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No substitute for real data: A cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses

The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth–death polytomy resolver is a method of accounting for phylogenetic uncertainty that places missing (uns... Full description

Journal Title: Evolution 2015, Vol.69 (12), p.3207-3216
Main Author: Rabosky, Daniel L.
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: United States: Blackwell Publishing Ltd
ID: ISSN: 0014-3820
Link: https://www.ncbi.nlm.nih.gov/pubmed/26552857
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title: No substitute for real data: A cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses
format: Article
creator:
  • Rabosky, Daniel L.
subjects:
  • Analysis
  • Animals
  • Bayesian
  • Bayesian statistical decision theory
  • Biogeography
  • Biological Evolution
  • Biological taxonomies
  • Birds
  • Birds - classification
  • BRIEF COMMUNICATIONS
  • Classification - methods
  • Datasets
  • diversification
  • Estimated taxes
  • Estimation bias
  • Evolution
  • Evolutionary biology
  • Genotype & phenotype
  • Mammals
  • Mammals - classification
  • Modeling
  • Models, Biological
  • phenotypic evolution comparative methods
  • Phenotypic plasticity
  • Phenotypic traits
  • phylogenetic uncertainty
  • Phylogenetics
  • Phylogeny
  • Population biology
  • Taxa
  • Usage
ispartof: Evolution, 2015, Vol.69 (12), p.3207-3216
description: The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth–death polytomy resolver is a method of accounting for phylogenetic uncertainty that places missing (unsampled) taxa onto phylogenetic trees, using taxonomic information alone. Recent studies of birds and mammals have used this approach to generate pseudoposterior distributions of phylogenetic trees that are complete at the species level, even in the absence of genetic data for many species. Many researchers have used these distributions of phylogenies for downstream evolutionary analyses that involve inferences on phenotypic evolution, geography, and community assembly. I demonstrate that the use of phylogenies constructed in this fashion is inappropriate for many questions involving traits. Because species are placed on trees at random with respect to trait values, the birth–death polytomy resolver breaks down natural patterns of trait phylogenetic structure. Inferences based on these trees are predictably and often drastically biased in a direction that depends on the underlying (true) pattern of phylogenetic structure in traits. I illustrate the severity of the phenomenon for both continuous and discrete traits using examples from a global bird phylogeny.
language: eng
source:
identifier: ISSN: 0014-3820
fulltext: no_fulltext
issn:
  • 0014-3820
  • 1558-5646
url: Link


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titleNo substitute for real data: A cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses
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descriptionThe statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth–death polytomy resolver is a method of accounting for phylogenetic uncertainty that places missing (unsampled) taxa onto phylogenetic trees, using taxonomic information alone. Recent studies of birds and mammals have used this approach to generate pseudoposterior distributions of phylogenetic trees that are complete at the species level, even in the absence of genetic data for many species. Many researchers have used these distributions of phylogenies for downstream evolutionary analyses that involve inferences on phenotypic evolution, geography, and community assembly. I demonstrate that the use of phylogenies constructed in this fashion is inappropriate for many questions involving traits. Because species are placed on trees at random with respect to trait values, the birth–death polytomy resolver breaks down natural patterns of trait phylogenetic structure. Inferences based on these trees are predictably and often drastically biased in a direction that depends on the underlying (true) pattern of phylogenetic structure in traits. I illustrate the severity of the phenomenon for both continuous and discrete traits using examples from a global bird phylogeny.
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subjectAnalysis ; Animals ; Bayesian ; Bayesian statistical decision theory ; Biogeography ; Biological Evolution ; Biological taxonomies ; Birds ; Birds - classification ; BRIEF COMMUNICATIONS ; Classification - methods ; Datasets ; diversification ; Estimated taxes ; Estimation bias ; Evolution ; Evolutionary biology ; Genotype & phenotype ; Mammals ; Mammals - classification ; Modeling ; Models, Biological ; phenotypic evolution comparative methods ; Phenotypic plasticity ; Phenotypic traits ; phylogenetic uncertainty ; Phylogenetics ; Phylogeny ; Population biology ; Taxa ; Usage
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abstractThe statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth–death polytomy resolver is a method of accounting for phylogenetic uncertainty that places missing (unsampled) taxa onto phylogenetic trees, using taxonomic information alone. Recent studies of birds and mammals have used this approach to generate pseudoposterior distributions of phylogenetic trees that are complete at the species level, even in the absence of genetic data for many species. Many researchers have used these distributions of phylogenies for downstream evolutionary analyses that involve inferences on phenotypic evolution, geography, and community assembly. I demonstrate that the use of phylogenies constructed in this fashion is inappropriate for many questions involving traits. Because species are placed on trees at random with respect to trait values, the birth–death polytomy resolver breaks down natural patterns of trait phylogenetic structure. Inferences based on these trees are predictably and often drastically biased in a direction that depends on the underlying (true) pattern of phylogenetic structure in traits. I illustrate the severity of the phenomenon for both continuous and discrete traits using examples from a global bird phylogeny.
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pmid26552857
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