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Title: Measuring phylogenetic signal between categorical traits and phylogenies

Abstract

Abstract Motivation Determining whether a trait and phylogeny share some degree of phylogenetic signal is a flagship goal in evolutionary biology. Signatures of phylogenetic signal can assist the resolution of a broad range of evolutionary questions regarding the tempo and mode of phenotypic evolution. However, despite the considerable number of strategies to measure it, few and limited approaches exist for categorical traits. Here, we used the concept of Shannon entropy and propose the δ statistic for evaluating the degree of phylogenetic signal between a phylogeny and categorical traits. Results We validated δ as a measure of phylogenetic signal: the higher the δ-value the higher the degree of phylogenetic signal between a given tree and a trait. Based on simulated data we proposed a threshold-based classification test to pinpoint cases of phylogenetic signal. The assessment of the test’s specificity and sensitivity suggested that the δ approach should only be applied to 20 or more species. We have further tested the performance of δ in scenarios of branch length and topology uncertainty, unbiased and biased trait evolution and trait saturation. Our results showed that δ may be applied in a wide range of phylogenetic contexts. Finally, we investigated our method in 14more » 360 mammalian gene trees and found that olfactory receptor genes are significantly associated with the mammalian activity patterns, a result that is congruent with expectations and experiments from the literature. Our application shows that δ can successfully detect molecular signatures of phenotypic evolution. We conclude that δ represents a useful measure of phylogenetic signal since many phenotypes can only be measured in categories. Availability and implementation https://github.com/mrborges23/delta_statistic. Supplementary information Supplementary data are available at Bioinformatics online.« less

Authors:
 [1];  [2];  [2]; ORCiD logo [3]; ORCiD logo [4];
  1. CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal, Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal, CMUP, Centre of Mathematics of the University of Porto, Porto, Portugal
  2. CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal
  3. Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal, CMUP, Centre of Mathematics of the University of Porto, Porto, Portugal
  4. CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal, Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal
Publication Date:
Sponsoring Org.:
USDOE Office of Nuclear Energy (NE), Nuclear Fuel Cycle and Supply Chain; USDOE Office of Nuclear Energy (NE), Fuel Cycle Technologies (NE-5)
OSTI Identifier:
1524121
Alternate Identifier(s):
OSTI ID: 1480148
Grant/Contract Number:  
RB: SFRH/BD/79850/2011; SFRH/BD/71041/2010; CG: SFRH/BD/71041/2010; PTDC/AAG-GLO/6887/2014; POCI-01-0124-FEDER-016845
Resource Type:
Published Article
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Name: Bioinformatics Journal Volume: 35 Journal Issue: 11; Journal ID: ISSN 1367-4803
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Borges, Rui, Machado, João Paulo, Gomes, Cidália, Rocha, Ana Paula, Antunes, Agostinho, and Hancock, ed., John. Measuring phylogenetic signal between categorical traits and phylogenies. United Kingdom: N. p., 2018. Web. doi:10.1093/bioinformatics/bty800.
Borges, Rui, Machado, João Paulo, Gomes, Cidália, Rocha, Ana Paula, Antunes, Agostinho, & Hancock, ed., John. Measuring phylogenetic signal between categorical traits and phylogenies. United Kingdom. doi:10.1093/bioinformatics/bty800.
Borges, Rui, Machado, João Paulo, Gomes, Cidália, Rocha, Ana Paula, Antunes, Agostinho, and Hancock, ed., John. Thu . "Measuring phylogenetic signal between categorical traits and phylogenies". United Kingdom. doi:10.1093/bioinformatics/bty800.
@article{osti_1524121,
title = {Measuring phylogenetic signal between categorical traits and phylogenies},
author = {Borges, Rui and Machado, João Paulo and Gomes, Cidália and Rocha, Ana Paula and Antunes, Agostinho and Hancock, ed., John},
abstractNote = {Abstract Motivation Determining whether a trait and phylogeny share some degree of phylogenetic signal is a flagship goal in evolutionary biology. Signatures of phylogenetic signal can assist the resolution of a broad range of evolutionary questions regarding the tempo and mode of phenotypic evolution. However, despite the considerable number of strategies to measure it, few and limited approaches exist for categorical traits. Here, we used the concept of Shannon entropy and propose the δ statistic for evaluating the degree of phylogenetic signal between a phylogeny and categorical traits. Results We validated δ as a measure of phylogenetic signal: the higher the δ-value the higher the degree of phylogenetic signal between a given tree and a trait. Based on simulated data we proposed a threshold-based classification test to pinpoint cases of phylogenetic signal. The assessment of the test’s specificity and sensitivity suggested that the δ approach should only be applied to 20 or more species. We have further tested the performance of δ in scenarios of branch length and topology uncertainty, unbiased and biased trait evolution and trait saturation. Our results showed that δ may be applied in a wide range of phylogenetic contexts. Finally, we investigated our method in 14 360 mammalian gene trees and found that olfactory receptor genes are significantly associated with the mammalian activity patterns, a result that is congruent with expectations and experiments from the literature. Our application shows that δ can successfully detect molecular signatures of phenotypic evolution. We conclude that δ represents a useful measure of phylogenetic signal since many phenotypes can only be measured in categories. Availability and implementation https://github.com/mrborges23/delta_statistic. Supplementary information Supplementary data are available at Bioinformatics online.},
doi = {10.1093/bioinformatics/bty800},
journal = {Bioinformatics},
number = 11,
volume = 35,
place = {United Kingdom},
year = {2018},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1093/bioinformatics/bty800

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Cited by: 5 works
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