S 9 Demographic Analysis Using G - PhoCS

Our main demographic analysis is based on the Generalized Phylogenetic Coalescent Sampler (G-PhoCS) developed by Gronau et al. [1]. G-PhoCS performs demographic inference conditioned on a given population phylogeny augmented by a collection of migration bands (see Fig. S9.1.1). Migration bands describe scenarios of post-divergence gene flow in the demographic model, and are defined by ordered pairs of branches in the population phylogeny, allowing different rates to be associated with the two directions of gene flow. G-PhoCS infers demographic parameters associated with the population phylogeny (i.e., ancestral population sizes, population divergence times, and migration rates) based on inferred genealogies at