The importance of fine-scale studies for integrating palaeogenomics and archaeology

Short review (behind paywall) The importance of fine-scale studies for integrating paleogenomics and archaeology, by Krishna R. Veeramah, Current Opinion in Genetics & Development (2018) 53:83-89.

Abstract (emphasis mine):

There has been an undercurrent of intellectual tension between geneticists studying human population history and archaeologists for almost 40 years. The rapid development of paleogenomics, with geneticists working on the very material discovered by archaeologists, appears to have recently heightened this tension. The relationship between these two fields thus far has largely been of a multidisciplinary nature, with archaeologists providing the raw materials for sequencing, as well as a scaffold of hypotheses based on interpretation of archaeological cultures from which the geneticists can ground their inferences from the genomic data. Much of this work has taken place in the context of western Eurasia, which is acting as testing ground for the interaction between the disciplines. Perhaps the major finding has not been any particular historical episode, but rather the apparent pervasiveness of migration events, some apparently of substantial scale, over the past ∼5000 years, challenging the prevailing view of archaeology that largely dismissed migration as a driving force of cultural change in the 1960s. However, while the genetic evidence for ‘migration’ is generally statistically sound, the description of these events as structured behaviours is lacking, which, coupled with often over simplistic archaeological definitions, prevents the use of this information by archaeologists for studying the social processes they are interested in. In order to integrate paleogenomics and archaeology in a truly interdisciplinary manner, it will be necessary to focus less on grand narratives over space and time, and instead integrate genomic data with other form of archaeological information at the level of individual communities to understand the internal social dynamics, which can then be connected amongst communities to model migration at a regional level. A smattering of recent studies have begun to follow this approach, resulting in inferences that are not only helping ask questions that are currently relevant to archaeologists, but also potentially opening up new avenues of research.

Interesting excerpts (emphasis mine, reference numbers removed for clarity):

There are two major, somewhat intertwined, problems that currently exist.

First, archaeologists are not critiquing whether the migrations identified by paleogenomics using sophisticated population genetic machinery are actually occurring. Instead, the technical criticism arrives in terms of how these migrations are being ascribed to specific cultures. In many paleogenomic papers, there is a tendency (and often an analytical and technical need) to associate samples with particular archaeological cultures, for which all samples are then treated as possessing some kind homogenous and pervasive social identity that is bound in space and time. The major critiques of this thus far have been directed to those studies examining Corded-Ware and Bell-Beaker-related individuals and their potential relationship to the Yamnaya [Vander Linden (2016), Heyd (2017), Furholt (2017)], but are applicable to many other ‘migration’ scenarios described in the recent literature. This is compounded by the use of sometimes small numbers of samples to represent certain cultures from a particular geographic area as representatives of the entire culture at a supra-regional level. Yet often these archaeological cultures such as Corded-Ware and Bell-Beaker themselves show considerable variability in space and time, and even within cemeteries, which is not factored into the genetic analysis.

From a population geneticists point of view, this kind of simplification is somewhat understandable and will often likely have very little impact on the final analysis, given that the primary goal is usually to use ancient samples to better understand modern genetic variation. Though there may be a specific historical interest in some of these past events, I would argue that the aim for most population geneticists at a higher level is to try and fit modern patterns of genetic variation using the simplest models possible that take into account past demographic events (for example fitting f-statistics using the ADMIXTUREGRAPH approach), as this is how we are trained. Although sharing an archaeological culture may not mean that a set of individuals are part of the same homogeneous social group in reality, this approach may be a good enough heuristic to find broad genetic connections compared to another group represented by a different culture, which can then ultimately help understand and model modern human population structure. However, for an archaeologists interested in the ancient individuals themselves and their social identity, this lumping is unsatisfactory, where sophisticated narratives of the individual migrants and their ancient communities are the intended goal.

eurasian-genomes
From the paper. Barplot showing cumulative number of ancient Eurasian genomes published on a yearly basis up to 8th July 2018. Includes samples undergoing both whole genome shotgun and SNP capture sequencing.

The second related problem is that ‘migration’ in the sense used currently in the paleogenomics literature lacks sufficient detail to be of much use for an archaeologists attempting to disentangle the complex social dynamics within and between communities. To truly understand the role of migration as a social process and its contribution towards cultural changes, it is necessary to describe it as a structured behaviour, rather than treating it as an explanatory ‘black box’. Are the migrations occurring as a result of short range waves-of-advance movements, or as long-distance movements via leapfrogging models or stream migrations along established routes dependent on key kinship networks. Are there return migrants, and are some subset of individuals more predisposed to migration driving the signals? Although such models were implemented in past studies (even with classical markers [1]) and are part of the population genetics literature, they are lacking in the current paleogenomics literature when discussing migration. The finding that there is an increase of 12.3% of ancestry type X in population A compared to the preceding population B that is suggestive of a migration, is not particularly useful for examining these kind of models. It is also unclear to what degree standard population genetic parameters estimated from genomic data such as effective population size, Ne, and gene flow are relevant to models studied in archaeology, given they reflect (somewhat undefined) long-term population sizes and average rates of movements over time, rather than reflecting any kind of reality of census size and mobility in the ancient communities the archaeologists are actually attempting to study.

The text goes on to talk about ways of studying fine-grained social dynamics of local cultures, such as:

define levels of genetic relatedness, but also in terms of material culture, age, sex, stress and activity indicators, stable isotopes for diet reconstruction (nitrogen, d13C and d15N, carbon, 13C/12C) and strontium and oxygen isotopes for mobility (87Sr/86Sr, d18O). Where possible, sites should be examined over multiple generations. In addition it will be incredibly useful to characterize the impact of disease in these communities, which is also proving to be a highly fruitful realm for paleogenomics.

I would say that the main problem is not the obvious limitations of palaeogenomics in terms of identifying prehistoric ethnolinguistic communities and their evolution, which is why it is just another tool to complement archaeology and linguistics. The main problem is the narrow understanding that some people have of the inherent limitations of palaeogenomics – especially when it interests them – , when publicizing simplistic conclusions based on these tools and their results. And I am not referring only to amateurs.

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