'Papuan' element there is primarily a later development although even the original Lapita settlers would have had a 'mixed' language to some degree. Quote:

"We suggest that it is just as likely that Papuan-speaking Melanesians, occupying the islands out to the end of the main Solomons chain for at least 30,000 years and having settled Manus by 20,000 years ago (Spriggs 1997), would have participated in the maritime
expansion that accompanied the spread of Lapita"

I think the following is far more likely than the authors' alternative option. This is especially likely to be so when we consider that the Santa Cruz population is remarkable in the relative lack of Y-DNA C2 and mt-DNA B4:

"One possible scenario for a Papuan influence on the linguistic ecology of Vanuatu
would be that the early Lapita horizon reflects settlement by people whose ancestors had
been resident in Melanesia for many millennia, [but almost certainly not in Vanuatu] and who adopted various aspects of a new
immigrant culture, including an Austronesian language. The language of these first colonizers
exhibited a number of structural features inherited from pre-Austronesian language(s) in
New Guinea, and these features were borne, more-or-less undiluted, to Vanuatu. These colonizers did not stay around in areas with a strong Austronesian influence long enough for
their Papuan 'accent' to be moderated".

That makes very likely the statement:

"suggesting ... a linguistically
complex initial settlement"

To me the most likely scenario in the Remote pacific is of a rapid Austronesian/Lapita expansion (mainly Y-DNAs O3 and C2 and mt-DNA B4) followed by the expansion of older populations from Melanesia (Y-DNAs K and M and mt-DNAs P, Q and M).

"did technologies expand with peoples, or did peoples adopt technologies?"

Both probably.

andrew said...

@MOCKBA I was about to suggest the scenario put forth by Pawley until you noted it. This is likely to me.

@terryt The genetics might not provide unequivocal support for either scenario, but I agree with you that that the archaeological data and information on boating technology strongly favor Austronesian settlement of the island.

terryt said...

"BTW did the AJHG mtDNA paper sample Vanuatus?"

I've just purchased the article and the answer to your question is: no. They didn't sample New Ireland either, nor New Caledonia. I guess they assumed these other groups would be similar to their neighbours. Probably justified judging from their conclusions:

"The heatmap contains pairwise distances for all sequences that belong to haplogroups of Near Oceanian origin and shows that, in general, sequences are most closely related to others originating from the same group."

However we do have some idea of those other regions from:

http://www.sciencedirect.com/science/article/pii/S0960982209021204

From this earlier paper we can see that both Vanuatu and New Caledonia have M29, absent in Santa Cruz (although 1 shown for Santa Cruz in the new paper). Further New Caledonia has M27 and P2, neither of which are found in Vanuatu or Santa Cruz (the 'P' shown for Santa Cruz in the new paper is probably P1 or P4a, shown to be present in the older paper). Otherwise the three regions are fairly similar, but it seems obvious there was no one, single migration route from Near to Remote Oceania.

"The genetics might not provide unequivocal support for either scenario, but I agree with you that that the archaeological data and information on boating technology strongly favor Austronesian settlement of the island".

The final sentence in the paper is actually:

"In addition, we do not find evidence to support a pre-Austronesian settlement of Santa Cruz, which remains a strong outlier in Remote Oceania because of its extraordinarily high frequency of autochthonous Near Oceanian haplogroups."

In other words the scenario is pretty much as I outlined it yesterday: 'a rapid Austronesian/Lapita expansion (mainly Y-DNAs O3 and C2 and mt-DNA B4) followed by the expansion of older populations from Melanesia (Y-DNAs K and M and mt-DNAs P, Q and M)'. The expansion that 'followed on' involved a lot of to and fro movement though.

terryt said...

A few further points that some may be interested in. The main findings are basically summarised in figure 5, a 'Network of all Haplogroupss of Putative Near Oceanian Origin'. Perhaps Dienekes could get in touch with the authors to get permission to post the figure as an update?

What becomes obvious in the paper is that we are dealing with more than just two movements from SE Asia to near Oceania. Mt-DNA E seems to have arrived some 6000 years ago, about the time the first evidence for humans beyond Bougainville appears in Guadalcanal. It is quite possible that the bulk of the Solomon Islands were not settled until that date, or even as late as 3500 years ago with the Austronesian expansion.

Another conclusion that is difficult to avoid is that M27 developed in Bougainville, M28 in New Ireland, M29 in New Britain and Q in New Guinea itself. The haplogroups spread, by several routes, through the Solomon Islands and out into Remote Oceania. M27b is almost ubiquitous through the islands, absent only from three of the very small ones and, notably, New Britain and Makira at opposite ends of its spread. M27a and M27c are much more restricted in their distribution being confined to islands closest to Bougainville.

terryt said...

In case anyone is interested:

I've just had a brain explosion after considering the current paper and returning to these ones:

http://mbe.oxfordjournals.org/content/26/8/1865.full.pdf

http://www.nature.com/nature/journal/v324/n6096/abs/324453a0.html

It has always interested me that it seems the Melanesian islands northeast of New Guinea were settled before the mainland was. At last, from extracting haplogroup ages and distributions from various sources, I can see why. Settlement of the region was far from simple with haplogroups moving backwards and forwards. Australia and New Guinea cannot have actually been 'connected' at any time. There was always water between them. Humans must have originally crossed from Timor to the Kimberly coast of Australia, and then moved east along Australia's north coast rather than along New Guinea's exposed northern coastline (mt-DNAs N13, N14, S, O, P, M14, M14 and M42 in Australia by 45,000 years ago). P1'2'8'10 moved back to eastern Indonesia. The swampy southern New Guinea region was of no use to anyone. Haplogroups M27, M28 and M29'Q (possibly as a single haplogroup) finally reached the more hilly southeastern New Guinea region by 40,000 years ago, and Q1'2 moved from there back to eastern Indonesia. By 35,000 M28 and M29 reached New Britain and New Ireland, and by 30,000 M27 reached Bougainville. About the same time P1 moved back from eastern Indonesia to northwest Australia and, finally, to western New Guinea. It was not until some 12,000 years ago that Q1 and Q2 also moved back into western New Guinea from eastern Indonesia, and to the Admiralty and Bismark Islands. P8 and P10's arrival in the Philipines may be part of the same movement. Humans did not reach the southeastern Solomon Islands, such as Guadalcanal, until some 6000 years ago, possibly associated with mt-DNA E's arrival. Around 3500 years ago the Austronesians arrived.

d6782388-e639-11e3-b3bd-fb578f794f7c said...

I have no comment about sequenced haplogroups... but unfortunately, I wouldn't trust the dates given in this paper, firstly it has no ancient DNA to prove any "first settlement" in this region, secondly, there is problem in calculating the haplogroup dates. The author does not disclose the posterior on each of the branches and conveniently hides the branches in a huge triangle... My guess is that there are many inconsistent haplogroup allocation problems, which the author claims with their previous paper (A highly unstable recent mutation in human mtDNA. http://www.ncbi.nlm.nih.gov/pubmed/23313375),so one would expect there are several back mutations among haplogroups in this region (yet no reason is provided as to why). In conclusion about haplogroup E, I do not know why the author entirely fails to mention the paper that links haplogroup E with Austronesian expansion when it was published before this paper (Early Austronesians: Into and Out Of Taiwan, http://www.cell.com/ajhg/abstract/S0002-9297(14)00061-5), my simple guess is the dating does not fit the author's analysis thus it was discredited.

terryt said...

"I wouldn't trust the dates given in this paper"

The authors certainly offer a wide margin of error for the ancient diversification but I'm inclined to accept dates given for the individual haplogroups' more recent expansions.

"firstly it has no ancient DNA to prove any 'first settlement" in this region'"

I think we can accept the 40,000 year date for the Huon settlement. Of course that need not be the date of 'first' New Guinea human presence but we know they were present 'by' that date.

"In conclusion about haplogroup E, I do not know why the author entirely fails to mention the paper that links haplogroup E with Austronesian expansion when it was published before this paper"

I am unable to access the whole paper but the abstract says:

"Bayesian phylogenetic analysis allows us to reconstruct a history of early Austronesians arriving in Taiwan in the north ~6,000 years ago, spreading rapidly to the south, and leaving Taiwan ~4,000 years ago to spread throughout Island Southeast Asia, Madagascar, and Oceania".

As far as I'm aware that fits exactly the generally accepted scenario. A paper out a few years ago showed that mt-DNA E had probably entered the Philippines/Taiwan region some reasonable time before the Austronesian expansion, almost certainly from Borneo. I can search for the paper if you wish. I am therefore unable to understand what you're getting at with:

"my simple guess is the dating does not fit the author's analysis thus it was discredited".

The authors' suggestion that at least some E haplogroups entered the Melanesia/New Guinea region before the Austronesian expansion is very likely to be correct. Quote:

"E1b is the most frequent lineage of haplogroup E found in this study (Table S2) and it is conspicuously absent in Taiwan and the Philippines, which would suggest a different source for entry into Near Oceania."