{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T23:16:18Z","timestamp":1774912578793,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,10,25]],"date-time":"2018-10-25T00:00:00Z","timestamp":1540425600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["RB: SFRH\/BD\/79850\/2011"],"award-info":[{"award-number":["RB: SFRH\/BD\/79850\/2011"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","award":["SFRH\/BD\/71041\/2010"],"award-info":[{"award-number":["SFRH\/BD\/71041\/2010"]}],"id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006753","name":"CMUP","doi-asserted-by":"publisher","award":["UID\/MAT\/00144\/2013"],"award-info":[{"award-number":["UID\/MAT\/00144\/2013"]}],"id":[{"id":"10.13039\/501100006753","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>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 \u03b4 statistic for evaluating the degree of phylogenetic signal between a phylogeny and categorical traits.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We validated \u03b4 as a measure of phylogenetic signal: the higher the \u03b4-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\u2019s specificity and sensitivity suggested that the \u03b4 approach should only be applied to 20 or more species. We have further tested the performance of \u03b4 in scenarios of branch length and topology uncertainty, unbiased and biased trait evolution and trait saturation. Our results showed that \u03b4 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 \u03b4 can successfully detect molecular signatures of phenotypic evolution. We conclude that \u03b4 represents a useful measure of phylogenetic signal since many phenotypes can only be measured in categories.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/mrborges23\/delta_statistic.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty800","type":"journal-article","created":{"date-parts":[[2018,10,25]],"date-time":"2018-10-25T03:23:21Z","timestamp":1540437801000},"page":"1862-1869","source":"Crossref","is-referenced-by-count":127,"title":["Measuring phylogenetic signal between categorical traits and phylogenies"],"prefix":"10.1093","volume":"35","author":[{"given":"Rui","family":"Borges","sequence":"first","affiliation":[{"name":"CIIMAR\/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leix\u00f5es, Matosinhos, Portugal"},{"name":"Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal"},{"name":"CMUP, Centre of Mathematics of the University of Porto, Porto, Portugal"}]},{"given":"Jo\u00e3o Paulo","family":"Machado","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leix\u00f5es, Matosinhos, Portugal"}]},{"given":"Cid\u00e1lia","family":"Gomes","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leix\u00f5es, Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3218-7001","authenticated-orcid":false,"given":"Ana Paula","family":"Rocha","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal"},{"name":"CMUP, Centre of Mathematics of the University of Porto, Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1328-1732","authenticated-orcid":false,"given":"Agostinho","family":"Antunes","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leix\u00f5es, Matosinhos, Portugal"},{"name":"Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2018,10,25]]},"reference":[{"key":"2023012810014264300_bty800-B1","first-page":"895","article-title":"A method for testing the assumption of phylogenetic independence in comparative data","volume":"1","author":"Abouheif","year":"1999","journal-title":"Evol. 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