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Interesting study of the performance of phylogenetic models for gene expression evolution, although they seem to have only investigated single-optimum OU models, which IMO limits conclusions on datasets with orthologs and paralogs. (Indeed they find poor performance for our 2016 dataset testing the ortholog conjucture.)
https://www.biorxiv.org/content/10.1101/2023.02.09.527893v2
#phylogeny #GeneExpression #MolecularEvolution #bioinformatics #phylogenetics
bioRxiv · Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression EvolutionPhylogenetic comparative methods are increasingly used to test hypotheses about the evolutionary processes that drive divergence in gene expression among species. However, it is unknown whether the distributional assumptions of phylogenetic models designed for quantitative phenotypic traits are realistic for expression data and importantly, the reliability of conclusions of phylogenetic comparative studies of gene expression may depend on whether the data is well-described by the chosen model. To evaluate this, we first fit several phylogenetic models of trait evolution to 8 previously published comparative expression datasets, comprising a total of 54,774 genes with 145,927 unique gene-tissue combinations. Using a previously developed approach, we then assessed how well the best model of the set described the data in an absolute (not just relative) sense. First, we find that Ornstein-Uhlenbeck models, in which expression values are constrained around an optimum, were the preferred model for 66% of gene-tissue combinations. Second, we find that for 61% of gene-tissue combinations, the best fit model of the set was found to perform well; the rest were found to be performing poorly by at least one of the test statistics we examined. Third, we find that when simple models do not perform well, this appears to be typically a consequence of failing to fully account for heterogeneity in the rate of the evolution. We advocate that assessment of model performance should become a routine component of phylogenetic comparative expression studies; doing so can improve the reliability of inferences and inspire the development of novel models.
### Competing Interest Statement
The authors have declared no competing interest.