After agriculture, before bronze


The above plot shows genetic distance/variation between highland and lowland populations in Papa New Guinea (PNG). It is from a paper in Science that I have been anticipating for a few months (I talked to the first author at SMBE), A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea.

What does “strong genetic structure” mean? Basically Fst is showing the proportion of genetic variation which is partitioned between groups. Intuitively it is easy to understand, in that if ~1% of the genetic variation is partitioned between groups in one case, and ~10% in another, then it is reasonable to suppose that the genetic distance between groups in the second case is larger than in the first case. On a continental scale Fst between populations is often on the order of ~0.10. That is the value for example when you pool the variation amongst Northern Europeans and Chinese, and assess how much of it can be apportioned in a manner which differentiates populations (so it’s about ~10% of the variation).

This is why ancient DNA results which reported that Mesolithic hunter-gatherers and Neolithic farmers in Central Europe who coexisted in rough proximity for thousands of years exhibited differences on the order of ~0.10 elicited surprise. These are values we are now expecting from continental-scale comparisons. Perhaps an appropriate analogy might be the coexistence of Pygmy groups and Bantu agriculturalists? Though there is some gene flow, the two populations exist in symbiosis and exhibit local ecological segregation.

In PNG continental scale Fst values are also seen among indigenous people. The differences between the peoples who live in the highlands and lowlands of PNG are equivalent to those between huge regions of Eurasia. This is not entirely surprising because there has been non-trivial gene flow into lowland populations from Austronesian groups, such as the Lapita culture. Many lowland groups even speak Austronesian languages today.

Using standard ADMIXTURE analysis the paper shows that many lowland groups have significant East Asian ancestry (red), while none of the highland groups do (some individuals with East Asian admixture seem to be due to very recent gene flow). But even within the highlands the genetic differences are striking. The  Fst values between Finns and Southern European groups such as Spaniards are very high in a European context (due to Finnish Siberian ancestry as well as drift through a bottleneck), but most comparisons within the highland groups in PNG still exceeds this.

The paper also argues that genetic differences between Papuans and the natives of Australia pre-date the rising sea levels at the beginning of the Holocene, when Sahul divided between its various constituents. This is not entirely surprising considering that the ecology of the highlands during the Pleistocene would have been considerably different from Australia to the south, resulting in sharp differences in the hunter-gatherer lifestyles. Additionally, there does not seem to have been a genetic cline. Papuans are symmetrically related to all Australian groups they had samples from.

Using coalescence-based genomic methods they inferred that separation between highlands and some lowland groups occurred ~10-20,000 years ago. That is, after the Last Glacial Maximum. For the highlands, the differences seem to date to within the last 10,000 years. The Holocene. Additionally, they see population increases in the highlands, correlating with the shift to agriculture (cultivation of taro).

None of the above is entirely surprising, though I would take the date inferences with a grain of salt. The key is to observe that large genetic differences, as well as cultural differences, accrued in the highlands of PNG during the Holocene. In the paper they have a social and cultural explanation for what’s going on:

  Fst values in PNG fall between those of hunter-gatherers and present-day populations of west Eurasia, suggesting that a transition to cultivation alone does not necessarily lead to genetic homogenization.

A key difference might be that PNG had no Bronze Age, which in west Eurasia was driven by an expansion of herders and led to massive population replacement, admixture, and cultural and linguistic change (7, 8), or Iron Age such as that linked to the expansion of Bantu-speaking
farmers in Africa (24). Such cultural events have resulted in rapid Y-chromosome lineage expansions due to increased male reproductive variance (25), but we consistently find no evidence for this in PNG (fig. S13). Thus, in PNG, wemay be seeing the genetic, linguistic, and cultural diversity that sedentary human societies can achieve in the absence of massive technology-driven expansions.

Peter Turchin in books like has aruged that one of the theses in Steven Pinker’s is incorrect: that violence has not decreased monotonically, but peaked in less complex agricultural societies. PNG is clearly a case of this, as endemic warfare was a feature of highland societies when they encountered Europeans. Lawrence Keeley’s gives so much attention to highland PNG because it is a contemporary illustration of a Neolithic society which until recently had not developed state-level institutions.

What papers like these are showing is that cultural and anthropological dynamics strongly shape the nature of genetic variation among humans. Simple models which assume as a null hypothesis that gene flow occurs through diffusion processes across a landscape where only geographic obstacles are relevant simply do not capture enough of the dynamic. Human cultures strongly shape the nature of interactions, and therefore the genetic variation we see around us.

3 thoughts on “After agriculture, before bronze

  1. The papers also detects footprints of vast population expansion, so the founder groups seem to have been small, and reproductive isolation, really long. Is it really surprising if the present genetic diversity may be shaped by the old founder events and extensive drift? Are the agriculturalist highlanders in other corners of the world also retaining comparably higher levels of diversity over shorter geographic distances? But yes, it’s sort of amazing to see how the absence of metal weapons yielded nothing like peace, yet no appreciable change of tribal landownership over millennia.

  2. Dm – Inter-tribal violence in the PNG highlands was/is a never ending pay-back system, like vendettas in Sicily, rather than seeking to invade and occupy others’ territory.

  3. Davidski, the blogger at Eurogenes, ran some Fst estimates in the past for between the European Early-Middle Neolithic-Copper Age sets of ancient dna samples we have (before expansions of steppe related ancestry).

    Those come out between the most extreme at Iberian Copper Age – Central European Linearbandkeramik: 0.016, or comarping similar time period pairs Iberian Early Neolithic – Central European Linearbandkeramik: 0.011 or Iberian Copper Age – Central European Middle Neolithic: 0.011. With Anatolia included as well, Anatolian Early Neolithic – Iberian Copper Age: 0.019.

    There’s about 25% WHG admixture into the most extreme European samples, with their Anatolian related ancestry. Still pretty far from the most extreme sets in PNG.

    (There is probably still some role for drift in determining the present day fine structure between the low Fst present day European population. Fst between Irish-Spanish 0.004 is about comparable to Fst Irish-Ukrainian 0.004 despite the latter pair seeming to be more similar in the deep proportions of WHG-Anatolia-Steppe ancestry).

    Modern day India is another example that might be interesting to compare with PNG. So long as both they’re fairly outbred on the world scale, Fst between fairly high and low ANI:ASI ratio group pairs isn’t actually very high compared to in PNG, as e.g. comparing Uttar Pradesh Brahmins to the Gond tribe only yields a Fst of about 0.007 (slightly less than 1% of their pooled variation).

    However, comparing high founder effects group like Chenchu, Pulliyar (high ASI), Kalash (high ANI) to each other can yield very high Fst, e.g. most extreme Chenchu-Pulliyar 0.081. (Some role here is for deep ancestry differences within the ANI-ASI abstractions, but it seems likely to mostly be founder effect). In India this can all happen in tandem with relatively high levels of heterozygosity for out of Africa populations, probably as they are pooling a lot of the out of Africa diversity due to migration.

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