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Comparing Evolutionary Rates for Different Phenotypic Traits on a Phylogeny Using Likelihood

In recent years, likelihood-based approaches have been used with increasing frequency to evaluate macroevolutionary hypotheses of phenotypic evolution under distinct evolutionary processes in a phylogenetic context (e.g., Brownian motion, Ornstein-Uhlenbeck, etc.), and to compare one or more evoluti... Full description

Journal Title: Systematic biology 2013-03-01, Vol.62 (2), p.181-192
Main Author: Adams, Dean C
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: England: Oxford University Press
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/23024153
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recordid: cdi_proquest_miscellaneous_1285467349
title: Comparing Evolutionary Rates for Different Phenotypic Traits on a Phylogeny Using Likelihood
format: Article
creator:
  • Adams, Dean C
subjects:
  • Animals
  • Biological Evolution
  • Biological taxonomies
  • Causal covariation
  • Covariance matrices
  • Evolution
  • Evolutionary biology
  • Forelimbs
  • Genotype & phenotype
  • Models, Statistical
  • Phenotype
  • Phenotypic traits
  • Phylogenetics
  • Phylogeny
  • Salamanders
  • Simulation
  • Systematic biology
  • Urodela - classification
  • Urodela - physiology
ispartof: Systematic biology, 2013-03-01, Vol.62 (2), p.181-192
description: In recent years, likelihood-based approaches have been used with increasing frequency to evaluate macroevolutionary hypotheses of phenotypic evolution under distinct evolutionary processes in a phylogenetic context (e.g., Brownian motion, Ornstein-Uhlenbeck, etc.), and to compare one or more evolutionary rates for the same phenotypic trait along a phylogeny. It is also of interest to determine whether one trait evolves at a faster rate than another trait. However, to date no study has compared phylogenetic evolutionary rates between traits using likelihood, because a formal approach has not yet been proposed. In this article, I describe a new likelihood procedure for comparing evolutionary rates for two or more phenotypic traits on a phylogeny. This approach compares the likelihood of a model where each trait evolves at a distinct evolutionary rate to the likelihood of a model where all traits are constrained to evolve at a common evolutionary rate. The method can also account for within-species measurement error and within-species trait covariation if available. Simulations revealed that the method has appropriate Type I error rates and statistical power. Importantly, when compared with existing approaches based on phylogenetically independent contrasts and methods that compare confidence intervals for model parameters, the likelihood method displays preferable statistical properties for a wide range of simulated conditions. Thus, this likelihood-based method extends the phylogenetic comparative biology toolkit and provides evolutionary biologists with a more powerful means of determining when evolutionary rates differ between phenotypic traits. Finally, I provide an empirical example illustrating the approach by comparing rates of evolution for several phenotypic traits in Plethodon salamanders.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


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descriptionIn recent years, likelihood-based approaches have been used with increasing frequency to evaluate macroevolutionary hypotheses of phenotypic evolution under distinct evolutionary processes in a phylogenetic context (e.g., Brownian motion, Ornstein-Uhlenbeck, etc.), and to compare one or more evolutionary rates for the same phenotypic trait along a phylogeny. It is also of interest to determine whether one trait evolves at a faster rate than another trait. However, to date no study has compared phylogenetic evolutionary rates between traits using likelihood, because a formal approach has not yet been proposed. In this article, I describe a new likelihood procedure for comparing evolutionary rates for two or more phenotypic traits on a phylogeny. This approach compares the likelihood of a model where each trait evolves at a distinct evolutionary rate to the likelihood of a model where all traits are constrained to evolve at a common evolutionary rate. The method can also account for within-species measurement error and within-species trait covariation if available. Simulations revealed that the method has appropriate Type I error rates and statistical power. Importantly, when compared with existing approaches based on phylogenetically independent contrasts and methods that compare confidence intervals for model parameters, the likelihood method displays preferable statistical properties for a wide range of simulated conditions. Thus, this likelihood-based method extends the phylogenetic comparative biology toolkit and provides evolutionary biologists with a more powerful means of determining when evolutionary rates differ between phenotypic traits. Finally, I provide an empirical example illustrating the approach by comparing rates of evolution for several phenotypic traits in Plethodon salamanders.
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subjectAnimals ; Biological Evolution ; Biological taxonomies ; Causal covariation ; Covariance matrices ; Evolution ; Evolutionary biology ; Forelimbs ; Genotype & phenotype ; Models, Statistical ; Phenotype ; Phenotypic traits ; Phylogenetics ; Phylogeny ; Salamanders ; Simulation ; Systematic biology ; Urodela - classification ; Urodela - physiology
ispartofSystematic biology, 2013-03-01, Vol.62 (2), p.181-192
rightsThe Author(s) 2012. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2012
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abstractIn recent years, likelihood-based approaches have been used with increasing frequency to evaluate macroevolutionary hypotheses of phenotypic evolution under distinct evolutionary processes in a phylogenetic context (e.g., Brownian motion, Ornstein-Uhlenbeck, etc.), and to compare one or more evolutionary rates for the same phenotypic trait along a phylogeny. It is also of interest to determine whether one trait evolves at a faster rate than another trait. However, to date no study has compared phylogenetic evolutionary rates between traits using likelihood, because a formal approach has not yet been proposed. In this article, I describe a new likelihood procedure for comparing evolutionary rates for two or more phenotypic traits on a phylogeny. This approach compares the likelihood of a model where each trait evolves at a distinct evolutionary rate to the likelihood of a model where all traits are constrained to evolve at a common evolutionary rate. The method can also account for within-species measurement error and within-species trait covariation if available. Simulations revealed that the method has appropriate Type I error rates and statistical power. Importantly, when compared with existing approaches based on phylogenetically independent contrasts and methods that compare confidence intervals for model parameters, the likelihood method displays preferable statistical properties for a wide range of simulated conditions. Thus, this likelihood-based method extends the phylogenetic comparative biology toolkit and provides evolutionary biologists with a more powerful means of determining when evolutionary rates differ between phenotypic traits. Finally, I provide an empirical example illustrating the approach by comparing rates of evolution for several phenotypic traits in Plethodon salamanders.
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pmid23024153
doi10.1093/sysbio/sys083
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