Testing phylogenetic signal with categorical traits and tree uncertainty

Diogo Ribeiro; Rui Borges; Ana Paula Rocha; Agostinho Antunes

doi:10.1093/bioinformatics/btad433

Testing phylogenetic signal with categorical traits and tree uncertainty

Bioinformatics. 2023 Jul 1;39(7):btad433. doi: 10.1093/bioinformatics/btad433.

Authors

Diogo Ribeiro^{1

2}, Rui Borges³, Ana Paula Rocha^{4

5}, Agostinho Antunes^{1

2}

Affiliations

¹ CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Porto, Portugal.
² Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
³ Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
⁴ CMUP, Centre of Mathematics of the University of Porto, 4169-007 Porto, Portugal.
⁵ Department of Mathematics, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.

Abstract

Summary: The phylogenetic signal, frequently used to identify signatures of adaptive evolution or important associations between genes and phenotypes, measures the tendency for recently diverged species to resemble each other more than distantly related species. An example of such a measure is the δ statistic, which uses Shannon entropy to measure the degree of phylogenetic signal between a categorical trait and a phylogeny. In this study, we refined this statistic to account for tree uncertainty, resulting in more accurate assessments of phylogenetic associations. In addition, we provided a more accessible and computationally efficient implementation of the δ statistic that will facilitate its use by the evolutionary community.

Availability and implementation: github.com/diogo-s-ribeiro/delta-statistic.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Phenotype
Phylogeny*
Uncertainty