Joint inference of adaptive and demographic history from temporal population genomic data
AbstractDisentangling the effects of selection and drift is a long-standing problem in population genetics. Theoretical works based on simulations show that the signal of selection may bias demographic inference when it is pervasive. Ideally, interactions between selection and demography should be considered in the estimation of parameters of demographic and adaptive models. One potential approach is to co-estimate demography and selection parameters using simulation-based likelihood-free methods such as Approximate Bayesian Computation (ABC). We propose a framework based on ABC via Random Forests to jointly infer demographic and selection parameters from temporal population genomic data (e.g. experimental evolution, monitored populations, ancient DNA). The proposed framework allows the separation of demography (census size,N) from genetic drift (effective population size,Ne) and the estimation of the genome-wide effect of selection as the scale mutation rate of beneficial mutations (θb). We applied this approach to a dataset of feral populations ofApis melliferacollected in California, and we estimated parameters consistent with the biology and the recent history of this species.