Summary tests of introgression are highly sensitive to rate variation across lineages

The evolutionary implications and frequency of hybridization and introgression are increasingly being recognized across the tree of life. To detect hybridization from multi-locus and genome-wide sequence data, a popular class of methods is based on summary statistics from subsets of 3 or 4 taxa. However, these methods often carry the assumption of a constant substitution rate across lineages and genes, which is commonly violated in many groups. In this work, we quantify the effects of rate variation on the D test (also known as ABBA-BABA test), the D3 test, and HyDe. All three tests are used widely across a range of taxonomic groups, in part because they are very fast to compute. We consider rate variation across species lineages, across genes, their lineage-by-gene interaction, and residual variation across gene-tree edges. We do so by simulating gene trees within species networks according to a birth-death-hybridization process so as to capture a range of realistic species phylogenies..., ,