Assessing biological factors affecting post-speciation introgression

An increasing number of phylogenomic studies have documented a clear ‘footprint’ of post-speciation introgression among closely-related species. Nonetheless, systematic genome-wide studies of factors that determine the likelihood of introgression remain rare. Here, we propose an a priori hypothesis-testing framework that uses introgression statistics—including a new metric of estimated introgression, Dp —to evaluate general patterns of introgression prevalence and direction across multiple closely related species. We demonstrate this approach using whole genome sequences from 32 lineages in 11 wild tomato species to assess the effect of three factors on introgression—genetic relatedness, geographical proximity, and mating system differences—based on multiple trios using the ‘ABBA-BABA’ test. Our analyses suggest each factor affects the prevalence of introgression, although our power to detect these is limited by the number of comparisons currently available. We find that of 14 species p...