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João Paulo Machado

dblp:242/5302 · DBLP profile ↗
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1ranked-venue papers
0as first author
0since 2021 · last 2019
0000-0002-7404-9670ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
phylogenetics
0.412019
Measuring phylogenetic signal between categorical traits and phylogenies · Bioinform. 2019
Bioinformatics and computational biology › phylogenetics › phylogenetic comparative methods
phylogenetic signal
0.412019
Measuring phylogenetic signal between categorical traits and phylogenies · Bioinform. 2019
Bioinformatics and computational biology
evolutionary biology
0.112019
Measuring phylogenetic signal between categorical traits and phylogenies · Bioinform. 2019

Methods — techniques the papers use, named apart from their topics

threshold-based classification test · 0.4simulation · 0.4shannon entropy · 0.4
YearPublicationVenuePosition
2019 Measuring phylogenetic signal between categorical traits and phylogenies
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.
Rui Borges, João Paulo Machado, Cidália Gomes, Ana Paula Rocha 0002, Agostinho Antunes
Bioinform.2