The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation.
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Resource type
Journal article
Date published
September 1, 2022
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.]
Contributor (person)
Alfaro, Michael
Project(s)
Plant and Fungal Tree of Life
Funder
| Funder name | Awards |
Aarhus Universitets Forskningsfond, Denmark | Grant AUFF-E 2017-7-19 |
David and Claudia Harding Foundation | Harding Alpine Programme |
Calleva Foundation, United Kingdom | Plant and Fungal Trees of Life Project |
Villum Fonden, Denmark | Research grant 00025354 |
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Switzerland | Grant 310030_185251 |
Journal title
Systematic Biology
Volume
71
Issue
5
Publisher
Oxford University Press (OUP)
Place of publication
Oxford, UK
ISSN
1063-5157
eISSN
1076-836X
Date accepted
February 8, 2022
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In Copyright
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