Inferring gene flow from phylogenies with ubiquitous genomes

It is now recognized that species often diverge while exchanging genetic material. There is plenty of evidence that gene flow has occurred across diverse biological groups and in numerous contexts (e.g., isolation with/after migration or secondary contact). However, the prevalence and impact of gene flow at phylogenetic time scales are less understood. The assessment is important, as it may contain clues on how species diverge and become different over time. Despite the many efforts to model speciation with gene flow, current models are insufficient to assess gene flow along multiple speciation events, particularly at deep time horizons. We propose a new and more realistic model of evolution that includes the joint action of evolutionary forces such as mutation bias, genetic drift, natural selection, and gene flow, along with processes such as population and migration histories and demography. We will use complex phylogenetic models and biological insights from grasshoppers, fruit flies, persimmon trees and fireflies to answer the following questions: What is the evolutionary significance of gene flow during species divergence? Are most regions of the genome affected by gene flow, or do some regions show an elevated impact of gene flow? What is the interplay between natural selection and gene flow during species evolution? Our main objective is to develop a powerful and more realistic framework to determine the macroevolutionary impact of gene flow and natural selection across evolutionary scales. This will expand the range of applications of current methods, allowing the analysis of extensive genomic datasets, now commonplace in evolutionary biology, and at evolutionary scales where gene flow has been less studied.

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