A geostatistical approach to modelling human Holocene migrations in Europe using ancient DNA

Abstract

The European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent's inhabitants, via admixture and population replacement processes. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. Here, we use a combination of paleogenomics and geostatistical modelling to produce detailed maps of the movement of these populations over time and space, and to understand how these movements impacted the European vegetation landscape. We find that the dilution of hunter-gatherer ancestries and the Yamnaya steppe migration coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture lands in the continent. We also show that climate played a role in these vegetational changes. Additionally, we find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings based on patterns of the cultural spread of farming from radiocarbon-dated archaeological sites. With thousands of ancient genomes publicly available and in production, we foresee that the integration of ancient DNA with geostatistical techniques and large-scale archaeological datasets will revolutionize the study of ancient populations movements, and their effects on local fauna and flora.

Beyond broad strokes: sociocultural insights from the study of ancient genomes

“…Now, the new abundance of radiocarbon-dated ancient genomes allows us to trace how genetic ancestry spread as a consequence of this cultural transformation 14,30 . Indeed, the "genetic expansion" of ancestry during the 3/28 Neolithic appears to have a similar shape to that evinced by archaeology 31 . This supports the idea that movements of people originating from Anatolia and the Middle East brought about this transformation throughout Europe ( Figure 2).…”

“…Grid data for building the left panel was obtained courtesy of Marc Vander Linden and Fabio Silva and is based on a figure from Linden and Silva 92 . The right panel was built after spatiotemporally kriging a collection of ancient genomes from Western Eurasian palaeogenomic studies mentioned in the main text, and recording the grid points at which one first encounters Anatolian farmer ancestry at a fraction higher than 75% 31 . White regions are regions where this ancestry did not reach levels above 75%.…”

Sometimes Hidden but Always There: Assumptions Behind Demographic Inference from Ancient DNA Data

“…SLiM [70] and msprime [69]) and analytical tools (e.g. [37,72,73]) will not only make linking past demographic events to the archaeological, historical and climate records more straightforward and robust but will also allow direct inclusion of data from these lines of evidence.…”