Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs

Abstract

Many recent phylogenetic methods have focused on accurately inferring species trees when there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of these methods, and for phylogenetic methods in general, the data for each locus is assumed to consist of orthologous, single-copy sequences. Loci that are present in more than a single copy in any of the studied genomes are excluded from the data. These steps greatly reduce the number of loci available for analysis. The question we seek to answer in this study is: What happens if one runs such species tree inference methods on data where paralogy is present, in addition to or without ILS being present? Through simulation studies and analyses of two large biological data sets, we show that running such methods on data with paralogs can still provide accurate results. We use multiple different methods, some of which are based directly on the multispecies coalescent (MSC) model, and some of which have been proven to be statistically consistent under it. We also treat the paralogous loci in multiple ways: from explicitly denoting them as paralogs, to randomly selecting one copy per species. In all cases the inferred species trees are as accurate as equivalent analyses using single-copy orthologs. Our results have significant implications for the use of ILS-aware phylogenomic analyses, demonstrating that they do not have to be restricted to single-copy loci. This will greatly increase the amount of data that can be used for phylogenetic inference.

Early diversification and karyotype evolution of flowering plants

“…First, the highly collinear and orthologous genes with all copies retained after WGD or WGT can be extracted across representative genomes for phylogenetic analyses. These genes may be superior to other homologs for phylogenetic constructions, for example, the single-copy or clustering-identi ed homologous genes [14][15][16][17]19 , for which paralogs with heterogeneous evolution after polyploidization may be randomly retained and ILS was modeled to occur more frequently during such phylogenetic analyses 23 .…”

<strong></strong> Recent Progress on Methods for Estimating and Updating Large Phylogenies

“…Yet there are other summary methods that may be competitive with ASTRAL for accuracy, and some of these are also fast. For example, ASTRID (which is much faster than ASTRAL) is sometimes more accurate than ASTRAL and sometimes less accurate, and it is not clear what the conditions are where each should be used (e.g., see Yan et al (2021)). Another method that is promising is wQFM (Mahbub et al, 2021), which uses a different technique to combine quartet trees and may provide better accuracy than ASTRAL (albeit at a computational cost).…”

“…Other methods that can estimate species trees from a set of MUL-trees have been developed, with gene tree parsimony the most well known (e.g., DupTree (Wehe et al, 2008)), but also including MixTrEm-DLRS (Ullah et al, 2015), MulRF (Chaudhary et al, 2015), FastMulRFS (Molloy and Warnow, 2020), and SpeciesRax (Morel et al, 2021). While not all of them have been compared to ASTRAL-Pro, those that have been evaluated have not been shown to be as reliably accurate as ASTRAL-Pro (Yan et al, 2021).…”

How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

“…If duplicated non-homologous sequences are not differentiated into their orthologous pairs, the orthology assumption for phylogenetic reconstruction is violated. Alignments that consist of paralogous sequences may lead to biased phylogenetic inference (Fitch, 1970;Gabaldón, 2008;Yang and Smith, 2014) or not (Yan et al, 2021). The best practice to account for paralogy in phylogenetic reconstruction is under debate.…”

“…The best practice to account for paralogy in phylogenetic reconstruction is under debate. Four strategies can be followed: (1) deleting paralogous loci from the analysis (Jones et al, 2019;Larridon et al, 2020); (2) retrieving both ortho-and paralogous copies of the loci without separating them into different alignments and proceeding with a gene duplication-aware species tree method (Zhang et al, 2020a); (3) retrieving both ortho-and paralogous copies without separating them into different alignments and proceeding with an ILS-aware species tree method (Yan et al, 2021); and (4) retrieving all copies, both ortho-and paralogous, and creating orthologous alignments, from which gene trees are inferred, before building the species tree (Gizaw et al, 2021;this study).…”