Data from: The genomic view of diversification

The process of species diversification is traditionally summarized by a
tree, the species tree, whose reconstruction from molecular data is
hindered by frequent conflicts between gene genealogies. Here, we argue
that instead of seeing these conflicts as nuisances, we can exploit them
to inform the diversification process itself. We adopt a gene-based view
of diversification to model the ubiquitous presence of gene flow among
diverging lineages, one of the most important processes explaining
disagreements among gene trees. We propose a new framework for modeling
the joint evolution of gene and species lineages relaxing the hierarchy
between the species tree and gene trees inherent to the standard view, as
embodied in a popular model known as the multi-species coalescent (MSC).
We implement this framework in two alternative models called the
gene-based diversification models (GBD): 1) GBD-forward following all
evolving genomes through time and 2) GBD-backward based on coalescent
theory. They feature four parameters tuning colonization, gene flow,
genetic drift and genetic differentiation. We propose a quick inference
method based on differences between gene trees. Applied to two empirical
data-sets prone to gene flow, we find better support for the GBD-backward
model than for the MSC model. Along with the increasing awareness of the
extent of gene flow, this work shows the importance of considering the
richer signal contained in genomic histories, rather than in the mere
species tree, to better apprehend the complex evolutionary history of
species.