Statistical methods to detect archaic admixture and identify introgressed sequences

Genome-scale sequencing data sets from many taxa have shown that hybridization across leaky species boundaries is common in natural populations. This observation extends to our own species, as gene flow between anatomically modern humans and other hominins, such as Neanderthal and Denisovans, has been well established. In this chapter, we describe statistical approaches that have been used to test hypotheses of gene flow between species and identify introgressed sequences. These methods provide powerful tools to investigate population history, understand mechanisms of evolutionary change, and better understand the heritable basis of phenotypic variation.