Data from: Parsimonious inference of hybridization in the presence of incomplete lineage sorting

Hybridization plays an important evolutionary role in several groups of
organisms. A phylogenetic approach to detect hybridization entails
sequencing multiple loci across the genomes of a group of species of
interest, reconstructing their gene trees, and taking their differences as
indicators of hybridization. However, methods that follow this approach
mostly ignore population effects, such as incomplete lineage sorting
(ILS). Given that hybridization occurs between closely related organisms,
ILS may very well be at play and, hence, must be accounted for in the
analysis framework. To address this issue, we present a parsimony
criterion for reconciling gene trees within the branches of a phylogenetic
network, and a local search heuristic for inferring phylogenetic networks
from collections of gene-tree topologies under this criterion. This
framework enables phylogenetic analyses while accounting for both
hybridization and ILS. Further, we propose two techniques for
incorporating information about uncertainty in gene-tree estimates. Our
simulation studies demonstrate the good performance of our framework in
terms of identifying the location of hybridization events, as well as
estimating the proportions of genes that underwent hybridization. Also,
our framework shows good performance in terms of efficiency on handling
large data sets in our experiments. Further, in analysing a yeast data
set, we demonstrate issues that arise when analysing real data sets.
Although a probabilistic approach was recently introduced for this
problem, and although parsimonious reconciliations have accuracy issues
under certain settings, our parsimony framework provides a much more
computationally efficient technique for this type of analysis. Our
framework now allows for genome-wide scans for hybridization, while also
accounting for ILS.