Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting
Author
Yu, Yun; Barnett, R. Matthew; Nakhleh, Luay
Date
2013Abstract
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 analyzing a
yeast data set, we demonstrate issues that arise when analyzing real data sets. While
a probabilistic approach was recently introduced for this problem, and while
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.
Citation
Published Version
Keyword
phylogenetic networks; hybridization; incomplete lineage sorting; coalescent; multi-labeled trees
Type
Journal article
Publisher
Citable link to this page
https://hdl.handle.net/1911/71341Rights
This is an author's peer-reviewed final manuscript, as accepted by the publisher.Metadata
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