The aggregate site frequency spectrum (aSFS) for comparative population genomic inference

Understanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, and an endeavor that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to gain complex demographic inference at unprecedented resolution across assemblages of non-model species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide polymorphism (SNP) datasets collected from multiple, co-distributed species for assemblage-level demographic inference. We describe how the aSFS is constructed over an arbitrary number of independent population samples and then demonstrate how the aSFS can differentiate various multi-species demographic histories under a wide range of sampling configurations while allowing effective population sizes and expansion magnitudes to vary independently. We subs...