10.5061/DRYAD.ZW3R2287M
Carruthers, Tom
Royal Botanic Gardens, Kew
Sun, Miao
Aarhus University
Baker, William
Royal Botanic Gardens, Kew
Smith, Stephen
University of Michigan–Ann Arbor
de Vos, Jurriaan
University of Basel
Eiserhardt, Wolf
Aarhus University
The implications of incongruence between gene tree and species tree
topologies for divergence time estimation
Dryad
dataset
2021
topological incongruence
gene trees
divergence time estimation
2022-03-30T00:00:00Z
2022-03-30T00:00:00Z
en
https://doi.org/10.5281/zenodo.6396398
https://doi.org/10.5281/zenodo.6396401
4891325 bytes
6
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Phylogenetic analyses are increasingly being performed with datasets 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 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 analysing 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 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.