Population genetics encompasses a wide range of questions related to the evolution of populations over time. The advent of ancient DNA (aDNA) analysis has further expanded this field, facilitating the development of methodological approaches like the population continuity test. Over time, there is a variation of the neutral genetic diversity in populations due to new mutations, genetic drift, and migration. If genetic samples collected from different time periods, in the same area, show no evidence of large genetic differentiation, it suggests a certain continuity in the population across the studied period. On the contrary, an extreme genetic divergence suggests a population replacement resulting from major immigration.
The objective of this master’s project is to develop an R package, called POPContinuity, that performs a structured population continuity test, investigating whether there has been a detectable population replacement in the time and area under study. The specificity of this approach is that it takes into account the continuous gene flow between the population of interest and neighboring populations, a factor that has proved important when investigating population continuity over time. Its main features are, first, the simulation of genetic data of different types (SNP, microsatellites, or sequences) under a null hypothesis of population continuity, and second, the comparison with observed data while accounting for both spatial and temporal dimensions of the population. POPcontinuity relies on the Approximate Bayesian Computation (ABC) analysis to optimize the goodness-of-fit of the simulations, based on intra-population genetic diversity, while the continuity test is based on inter-population genetic divergence. Integrating simulations and analysis into a single, easy-to-use R package simplifies the user approach to population continuity testing. POPcontinuity also provides various complete summary files for detailed results, making it a flexible tool, adaptable to various research contexts when molecular data in temporal series is available.
To illustrate the usefulness of our package and to validate its results, we applied it to two case studies from different research fields: the evolutionary history of modern human populations in Europe and the conservation of the butterfly Vanessa atalanta in Switzerland. In the first case study, two cases of population discontinuity have been identified: first between Hunter-gatherers and early Neolithic farmers, and second between final Neolithic and Bronze Age. For Vanessa atalanta, no cases of population discontinuity have been identified in Switzerland for the period considered.
