Data from: Using genomic location and coalescent simulation to investigate gene tree discordance in Medicago L.

Several well-documented evolutionary processes are known to cause conflict
between species-level phylogenies and gene-level phylogenies. Three of the
most challenging processes for species tree inference are incomplete
lineage sorting, hybridization and gene duplication, which may result in
unwarranted comparisons of paralogous genes. Several existing methods have
dealt with these processes but none has yet been able to untangle all
three at once. Here, we propose a stepwise method by which these processes
can be discerned using information on genomic location coupled with
coalescent simulations. In the first step, highly discordant genes within
genomic blocks (putative paralogs) are identified and excluded from the
data set and, in the second step, blocks of linked genes are grouped
according to their hybrid history. Existing multispecies coalescent
software can then be applied to recover the principal tree(s) that make up
the species tree/network without violating the underlying model. The
potential of the approach is evaluated on simulated data derived from a
species network composed of nine species, of which one is of hybrid
origin, and displaying a single-gene duplication that leads to paralogous
comparisons. We apply our method to an empirical set of 12 genes from 7
species sampled in the plant genus Medicago that display phylogenetic
discordance. We identify the causes of the discordance and demonstrate
that the Medicago orbicularis lineage experienced an episode of ancient
hybridization. Our results show promise as a new way to explore
phylogenetic sequence data that can significantly improve species tree
inference in presence of hybridization and undetected paralogy or other
causes leading to extremely discordant gene trees.