The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation

Tom Carruthers; Miao Sun; William J. Baker; Stephen A. Smith; Jurriaan M. De Vos; Wolf L. Eiserhardt

doi:10.1093/sysbio/syac012

The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation

Tom Carruthers^*, Miao Sun, William J. Baker, Stephen A. Smith, Jurriaan M. De Vos, Wolf L. Eiserhardt

^*Corresponding author af dette arbejde

Institut for Biologi - Økoinformatik og biodiversitet

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

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Abstract

Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from the erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analyzing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with the species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation. [Divergence time estimation; gene trees; species tree; topological incongruence.]

Originalsprog	Engelsk
Tidsskrift	Systematic Biology
Vol/bind	71
Nummer	5
Sider (fra-til)	1124-1146
Antal sider	23
ISSN	1063-5157
DOI	https://doi.org/10.1093/sysbio/syac012
Status	Udgivet - sep. 2022

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10.1093/sysbio/syac012Licens: CC BY

syac012Forlagets udgivne version, 1,08 MBLicens: CC BY

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abstract = "Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from the erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analyzing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with the species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation. [Divergence time estimation; gene trees; species tree; topological incongruence.]",

author = "Tom Carruthers and Miao Sun and Baker, {William J.} and Smith, {Stephen A.} and {De Vos}, {Jurriaan M.} and Eiserhardt, {Wolf L.}",

note = "Publisher Copyright: {\textcopyright} 2022 The Author(s). Published by Oxford University Press on behalf of the Society of Systematic Biologists.",

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AU - Eiserhardt, Wolf L.

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AB - Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from the erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analyzing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with the species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation. [Divergence time estimation; gene trees; species tree; topological incongruence.]

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The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation

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