DILS: Demographic inferences with linked selection by using ABC
Christelle Fraïssé, Iva Popovic, Clément Mazoyer, B. Spataro, Stéphane Delmotte, Jonathan Romiguier, Étienne Loire, Alexis Simon, Nicolas Galtier, Laurent Duret, Nicolas Bierne, Xavier Vekemans, Camille Roux
Abstract
We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.