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

Diogo Ribeiro, Rui Borges, Ana Paula Rocha, Agostinho Antunes^*

^*Corresponding author for this work

School of Mathematics and Statistics

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Article number	btad433
Number of pages	3
Journal	Bioinformatics
Volume	39
Issue number	7
DOIs	https://doi.org/10.1093/bioinformatics/btad433
Publication status	Published - 27 Jul 2023

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Ribeiro_2023_Bioinformatics_Testing-phylogenetic-signal-categorical-traits_CC
© The Author(s) 2023. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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Cite this

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title = "Testing phylogenetic signal with categorical traits and tree uncertainty",

abstract = "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.",

author = "Diogo Ribeiro and Rui Borges and Rocha, {Ana Paula} and Agostinho Antunes",

note = "Funding: This work was supported by the Austrian Science Fund [P34524-B] to R.B.; partially supported by Centre of Mathematics of the University of Porto - Intelligent Systems Associate Laboratory (CMUP-LASI) through the Funda{\c c}{\~a}o para a Ci{\^e}ncia e a Tecnologia (FCT) project [UIDB/00144/2020] to A.P.R.; and the FCT projects UIDB/04423/2020, UIDP/04423/2020, PTDC/CTA-AMB/31774/2017 [POCI-01-0145-FEDER/031774/2017], and Atlantida [NORTE-01-0145-FEDER-000040] to A.A.",

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doi = "10.1093/bioinformatics/btad433",

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AU - Ribeiro, Diogo

AU - Borges, Rui

AU - Rocha, Ana Paula

AU - Antunes, Agostinho

N1 - Funding: This work was supported by the Austrian Science Fund [P34524-B] to R.B.; partially supported by Centre of Mathematics of the University of Porto - Intelligent Systems Associate Laboratory (CMUP-LASI) through the Fundação para a Ciência e a Tecnologia (FCT) project [UIDB/00144/2020] to A.P.R.; and the FCT projects UIDB/04423/2020, UIDP/04423/2020, PTDC/CTA-AMB/31774/2017 [POCI-01-0145-FEDER/031774/2017], and Atlantida [NORTE-01-0145-FEDER-000040] to A.A.

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AB - 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.

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DO - 10.1093/bioinformatics/btad433

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JO - Bioinformatics

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Testing phylogenetic signal with categorical traits and tree uncertainty

Abstract

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