One can appreciate a work of art on two levels. When one beholds the sculpted renderings of the Classical Greeks, across the distance of more than 2,000 years we can feel viscerally that they have touched something beautiful, and made it stone. To reduce this to biology, our perception maps onto to deep grooves in our evolutionary landscape of aesthetic judgments. As a savanna ape the darkness of the forest haunts us with its beauty and majesty; but we are the children of the meadows and edges of the Paleolithic pastoral. Similarly, on some level we acknowledge physical beauty when we see it, before we even think it.*

Another level of appreciation is narrower, and that is one where you have awareness of the ingenuity of technique, the deep virtuosity and fluency of execution. This aspect of understanding aesthetics is naturally delimited to those with equivalent skills, or whose skills aspire toward the plane of the masters.

Reading Iosif Lazaridis’ The genetic structure of the world’s first farmers you can evaluate on both levels. The results are broadly accessible, but the depth of the analysis is clear to anyone who has ever attempted something analogous. These papers coming out of David Reich’s lab have a certain template, but they are definitely not paint-by-numbers. For those who are interested in technical details, you have to read the supplements.

Ten years ago the insights gleaned from this preprint were only glimmers in the eyes of assorted researchers and “genome bloggers.” The problem now is one of going from the raw result, back to the dynamics which produced the result. A deep problem of inference.

To get to where we are now, and the embarrassment of copious conclusions, researchers needed three things:

1) Lots of genetic data, and methods designed to leverage that data (basically, genomics, and the statistical genetics geared toward analyzing large data sets).

2) Genetic data from time points in the human past, and not just present.

3) The technological infrastructure necessary to handle the data (from computational power to the arcane arts of the ancient DNA lab).



What have we learned? Ancient DNA has revealed that genetic variation in the human past has been characterized by very strong discontinuities, both over time and space. What do I mean by this?

As a stylized fact it has been fashionable in some quarters to describe human variation as being overwhelmingly clinal. That is, a continuous change in gene frequencies as a function of space. One associated fact has been the expectation that gene frequencies will change over time in a similar steady and regular fashion.

Obviously there is some truth to the clinal variation in our species. If, for example, you walked form France to the Punjab, it would be difficult to establish a hard-and-fast line where there was a definite discontinuity in genes. But there could be candidates. In particular, in Central Asia there would be regions where you would find rather high frequencies of alleles more typical of East Asia, while in Afghanistan the genetic signatures of non-West Eurasian peoples of a different sort, typically found in South Asia, would start to crop up.

But these two points of discontinuity illustrate the general principle that discontinuity emerges from specific historical-demographic events. In the case of the rather high fraction of East Asian associated genes in Central Asia, this is almost certainly a product of the Turkic expansion, which occurred in starts and fits over the ~1,000 years between 500 and 1500. In South Asia, we now suspect that there was a relatively recent intrusion of West Eurasian populations, and likely some reciprocal gene flow between indigenous groups and the incomers.

These two instances point out that major disruptions in gene flow are likely correlated with major cultural disruptions. The Turkic expansion occurred in historical time, so we can inspect it and note that the decline of Iranian populations within Central Asia began during the late Sassanian period, but came to near completion with the major shocks of the Mongol period 700 years later. These were events of geopolitical note.

This is important to consider, because the older models which posit clinal variation assume that genetic change occurs through a ‘mass action’ process, whereby small family or village groups enter into a phase of demographic expansion, and literally outbreed others. This was to some extent the model implicit in the ‘demic diffusion’ theories of the expansion of the Neolithic lifestyle into Europe from the Near East, pioneered by Colin Renfew, and extended by L. L. Cavalli-Sforza and colleagues.

In a classical economic framework one can simply assume that those who practice the farming lifestyle will be in a state of land surplus on the frontier. Therefore, they will have large families, and keep expanding their range. In such a fashion individual decisions of Homo economicus can drive cultural and demographic change over large regions in relatively short time periods.

The decisions of the many in an uncoordinated fashion can lead to the ordered patterns we see around us, with clines of variation, as well as signals of genetic expansion. As L. L. Cavalli-Sforza noted the argument here is not that most of the ancestry of modern Europeans is exogenous to the continent when using Pleistocene groups as the indigenous reference, but that the demographic wave of advance is responsible for agriculture, not cultural emulation. Even with this wave of advance model, which has been widely explored in population genetics, assimilation of native groups on the frontier means that most of the ancestry on the frontier by the end of the process could be “indigenous.”

Cavalli-Sforza’s assertions came in the wake of a series of results in the early 2000s which were interpreted to suggest that most of the ancestry of modern Europeans derives from populations resident during the Pleistocene. These results were taken to suggest that agriculture must have then spread by cultural diffusion, not demographic expansion. All Cavalli-Sforza was pointing out was that the model he was supporting was about a dynamic process, not some specific value of haplotype counting by region.

Ultimately this rearguard apologia was not necessary. It turns out that a majority of the ancestry of modern Europeans is likely exogenous to the continent over the last ~10,000 years. The earlier results which were used to support the converse were right in their results, but were misinterpreted. Additionally, I also think that the model outlined by Cavalli-Sforza and his colleagues is in some ways too elegant and stylized to be useful. If you read The War Before Civilization there are plenty of archaeological hints that there were massive inter-group conflicts during prehistory, and the arrival of farmers to the continent probably exhibited some coordination and collective action beyond the village. The 3,200 year old battle on the Baltic is probably the continuation of a long tradition in Europe, and the world, of collective action and conflict.

This is a “problem” because inter-group conflicts on a geopolitical scale are not as tractable in terms of a general model as a “wave of advance” demographic scenario where endogenous growth parameters rule supreme. Rather, demographic patterns are not due to continuous predictable dynamics, but the intersection of such parameters and contingent events. History has no guarantees, though its wheels tend toward certain favored grooves.

Twenty years ago L. L. Cavalli-Sforza wrote a book geared toward the lay audience, Great Human Diasporas. The culmination of a lifetime’s work, it surveyed what we then knew about human genetic variation with classical markers derived from contemporary populations. The tools we have today are far more precise, with hundreds of thousands of markers rather than hundreds, and DNA samples from populations thousands or tens of thousands of years in the past. Instead of simply inferring the tree of life, researchers are now constructing a lattice of relationships derived not only from the nodes visible today, but also positions within the lattice from the deep past.

The evidence which is coming back is that pre-modern populations exhibited a great deal of genetic differentiation over even small distances, and, that differentiation could persist for thousands of years. Between group proportions of variation on the order of 10% of the total variance, what you see between Europeans and Han Chinese, were not atypical for nearby peoples, even though one migrant between them per generation would have eliminated that difference in short order. This equilibrium of difference would eventually get disrupted by radical demographic turnover, as location populations went extinct or were absorbed by newcomers, who reshaped whole landscapes through their expansions. In other words, if Cavalli-Sforza were to write a book today I believe it would be titled “Great Human Disruptions and their Diasporas.”

And this isn’t just about agriculture. Ancient DNA from Pleistocene Europe indicates turnover there too. There may be meta-population dynamics which are at work on the edge of the modern human range in Eurasia. As local populations go extinct, new populations expand to occupy their territory. The ancient human landscape may have been relatively sparsely populated, diminishing opportunities for gene flow.

But this is likely not the whole story. Inter-group conflict certainly played a role, and ancient DNA has uncovered evidence of long periods of genetic distinctiveness between neighboring populations. This suggests cultural practices serving as a barrier to gene flow. We do have one case where this occurs today: India. The caste system is such that continental wide genetic distances can be found within local populations in the same region, which have coexisted for thousands of years.

So what are the results of the the Lazaridis’ paper? The figure at the top gives you a PCA-centric view. Basically, all West Eurasian populations today can be modeled to a first approximation as a mixture of four ancestral groups which flourished on the order of ~10,000 years ago. If modern genetic variation can be conceived of as an algebra, then for West Eurasia these are the four variables with differential weights you need to produce any reasonable output.

The four are:

1) Western hunter-gatherers (WHG), the indigenous populations of Europe and surrounding areas.

2) Eastern hunter-gatherers (EHG), the indigenous populations of the the northeastern fringe of Europe.

3) Western farmers, the ancestors of Early European Farmers (EEF), with roots in the zone from the southern Levant north into Anatolia.

4) Eastern farmers, who are rooted populations which flourished in the Zagros mountains of western Iran (Central Asian Farmers, CAF).

These four themselves exhibit some compound ancestry. On the order of half the ancestry of EEF and and CAF was basal Eurasian (BEu), a population which seems to have diverged from other non-Sub-Saharan Africans more than 50,000 years ago, before Neanderthal admixture. To be clear, BEu seems to be an outgroup to populations as diverse as Pleistocene European hunter-gatherers, Australian indigenous groups, and Andaman Islanders. The other half of EEF and CAF ancestry derives from two distinct sources, which explain their different positions on the PCA plot. The EEF have a WHG-like admixture. That is, some of their ancestors are nested within the broader clade which includes European hunter-gatherers, and far more distantly the Ancestral North Eurasians (ANE). Work on Pleistocene genomics indicates that there was a major increase in affinity between European hunter-gatherers and Near Easterners ~15,000 years before the present, suggesting that there was major gene flow uniting these two regions. The Near Eastern element of this movement probably fused with BEu.

Second, the CAF population, which is known from far fewer samples, seems to have shared a lot of ancestry with EHG, so the two must have shared common ancestry from related groups. It seems that the mostly likely source of this was ANE. Due to the genetic distance between ANE and WHG, the Fst between EEF and CAF was on the order of ~0.10, similar to that between Chinese and Europeans today. These two groups seem to have stumbled upon agriculture very near to each other at similar times.

Where they independent events? I suspect that they weren’t. I’m not implying here cultural diffusion. There is evidence of independent domestication of landraces in the Zagros. Rather, these two populations were part of a broader network of trade connections within a similar ecological landscape. It was not coincidental that both stumbled upon agriculture. Likely there was diffusion between the two of similar cultural precursors to agriculture. Their location in such proximity can not be coincidence, though the details are to be worked out.

Interestingly once these two populations stumbled onto agriculture they expanded in opposite directions. Why? Probably because they could. That is, both of them had high population densities and social complexity, and rather than impinging upon each other’s territories they expanded into “empty” landscape. Regions inhabited by hunter-gatherers who were easier to eliminate or assimilate. The spread of Cardial and LBK people in Europe was so fast that it is almost certain that they were all one cultural unit initially. Something similar probably applies to the CAF groups which expanded east into South Asia, and north to the steppe.

Another intriguing result in this paper is that WHG themselves seem to have had admixture from eastern populations. More precisely, the Mesolithic hunter-gatherers used in earlier analyses as “pure” exemplars of WHG turn out not to be, but exhibit some admixture with other groups. This is probably why the ANE proportion of EHG is much higher in this paper. An older sample from Bichon in Switzerland lacks the eastern admixture, and so serves as a better reference for WHG. Though not definitive, it now looks as if ANE admixture into East Eurasians (e.g., Han Chinese) has resulted in some affinity between these populations and Europeans today, going back to, but not limited to, the WHG. This is no surprise. The emergence of agriculture is not singularly new, cultural innovation seems to trigger demographic disruptions, no matter the time or place.

Though the centerpiece of this preprint is the fact that four populations are sufficient to explain the genetic variation, and demographic history, of West Eurasian populations, I think perhaps a more interesting element is the role of ANE and BEu. Neither of these groups exist in “pure” form today. We don’t know who BEu were. We don’t know where they came from. To me it is suspicious that BEu ancestry exists in about the same fractions in both EEF (at least their precursors in the Middle East) and in CAF. It does not seem that the two BEu components were very differentiated. To me that indicates that BEu may have expanded relatively recently. I also believe that BEu may have a role mediating “back to Africa” gene flow. As BEu lacks Neanderthal admixture that would explain the very low levels in most of the continent, and yet the presence of what now look to be Eurasian origin E Y chromosomal haplotypes.

As for the ANE, their geographic coverage is incredible, from Western Europe all the way to the New World. It seems that as a unadmixed group they persisted into the Holocene, but in numbers they were always stretched thin. Through their amalgamation into agriculturalists they’ve persisted, but likely many of their Paleo-Siberian folkways diminished. I do believe though the R1 haplogroups on the Y chromosome likely derive from them, as it is a sister to the Amerindian Q.

There’s a lot in the paper to chew on, especially the supplements. For example, the percentages of “steppe” ancestry are non-trivial throughout South Asia. What to make of this? I think I’ll hold off until ancient DNA comes in, as it will in the next 6 months.

But, I do think ancient DNA and the model of disruptions and discontinuity supports the proposition that punctuated equilibrium as a thesis has much more validity for cultural evolution than it does for biology. Cultures exhibit inertia and a tendency toward conformity. Learning new things is difficult. Very special conditions must have existed for agriculture to “take” in the Near East, as hunter-gatherers shifted form facultative cultivation to obligate modes of production of crops. Once these cultures became farming cultures, it wasn’t easy for neighbors to easily adopt them, as cultural packages often come as a whole, with many contingent parts. The advantage of agriculture is that it extracts more yield from the ground, and population densities go up. Higher population densities means more resources in inter-group conflict, if it comes to that, and the need to expand to continue to race beyond the Malthusian limit. Once the space is occupied, a new equilibrium is reached.

And I want to reiterate, this model does not apply to just agriculture. A tweet from Spencer Wells:

Papua New Guinea is fascinating – looking forward to seeing this published. #SMBE16 pic.twitter.com/8fhB8Pcaqv — Spencer Wells (@spwells) July 4, 2016

New Guinea is a horticultural society, and the highlands are very densely populated. The high Fst is in line with what you see in early Holocene Western Eurasia, or in India today. But observe that the genetic differentiation is from the past 10,000 years, not the past 50,000. 10,000 years ago is when horticulture began. In all likelihood one population in the highlands began to practice this, and expanded demographically, eliminating or absorbing its neighbors. But the landscape of New Guinea sets tight limits to the range of possibilities, as the highlands of the island are a very isolated ecosystem. The genetic differentiation began once the expansion phase ceased, and groups began to struggle for existence at the Malthusian limit.

One of the insights of Lazaridis et al.’s paper is that this didn’t happen in Eurasia. The differences between EEF and CAF diminished, as the Near East saw reciprocal gene flow during the Bronze Age. The difference was not in agriculture, but post-agricultural social complexity, which allowed for the emergence of what Peter Turchin would term “meta-ethnic” identities, and complex institutions which transcend locality. In the new equilibrium state the Fst did not begin to go up as populations jostled for resources, as innovation began to gently push the production frontier outward, and foster connections of material (e.g., trade) and ideas (e.g., religion).

The whole story is not written in stone yet. The next few years are going to be interesting. China is the next frontier, and ancient DNA will open up its history soon enough. But it’s an exciting time to be witnessing the unveiling of prehistory before our eyes.

* There is a dimension of aesthetic judgement which is culturally conditional, and another which is not. I speak of the latter here.