A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation

Abstract

BackgroundBranching events in phylogenetic trees reflect bifurcating and/or multifurcating speciation and splitting events. In the presence of gene flow, a phylogeny cannot be described by a tree but is instead a directed acyclic graph known as a phylogenetic network. Both phylogenetic trees and networks are typically reconstructed using computational analysis of multi-locus sequence data. The advent of high-throughput sequencing technologies has brought about two main scalability challenges: (1) dataset size in terms of the number of taxa and (2) the evolutionary divergence of the taxa in a study. The impact of both dimensions of scale on phylogenetic tree inference has been well characterized by recent studies; in contrast, the scalability limits of phylogenetic network inference methods are largely unknown.ResultsIn this study, we quantify the performance of state-of-the-art phylogenetic network inference methods on large-scale datasets using empirical data sampled from natural mouse populations and a range of simulations using model phylogenies with a single reticulation. We find that, as in the case of phylogenetic tree inference, the performance of leading network inference methods is negatively impacted by both dimensions of dataset scale. In general, we found that topological accuracy degrades as the number of taxa increases; a similar effect was observed with increased sequence mutation rate. The most accurate methods were probabilistic inference methods which maximize either likelihood under coalescent-based models or pseudo-likelihood approximations to the model likelihood. The improved accuracy obtained with probabilistic inference methods comes at a computational cost in terms of runtime and main memory usage, which become prohibitive as dataset size grows past twenty-five taxa. None of the probabilistic methods completed analyses of datasets with 30 taxa or more after many weeks of CPU runtime.ConclusionsWe conclude that the state of the art of phylogenetic network inference lags well behind the scope of current phylogenomic studies. New algorithmic development is critically needed to address this methodological gap.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1277-1) contains supplementary material, which is available to authorized users.

Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l

“…These methods have been increasingly used in phylogenetic studies (e.g., Wen et al 2016;Copetti et al 2017;Morales-Briones et al 2018a;Crowl et al 2020). To date, however, species network inference is still computationally intensive and limited to a small number of species and a few hybridization events (Hejase and Liu 2016; but see Hejase et al 2018 andZhu et al 2019). Furthermore, studies evaluating the performance of different phylogenetic network inference approaches are scarce and restricted to simple hybridization scenarios.…”

Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting

“…22,50 The computational cost, particularly for likelihood methods, can become prohibitive quickly if the number of taxa grows to ~25 or more. 50 …”

Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization

“…Therefore this method cannot distinguish the correct network when other networks induce the same sets of rooted triples [128]. However, it is much more scalable than ML methods in terms of the number of taxa [46].…”

“…SNaQ is based on unrooted quartets, akin to the ASTRAL method for species tree inference [78]. It is even more scalable than InferNetwork MPL [46], but can only infer level-1 networks (Fig. 12).…”