Prehistory – Gene Expression

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.

When it comes to the arrival of Indo-Aryans to South Asia a major question Indians always post is “if they are invaders why don’t they mention that in their mythology?” My standard rejoinder is straightforward: we have plenty of paleogenetic evidence that many populations are intruders, but their mythology doesn’t indicate that. If the Indian objection is to hold then why not others? Are all human populations autochthonous in their native lands?

And yet the most recent work suggests that steppe ancestry didn’t arrive in the BMAC region until 2000 BC. That means that the Cemetery H culture in Punjab dating to 1900 BC is the earliest likely candidate for Indo-Aryans in South Asia. The Rigveda was composed as early as 200 years after this date, or as late as 700 years. Could they have “forgotten” where they came from?

The Irish are one people who have preserved their mythology due to the gradual and indigenous nature of Christianization. But 2,500 years after their arrival en masse from the continent they had forgotten the details. But, the motif of invasion was preserved, though we don’t know if that is a memory of their past, or just a channeling of the mythos of the period when their folklore was written down. Another example might be the Japanese, who arrived about 1,100 years before the Heian period, the first flowering of literate civilization on the island. To my knowledge, their mass migration from southern Korea was mostly forgotten by then.

With all this in mind, I decided to reread Genetic origins of the Minoans and Mycenaeans. The conclusion of the paper is that it’s clear an appreciable, though minority, component of Mycenaean ancestry seems to have some affinity with Indo-European groups. The two candidates for the donors are people from the Eurasian steppe, or Copper age Armenians. For linguistic reasons that I can barely evaluate, I lean toward the former. This implies that the proto-Greeks arrived in the late 3rd millennium or early 2nd millennium. The mythology of ancient Greek as recorded by Hesiod and others in the Archaic period probably dates in part to the Bronze Age (some of the Greek gods are recorded in the Linear B tablets). To my knowledge the Greeks do not record when they arrived from outside of Greece.

This suggests that 1,000 years is sufficient for a forgetting, at least for a semi-literate society.

The last is key. Societies with written histories can maintain continuity. But what about oral societies?