Special care is needed in applying phylogenetic comparative methods to gene trees with speciation and duplication nodes.

Details

Serval ID
serval:BIB_C4CAC6CE8CD6
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Special care is needed in applying phylogenetic comparative methods to gene trees with speciation and duplication nodes.
Journal
Molecular biology and evolution
Author(s)
Begum T., Robinson-Rechavi M.
ISSN
1537-1719 (Electronic)
ISSN-L
0737-4038
Publication state
In Press
Peer-reviewed
Oui
Language
english
Notes
Publication types: Journal Article
Publication Status: aheadofprint
Abstract
How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, since genes, like species, are phylogenetically related. Phylogenetic comparative methods should be used to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the "ortholog conjecture", the hypothesis that functional evolution is faster in paralogs than in orthologs. Whereas pairwise comparisons of tissue specificity (τ) provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue-specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows successful use of phylogenetic methods to study the evolution of gene function, and provides some support for the ortholog conjecture using three different phylogenetic approaches.
Keywords
Brownian, Ornstein-Uhlenbeck, gene expression, ortholog, paralog, phylogenetic comparative methods
Pubmed
Open Access
Yes
Create date
16/11/2020 14:39
Last modification date
20/11/2020 6:26
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