Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

Abstract

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.

Avian introgression in the genomic era

“…Some methods for constructing phylogenetic networks allow for hybridization while ignoring incomplete lineage sorting (Beiko and Hamilton 2006), whereas other methods take into account incomplete lineage sorting while ignoring hybridization (Maddison and Knowles 2006; Than and Nakhleh 2009). New methods are being developed to reconstruct phylogenetic networks taking both incomplete lineage sorting and hybridization into account (Joly et al 2009;Kubatko 2009;Meng and Kubatko 2009;Yu et al 2013;Wen et al 2016). This network approach has not been applied to avian genomic data yet, but promises to be a fruitful strategy for the detection of introgression.…”

Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks

“…It is precisely the structure on tree space and the efficient computation of a so-called tree neighbourhood that the above-mentioned tree reconstruction methods take advantage of in order to search tree space. To date, the only available metric that induces some structure on the space of phylogenetic networks and that can therefore be used to traverse phylogenetic network space in search of an optimal (rooted) phylogenetic network is rather ad hoc and based on a search that works in layers from trees to networks of increasing complexity (Yu et al, 2013(Yu et al, , 2014. Indeed, the mathematical properties of this search (e.g.…”

Maximum likelihood inference of reticulate evolutionary histories

“…To the best of our knowledge, the first method to conduct a search of the phylogenetic network space in search of optimal phylogenies is described in a study by our group (18). However, this method is based on the maximum parsimony criterion: It seeks a phylogenetic network that minimizes the number of "extra lineages" resulting from embedding the set of gene tree topologies within its branches.…”