The new post-genetic paradigm will come

Oftentimes the domain on which a technical framework is applied matters a great deal. Imagine, if you will, an explicit statistical test for a phylogenetic relationship between a set of extant populations, whereby one infers a group of ancestral populations. If the genus is Drosophila, it’s academic. Interesting, but academic. If the genus is Homo, then it gets complicated.

People care a great deal about the historical inferences made from human population genomic datasets. I say genomic, and not genetic, because the last ten years with genome-wide analyses and ancient DNA is very different from what we saw in the late 20th century and aughts. The definitive granularity is such that population genomics has touched upon very sensitive and precious issues, both in a scholarly and non-scholarly context.

A lot of the time I have my head down reading supplements where the statistical methods are. The reality is that this sort of science is cutting edge, and there are always later revisions. Usually you can see where those revisions might come from if you look at the detailed methods and conclusions that are found in the supplements. Also, you will find that that is where you see the limitations, and the reasons that the authors chose particular parameters.

To give you a sense of what I’m talking about, consider 2016’s Genomic insights into the origin of farming in the ancient Near East. The paper proper is 24 pages. But the supplemental text is 148 pages. There is a lot of interesting stuff in there, but I would just jump to page 125 and read the whole section there and down to the end. The method portion is important because you always need to take number values in results with a grain of salt. You see for example later work which refines fractions significantly when it comes to estimating admixture between a finite set of putative populations. And the last section seems likely to become a paper in and of itself at some point

But that doesn’t mean that the genetic inferences are not robust and come out of a vacuum. In the details the phylogenetic models being tested are going to be wrong on many particulars, but in relation to hypotheses being tested they are often entirely sufficient to reject to accept.

For example, there was long the idea that the Basque people of the western trans-Pyrenees region of Spain and France descended from pre-farming Europeans, and therefore the Basque language, which is an isolate, might have local roots which went back to the Pleistocene. Today, ancient DNA along with explicit testing of various phylogenetic scenarios makes it clear that the largest fraction of Basque ancestry derives from “Early European Farmers,” who represent a demographic pulse which radiated out of the Eastern Mediterranean and reached Spain 7,500 years ago. Of course Basques do have local hunter-gatherer ancestry, but these Mesolithic peoples themselves were the last in a sequence of very distinctive populations in Pleistocene Europe. Finally, Basques do have admixture from Indo-European peoples, just less than other people in Iberia.

Of course, genetics can’t tell us about languages. Using linguistic labels in population genetic papers is to some extent a lexical convenience, but it is also one we use because of the constellation of information we have. The last major demographic pulse into Iberia is associated with an ancestry which derives from Central Eurasia. This ancestry is copious in Northern Europe, but is also found in South Asia, and ancient DNA suggests its expansion occurred between 5,000 and 3,500 years ago. It also happens that the Indo-European languages are spoken in both India and Europe. The natural inference then is to make an association between this language family, and this demographic pulse.

Some observers note discordance between estimated fractions from paper to paper, but don’t seem to understand that the point isn’t to estimate fractions of ancestry as ends in and of themselves, but to estimate fractions of ancestry to expose and highlight demographic change (or lack thereof). We can say with a very high degree of certainty that the period between 3000 and 2000 BC witnessed massive demographic change in Northern Europe. Somewhat later there was a similar change in Southern Europe, but more demographically modest. These are simple facts.

There are some scholars, frankly often archaeologists, who dismiss the relevance of the genetic findings. But anyone who has read archaeology knows that there are many cases where researchers see demographic continuity, and posit in situ cultural evolution, where it is just as possible that a new people arrived. The reason ancient DNA has revolutionized our understanding of prehistory isn’t because it has brought us new knowledge, it has foregrounded old and buried knowledge. The knowledge being that migration matters.

But genetics is only a skeleton. A framework. True flesh on the bones of the story needs the input of archaeologists, linguistics, and other scholars. In Who We Are and How We Got Here David Reich expresses his ambition to construct a historical genetic atlas of the world. But that atlas will be all the poorer without the input from other fields besides genetics. Many archaeologists have gotten on board with genetics as a tool, but the reality is that there needs to occur the rejection of some theories precious to some scholars if there is going to be total buy-in. Eventually that will happen, and a new synthesis will arise.

Before the Indo-Europeans in Ukraine

It’s been ten years since I read The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. It’s a great book, but some of the material was very wrong. The author, David Anthony, helped provide samples which undercut his thesis that Indo-Europeanization in Europe was mostly a matter of elite cultural diffusion. Rather, it looks as if there was a massive migration from the steppes.

The Horse, the Wheel, and Language was heavy on archaeology which I found hard to follow. The Cucuteni–Trypillia culture plays a major role in the narrative since it seems to have been a source of cultural influence on the Yamnaya steppe culture which eventually overran it. A new preprint seems to confirm that there was a genetic discontinuity. Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the origins and expansions of the Late Neolithic-Chalcolithic Cututeni-Tripolye Culture

…Burials at Verteba Cave are largely commingled and secondary in nature. A total of 68 individual bone specimens were analyzed. Most of these specimens were found in association with well-defined Tripolye artifacts. We determined 28 mtDNA D-Loop (368 bp) sequences and defined 8 sequence types, belonging to haplogroups H, HV, W, K, and T. These results do not suggest continuity with local pre-Eneolithic peoples, but rather complete population replacement. We constructed maximum parsimonious networks from the data and generated population genetic statistics…We find different signatures of demographic expansion for the Tripolye people that may be caused by existing population structure or the spatiotemporal nature of ancient data. Regardless, peoples of the Tripolye Culture are more closely related to early European farmers and lack genetic continuity with Mesolithic hunter-gatherers or pre-Eneolithic groups in Ukraine.

There is stuff in the preprint about population expansion. My personal opinion is that in most cases genetics doesn’t add much beyond what archaeology does for humans in reconstructing population history. Rather, these results in concern with others are strongly indicative of population turnover. Uniparental lineages are still useful, but only in the context of other data.

The great thing about genetics when it is so clear and striking is that it clears up confusions about relationships in the past that otherwise would be unclear. It’s like having a time machine. So we now know that early European farmers (EEF) were ancestors of this particular culture. Over the next decade or so we’ll get a really granular understanding of the ebb and flow of populations across prehistoric and historic Europe. This won’t abolish all controversy, but it will reduce the space of the unknown….

The revolution which came to archaeology without archaeologists?

The recent letter to Nature, Genetic origins of the Minoans and Mycenaeans, has elicited some response from those outside of genetics. The first author of the paper linked to these two, Who are you calling Mycenaean? and On genetics and the Aegean Bronze Age.

One of the common elements to both reactions was that the paper’s definition, or reification, of Mycenaean and Minoan constructs was naive. From one of the posts:

In a press interview following the publication of the study, one of the main authors claimed that ‘there is no doubt that our findings reflect historical events in the Greek lands’: ‘the picture of historical continuity is crystal clear, as is very clear the fact that through the centuries Greeks evolved receiving genetic influences from other populations.’ The category of ‘Greekness’ here appears more or less given and stable, despite the ‘influences’, from the Early Bronze Age to the present. It sounds like a version of the 19th-century national narrative of the power of eternal Hellenism to absorb external influences.

Context is important here. The last ten years have seen a massive updating of our assumptions about the nature of demographic change in the pre-modern world. Geneticists using ancient DNA have been central to this process. They’ve overturned a lot of archaeological orthodoxies.

One of the major assumptions seemingly at the heart of the two critical posts is that modern ideas of nationhood were a recent construction. The stylized assertion is that modern nationalism begins with the French Revolution. To me this is like the assertion that the troubadours invented romantic love during the High Middle Ages. While it is true that the troubadours popularized a particular form of romantic love, the core emotional impulses are primal, and didn’t need “inventing.” Similarly, ideas of nationality are clearly primal, because they derive from the tribal structures of prehistoric humanity. Tribes are an evoked part of human culture. That is, given similar cognitive hardware, the same software seems to get installed for the same tasks (group cohesion and inter-group competition).

Ironically, the period between the “rise of civilization” and the modern era may have been one defined by the regression of nationalistic thinking, because tribalism had to be suppressed with the rise of multiethnic agricultural states. Only with early modern information technology, and the spread of a literate middle class culture united by common mores and touchstones, could primal tribalism be transformed into modern nationalism (to this way of thinking it is not a coincidence that German nationalism with the Lutheran Reformation was supercharged by the arrival of the printing press).

Peter Heather in Empires and Barbarians and Azar Gat in Nations outline the revisionist views I’m alluding to in regards to the ancient origins of nationalism. But from a perspective of a geneticist the very high differentiation between nearby groups that persist for hundreds and even thousands of years is indicative of high levels of cultural distinction and consciousness (because only small amounts of gene flow between groups is enough to eliminate differences very rapidly). Genetics can’t maintain these sorts of differences, only strong cultural ideologies can.

Finally, quoting from the same post:

First, there’s not much new here. I mean, the data are new, but the conclusions are largely consistent with the archaeological consensus: there’s no big genetic difference between “Minoans” (Late Bronze Age Cretans) and “Mycenaeans” (Late Bronze Age inhabitants of the Greek mainland), and both are pretty close genetically to Late Bronze Age southwestern Anatolians….

The archaeological consensus was correct here to a great extent. But in other areas it has not been right of late. That’s why it is not so ho-hum. In The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe the authors show that:

1) the spread of Beaker culture from Southwest Europe to Central Europe was one of cultural transmission (archaeologists would not be surprised).

2) the spread of Beaker culture to England from Central Europe was one of demographic replacement on the order of 90% over a few hundred years (archaeologists would be surprised).

It’s easy for archaeologists to be surprised that geneticists are presenting ideas that they “refuted” in the 1960s. But it turns out that the predictions on a demographic scale are easily refuted in many places and times by genetics. The issue isn’t whether it’s pots or peoples, but what the mix of pots and people are. This research is part of a broad program of nailing down the values in these parameters, as opposed to simply going along with archaeological orthodoxy.

Addendum: The title is somewhat unfair now that I think about it. Many archaeologists have been instrumental in the revolution triggered by ancient DNA. But, the vast majority of archaeologist and historians who are outside of these collaborations, I’m not so sure they are aware of the recent developments.