Investigating population continuity with ancient DNA under a spatially explicit simulation framework

Abstract

BackgroundRecent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory. Comparing samples taken in the same region but at different times, hereafter called “serial samples”, may indicate whether there is continuity in the peopling history of that area or whether an immigration of a genetically different population has occurred between the two sampling times. However, the exploration of genetic relationships between serial samples generally ignores their geographical locations and the spatiotemporal dynamics of populations. Here, we present a new coalescent-based, spatially explicit modelling approach to investigate population continuity using aDNA, which includes two fundamental elements neglected in previous methods: population structure and migration. The approach also considers the extensive temporal and geographical variance that is commonly found in aDNA population samples.ResultsWe first showed that our spatially explicit approach is more conservative than the previous (panmictic) approach and should be preferred to test for population continuity, especially when small and isolated populations are considered. We then applied our method to two mitochondrial datasets from Germany and France, both including modern and ancient lineages dating from the early Neolithic. The results clearly reject population continuity for the maternal line over the last 7500 years for the German dataset but not for the French dataset, suggesting regional heterogeneity in post-Neolithic migratory processes.ConclusionsHere, we demonstrate the benefits of using a spatially explicit method when investigating population continuity with aDNA. It constitutes an improvement over panmictic methods by considering the spatiotemporal dynamics of genetic lineages and the precise location of ancient samples. The method can be used to investigate population continuity between any pair of serial samples (ancient-ancient or ancient-modern) and to investigate more complex evolutionary scenarios. Although we based our study on mitochondrial DNA sequences, diploid molecular markers of different types (DNA, SNP, STR) can also be simulated with our approach. It thus constitutes a promising tool for the analysis of the numerous aDNA datasets being produced, including genome wide data, in humans but also in many other species.Electronic supplementary materialThe online version of this article (10.1186/s12863-017-0575-6) contains supplementary material, which is available to authorized users.

Inference of natural selection from ancient DNA

“…2009), an approach that was recently extended to include structured populations (Silva et al. 2017). However, a comprehensive investigation into how these confounding variables violate the assumptions and impact the inferences of the methods outlined above is currently lacking.…”

Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations

“…Then, the proportion of simulated F st that are greater than that observed is computed, and if it is smaller than 5%, the genetic shift is considered to be large enough to reject the population continuity hypothesis. This test has been recently improved by including two fundamental elements that were not considered in previous approaches: population subdivision and migration (Silva, Rio, & Currat, ). Under these continuity model assumptions, the genetic difference between the serial samples is due to sampling, genetic drift and ongoing gene flow with neighbours (Silva et al., ).…”

“…This test has been recently improved by including two fundamental elements that were not considered in previous approaches: population subdivision and migration (Silva, Rio, & Currat, ). Under these continuity model assumptions, the genetic difference between the serial samples is due to sampling, genetic drift and ongoing gene flow with neighbours (Silva et al., ). A rejection of the continuity hypothesis may thus indicate that genetic input due to immigration occurred during the period separating the two sampling times and was sufficient to create a detectable shift in allele frequency.…”

The female ancestor's tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany

“…Evidence of long‐term genealogical continuity was found in several genetic isolates, such as the Basques in Iberia, Ogliastra in Sardinia, and Casentino in Tuscany (Ghirotto et al, , ; Günther et al, ; Sampietro et al, ) but were often rejected in more open areas (Bramanti et al, ; Gamba et al, ; Guimaraes et al, ; Malmström et al, ). Only very recently serial coalescent simulations supported genetic continuity from the Neolithic to this day in nonisolated regions such as the Paris basin (Rivollat et al, ; Silva, Rio, & Currat, ) and the Southern Caucasus (Margaryan et al, ).…”