Genetic evidence for the colonization of Australia

Quaternary International Volume 285, 8 February 2013, Pages 44–56

Genetic evidence for the colonization of Australia

Sheila van Holst Pellekaan et al.

Mitochondrial DNA (mtDNA), Y-chromosome and, more recently, genome studies from living people have produced powerful evidence for the dispersal of modern human populations. The prevailing model of global dispersion assumes an African origin in which Australia and the American continents represent some of the extreme regions of human migration, though the relative timing of dispersal events remains debatable. Here, a focus on Australia and New Guinea discusses currently available genetic evidence from the two regions, compared with that from Asia. Mt haplotypes indicate ancient ancestry for both Australia and New Guinea peoples, with evidence of some shared genetic connection and other unshared haplogroups apparently specific to both places. Migration into Sahul from south-east Asia may have been by more complex routes than only along a ‘southern coastal route’, raising the question of possible common ancestry in central or northern Asia for some Australian and American peoples for which current genetic evidence is tenuous. Although current dating methods for genetic diversity rely heavily on several assumptions, best estimates provide support for archaeological dates, indicating that, relative to the colonization of America, Australia was inhabited very early. Genetic diversity of living descendants of Australia’s founding populations is informative for dispersal within Australia and for understanding complex population histories of Asia.

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Sailing across the Pacific to settle Polynesia (Soares et al. 2011)

I always have a hard time following these easy archaeological interpretations on the basis of uniparental markers, both because I'm convinced that they are not supported by the wide confidence intervals of age estimates, and because, as I've argued countless times, age of colonization != age of most recent common ancestor of colonists' descendants.

With respect to the latter point, let me just reiterate that:

• The common founder of a set of lineages may postdate the colonization event, if the number of colonists was small enough so that attrition was high enough, and a founder that lived long after the colonization effect contributed most of the present-day population
• The common founder of a set of lineages may predate the colonization event, if the number of colonists was high enough, so that multiple related lineages with a founder who lived before the event, survived into the modern population.

We should all take modern genetic-archaeological-prehistorical correlations (including my own!) with a huge grain of salt. Polynesia seems like the last place on earth likely to yield ancient DNA of any antiquity, due to the combination of heat and moisture, but, on the whole, a single well-dated and authenticated ancient DNA sample carries much more weight than all the modern DNA put together.

From the press release:

Surprising new evidence which overturns current theories of how humans colonised the Pacific has been discovered by scientists at the University of Leeds, UK.

The islands of Polynesia were first inhabited around 3,000 years ago, but where these people came from has long been a hot topic of debate amongst scientists. The most commonly accepted view, based on archaeological and linguistic evidence as well as genetic studies, is that Pacific islanders were the latter part of a migration south and eastwards from Taiwan which began around 4,000 years ago.

But the Leeds research – published today in The American Journal of Human Genetics – has found that the link to Taiwan does not stand up to scrutiny. In fact, the DNA of current Polynesians can be traced back to migrants from the Asian mainland who had already settled in islands close to New Guinea some 6-8,000 years ago.

...

Professor Richards and co-researcher Dr Pedro Soares (now at the University of Porto), argue that the linguistic and cultural connections are due to smaller migratory movements from Taiwan that did not leave any substantial genetic impact on the pre-existing population.

The American Journal of Human Genetics, 03 February 2011
doi:10.1016/j.ajhg.2011.01.009

Ancient Voyaging and Polynesian Origins

Pedro Soares et al.

Abstract
The “Polynesian motif” defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ∼4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3–4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a “voyaging corridor” between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia.

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Demographic history of Oceania (Wollstein et al. 2010)

frappe analysis on the left: New Guinea Highlanders split at K=4 (light blue), with Polynesian-Fijians remaining aligned with East Asians; at K=5 the specificity of the East Eurasian component in Polynesians-Fijians (teal) is revealed; at K=5 the specificity of Borneo is apparent (red), but there are individuals of clearer East Asian ancestry remaining.

From the paper:

Among the three demographic models examined for the peopling of Near Oceania (Figure 4, models 2a–2c), the model receiving the highest support involves a split of New Guineans from a common European-East Asian (i.e., Eurasian) ancestor population. This finding does not support the southern dispersal hypothesis of separate human migrations from Africa to Near Oceania and to East Asia [33, 34]. The existence of a single ancestral population for all present-day non-Africans is supported, among other genetic evidence, by recent data from the Neandertal genome sequence, indicating that all present-day non-African genome sequences studied(including one from a Papua New Guinean) have equivalent amounts of Neandertal admixture [46].

However, the authors date the split of Near Oceanians from the common Eurasians at 27ky and of East Asians from Europeans at only 18ky. These dates are far too low, in my opinion, as there is evidence that Upper Paleolithic Europeans were already robust versions of modern Caucasoids.

Moreover, if Eurasian unity broke down at 27ky, then where were the Eurasians since the time they acquired "Neandertal admixture" until 27ky?

It is difficult to imagine Eurasians camping in the Near East or Europe (where Neandertals are attested) for tens of thousands of years before starting to split off at 27ky. And indeed, the fact that there are anatomically modern humans from South China and the Levant at around 100ky, make the idea that Eurasians got Neandertal admixture in one place before starting to disperse a few tens of thousands of years ago hard to believe.

I personally don't buy the idea that New Guineans have the same "Neandertal admixture" as Europeans. In fact, I doubt there is any substantial Neandertal admixture in Eurasians at all, and if there is, it is certainly not the 1-4% evenly distributed element across Eurasia that was discovered in the recent paper.

In any case, this issue is peripheral to this paper which offers important new data on the question of Oceanian origins.

Related:

• Bayesian phylogenetics of languages and the timing of Austronesian settlement of the Pacific from Taiwan
• 500K SNP study of Oceanian populations
• Genetic structure of Pacific Islanders
• Polynesians more Asian than Melanesian
• A rare genomic look at Aboriginal Australians

Curr Biol. 2010 Nov 10. [Epub ahead of print]

Demographic History of Oceania Inferred from Genome-wide Data.

Wollstein A, Lao O, Becker C, Brauer S, Trent RJ, Nürnberg P, Stoneking M, Kayser M.

Abstract

BACKGROUND: The human history of Oceania comprises two extremes: the initial colonizations of Near Oceania, one of the oldest out-of-Africa migrations, and of Remote Oceania, the most recent expansion into unoccupied territories. Genetic studies, mostly using uniparentally inherited DNA, have shed some light on human origins in Oceania, particularly indicating that Polynesians are of mixed East Asian and Near Oceanian ancestry. Here, we use ∼1 million single nucleotide polymorphisms (SNPs) to investigate the demographic history of Oceania in a more detailed manner.

RESULTS: We developed a new approach to account for SNP ascertainment bias, used approximate Bayesian computation simulations to choose the best-fitting model of population history, and estimated demographic parameters. We find that the ancestors of Near Oceanians diverged from ancestral Eurasians ∼27 thousand years ago (kya), suggesting separate initial occupations of both territories. The genetic admixture in Polynesian history between East Asians (∼87%) and Near Oceanians (∼13%) occurred ∼3 kya, prior to the colonization of Polynesia. Fijians are of Polynesian (∼65%) and additional Near Oceanian (∼35%) ancestry not found in Polynesians, with this admixture occurring considerably after the initial settlement of Remote Oceania. Our data support a greater contribution of East Asian women than men in the admixture history of Remote Oceania and highlight population substructure in Polynesia and New Guinea.

CONCLUSIONS: Despite the inherent ascertainment bias, genome-wide SNP data provide new insights into the genetic history of Oceana. Our approach to correct for ascertainment bias and obtain reliable inferences concerning demographic history should prove useful in other such studies.

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Y chromosome variation in NW New Guinea

A 2007 paper that slipped through my net at the time it appeared, but is interesting to read as it was cited in the recent study by Cox et al. (2010)

Molecular Biology and Evolution 2007 24(11):2546-2555; doi:10.1093/molbev/msm187

Patterns of Y-Chromosome Diversity Intersect with the Trans-New Guinea Hypothesis

Stefano Mona et al.

Abstract

The island of New Guinea received part of the first human expansion out of Africa (>40,000 years ago), but its human genetic history remains poorly understood. In this study, we examined Y-chromosome diversity in 162 samples from the Bird's Head region of northwest New Guinea (NWNG) and compared the results with previously obtained data from other parts of the island. NWNG harbors a high level of cultural and linguistic diversity and is inhabited by non-Austronesian (i.e., Papuan)–speaking groups as well as harboring most of West New Guinea's (WNG) Austronesian-speaking groups. However, 97.5% of its Y-chromosomes belong to 5 haplogroups that originated in Melanesia; hence, the Y-chromosome diversity of NWNG (and, according to available data, of New Guinea as a whole) essentially reflects a local history. The remaining 2.5% belong to 2 haplogroups (O-M119 and O-M122) of East Asian origin, which were brought to New Guinea by Austronesian-speaking migrants around 3,500 years ago. Thus, the Austronesian expansion had only a small impact on shaping Y-chromosome diversity in NWNG, although the linguistic impact of this expansion to this region was much higher. In contrast, the expansion of Trans-New Guinea (TNG) speakers (non-Austronesian) starting about 6,000–10,000 years ago from the central highlands of what is now Papua New Guinea, presumably in combination with the expansion of agriculture, played a more important role in determining the Y-chromosome diversity of New Guinea. In particular, we identified 2 haplogroups (M-P34 and K-M254) as suggestive markers for the TNG expansion, whereas 2 other haplogroups (C-M38 and K-M9) most likely reflect the earlier local Y-chromosome diversity. We propose that sex-biased differences in the social structure and cultural heritage of the people involved in the Austronesian and the TNG expansions played an important role (among other factors) in shaping the New Guinean Y-chromosome landscape.

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Genetic methods applied to linguistic diversity of the Sahul

It is great to see cross-pollination between the sciences; in this case, use of STRUCTURE has led to insights about languages of the Sahul.

From the paper:

Although we cannot specify how many different migrations have colonized Sahul since the first settlement approximately 50,000 years ago, our results indicate ancient splits into seven major plausible groups: TNG, South-Papuan, North-West Papuan, North-East Papuan, West-Papuan, PN, and non-PN. The wide-spread families (TNG and PN) on both sides of the Torres Strait divide (~9,000 BP) are the result of more recent expansions of two of those groups, in the case of TNG probably linked to the development of agriculture, ~9,000 to 6,000 years ago, see [35],[37].

The AN expansion is much more recent and has only had effects in eastern Indonesia, along the north coast of New Guinea and the islands east of the New Guinea mainland. We know on the basis of the comparative method correlated with archaeological data that approximately 3,200 years ago the Oceanic subgroup dispersed from its homeland on New Britain in three directions [9]: (1) back along the north coast, (2) around the eastern tip of New Guinea along the south coast, and (3) much further into the Pacific. The results of our analysis capture some of the impact of this great expansion on the languages that were already in the region. We find that in the eastern islands there are clearly distinct AN and non-AN groups, with good evidence of a deep structural phylogenetic signal, albeit with some admixture [16]. In the western islands however there is considerably more typological convergence between AN and non-AN languages (see also [38]). The linguistic population identified as Red appears to have members along the north coast (Mairasi, I'saka, and Kamasau) and on New Britain, where again both AN (Mangseng) and Papuan languages (Kol and Sulka) have contributions from the same cluster. This finding suggests an area of millennia of contact between AN and Papuan non-TNG speaking groups.

Gene Expression has more.

PLoS Biology doi:10.1371/journal.pbio.1000241

Explaining the Linguistic Diversity of Sahul Using Population Models


Ger Reesink et al.

Abstract

The region of the ancient Sahul continent (present day Australia and New Guinea, and surrounding islands) is home to extreme linguistic diversity. Even apart from the huge Austronesian language family, which spread into the area after the breakup of the Sahul continent in the Holocene, there are hundreds of languages from many apparently unrelated families. On each of the subcontinents, the generally accepted classification recognizes one large, widespread family and a number of unrelatable smaller families. If these language families are related to each other, it is at a depth which is inaccessible to standard linguistic methods. We have inferred the history of structural characteristics of these languages under an admixture model, using a Bayesian algorithm originally developed to discover populations on the basis of recombining genetic markers. This analysis identifies 10 ancestral language populations, some of which can be identified with clearly defined phylogenetic groups. The results also show traces of early dispersals, including hints at ancient connections between Australian languages and some Papuan groups (long hypothesized, never before demonstrated). Systematic language contact effects between members of big phylogenetic groups are also detected, which can in some cases be identified with a diffusional or substrate signal. Most interestingly, however, there remains striking evidence of a phylogenetic signal, with many languages showing negligible amounts of admixture.

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