To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

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With the increasing availability of whole genome data, many species trees are being constructed from hundreds to thousands of loci. Although concatenation analysis using maximum likelihood is a standard approach for estimating species trees, it does not account for gene tree heterogeneity, which can occur due to many biological processes, such as incomplete lineage sorting. Coalescent species tree estimation methods, many of which are statistically consistent in the presence of incomplete lineage sorting, include Bayesian methods that coestimate the gene trees and the species tree, summary methods that compute the species tree by combining estimated gene trees, and site-based methods that infer the species tree from site patterns in the alignments of different loci. Due to concerns that poor quality loci will reduce the accuracy of estimated species trees, many recent phylogenomic studies have removed or filtered genes on the basis of phylogenetic signal and/or missing data prior to inferring species trees; little is known about the performance of species tree estimation methods when gene filtering is performed. We examine how incomplete lineage sorting, phylogenetic signal of individual loci, and missing data affect the absolute and the relative accuracy of species tree estimation methods and show how these properties affect methods' responses to gene filtering strategies. In particular, summary methods (ASTRAL-II, ASTRID, and MP-EST), a site-based coalescent method (SVDquartets within PAUP*), and an unpartitioned concatenation analysis using maximum likelihood (RAxML) were evaluated on a heterogeneous collection of simulated multilocus data sets, and the following trends were observed. Filtering genes based on gene tree estimation error improved the accuracy of the summary methods when levels of incomplete lineage sorting were low to moderate but did not benefit the summary methods under higher levels of incomplete lineage sorting, unless gene tree estimation error was also extremely high (a model condition with few replicates). Neither SVDquartets nor concatenation analysis using RAxML benefited from filtering genes on the basis of gene tree estimation error. Finally, filtering genes based on missing data was either neutral (i.e., did not impact accuracy) or else reduced the accuracy of all five methods. By providing insight into the consequences of gene filtering, we offer recommendations for estimating species tree in the presence of incomplete lineage sorting and reconcile seemingly conflicting observations made in prior studies regarding the impact of gene filtering.

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