Our new paper on the impacts of gene flow on species tree estimation is in press at Systematic Biology. Gene flow can cause gene trees to conflict with one another, and therefore we typically try to shelter our species tree analyses from anything other than incomplete lineage sorting. What happens if some gene flow sneaks into the analysis?
We use simulations to characterize estimation errors that result from various models of gene flow. Even in cases where the topology of the species tree is estimated with high accuracy, we find that gene flow can still result in overestimates of population sizes (species tree dilation) and underestimates of divergence times (species tree compression).
Species tree distortion is illustrated below using species trees and Homer Simpson.
Leaché, A. D., R. B. Harris, B. Rannala, and Z. Yang. The influence of gene flow on species tree estimation: A simulation study. Systematic Biology, In Press.