Abstract
Original language | English (US) |
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Pages (from-to) | 994-1005 |
Number of pages | 12 |
Journal | Methods in Ecology and Evolution |
Volume | 9 |
Issue number | 4 |
DOIs | |
State | Published - 2018 |
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In: Methods in Ecology and Evolution, Vol. 9, No. 4, 2018, p. 994-1005.
Research output: Contribution to journal › Research Article › peer-review
TY - JOUR
T1 - Comparing evolutionary rates between trees, clades and traits
AU - Revell, L.J.
AU - González-Valenzuela, L.E.
AU - Alfonso, A.
AU - Castellanos-García, L.A.
AU - Guarnizo, C.E.
AU - Crawford, A.J.
N1 - Export Date: 17 April 2018 Correspondence Address: Revell, L.J.; Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del RosarioColombia; email: [email protected] Funding details: 120456934310, COLCIENCIAS, Departamento Administrativo de Ciencia, Tecnología e Innovación Funding details: BSF, United States-Israel Binational Science Foundation Funding details: 1350474, DEB, Division of Environmental Biology Funding details: DEB 1350474, BSF, United States-Israel Binational Science Foundation Funding text: Departamento Administrativo de Ciencia, Tecnología e Innovación, Grant/Award Number: 120456934310; United States National Science Foundation, Division of Environmental Biology, Grant/Award Number: 1350474 Funding text: The authors thank the United States National Science Foundation (DEB 1350474 to L.J.R.) and Colombia’s Departamento Administrativo de Ciencia, Tecnología e Innovación (Colciencias), Programa Nacional en Ciencias Básicas (award number 120456934310 to A.J.C.) for supporting portions of this research. The majority of this research was undertaken by L.J.R. during a sabbatical at the Universidad de los Andes in Bogotá, Colombia. 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PY - 2018
Y1 - 2018
N2 - The tempo of evolutionary change through time is among the most heavily studied dimensions of macroevolution using phylogenies. Here, we present a simple, likelihood-based method for comparing the rate of phenotypic evolution for continuous characters between trees. Our method is derived from a previous approach published by Brian O'Meara and colleagues in 2006. We examine the statistical performance of the method and find that it suffers from the typical downward bias expected for maximum likelihood estimates of the variance, but only for very small trees. We find that evolutionary rates are estimated with minimal bias for trees of even relatively modest size. We also find that type I error rates based on a likelihood-ratio test are minimally elevated above the nominal level, even for small phylogenies. The type I error rate can be reduced to a level at or below its nominal value by substituting a test-statistic distribution obtained via simulation under the null hypothesis of no difference in evolutionary rate among trees. We discuss the consequences of failing to account for uncertainty in the estimation of species means or in the phylogeny, and describe strategies for taking this uncertainty into consideration during estimation. We also identify how our approach is related to previous methods for comparing the rate of evolution among different clades of a single tree or between different phenotypic traits. Finally, we describe how the method can be applied to different evolutionary models and to discrete characters—options that are already implemented in software. Evolutionary biologists continue to be intrigued by changes in the tempo of phenotypic evolution across the tree of life. The method described herein should be useful for contexts in which changes in the evolutionary rate or process between two or more clades of distant or unknown relationship are of interest. © 2018 The Authors. Methods in Ecology and Evolution © 2018 British Ecological Society
AB - The tempo of evolutionary change through time is among the most heavily studied dimensions of macroevolution using phylogenies. Here, we present a simple, likelihood-based method for comparing the rate of phenotypic evolution for continuous characters between trees. Our method is derived from a previous approach published by Brian O'Meara and colleagues in 2006. We examine the statistical performance of the method and find that it suffers from the typical downward bias expected for maximum likelihood estimates of the variance, but only for very small trees. We find that evolutionary rates are estimated with minimal bias for trees of even relatively modest size. We also find that type I error rates based on a likelihood-ratio test are minimally elevated above the nominal level, even for small phylogenies. The type I error rate can be reduced to a level at or below its nominal value by substituting a test-statistic distribution obtained via simulation under the null hypothesis of no difference in evolutionary rate among trees. We discuss the consequences of failing to account for uncertainty in the estimation of species means or in the phylogeny, and describe strategies for taking this uncertainty into consideration during estimation. We also identify how our approach is related to previous methods for comparing the rate of evolution among different clades of a single tree or between different phenotypic traits. Finally, we describe how the method can be applied to different evolutionary models and to discrete characters—options that are already implemented in software. Evolutionary biologists continue to be intrigued by changes in the tempo of phenotypic evolution across the tree of life. The method described herein should be useful for contexts in which changes in the evolutionary rate or process between two or more clades of distant or unknown relationship are of interest. © 2018 The Authors. Methods in Ecology and Evolution © 2018 British Ecological Society
U2 - 10.1111/2041-210X.12977
DO - 10.1111/2041-210X.12977
M3 - Research Article
SN - 2041-210X
VL - 9
SP - 994
EP - 1005
JO - Methods in Ecology and Evolution
JF - Methods in Ecology and Evolution
IS - 4
ER -