Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited

In 1973, the statistician Francis Anscombe used a clever set of bivariate datasets (now known as Anscombe's quartet) to illustrate the importance of graphing data as a component of statistical analyses. In his example, each of the four datasets yielded identical regression coefficients and mode...

Full description

Autores:
Revell, Liam J.
Schliep, Klaus
Valderrama, Eugenio
Richardson, James E.
Tipo de recurso:
Article of journal
Fecha de publicación:
2020
Institución:
Universidad El Bosque
Repositorio:
Repositorio U. El Bosque
Idioma:
eng
OAI Identifier:
oai:repositorio.unbosque.edu.co:20.500.12495/3625
Acceso en línea:
http://hdl.handle.net/20.500.12495/3625
https://doi.org/10.1111/2041-210X.13067
https://repositorio.unbosque.edu.co
Palabra clave:
Comparative methods
Macroevolution
Phylogeny
Plotting
Visualization
Rights
openAccess
License
Acceso abierto
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dc.title.spa.fl_str_mv Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited
dc.title.translated.spa.fl_str_mv Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited
title Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited
spellingShingle Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited
Comparative methods
Macroevolution
Phylogeny
Plotting
Visualization
title_short Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited
title_full Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited
title_fullStr Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited
title_full_unstemmed Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited
title_sort Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited
dc.creator.fl_str_mv Revell, Liam J.
Schliep, Klaus
Valderrama, Eugenio
Richardson, James E.
dc.contributor.author.none.fl_str_mv Revell, Liam J.
Schliep, Klaus
Valderrama, Eugenio
Richardson, James E.
dc.subject.keywords.spa.fl_str_mv Comparative methods
Macroevolution
Phylogeny
Plotting
Visualization
topic Comparative methods
Macroevolution
Phylogeny
Plotting
Visualization
description In 1973, the statistician Francis Anscombe used a clever set of bivariate datasets (now known as Anscombe's quartet) to illustrate the importance of graphing data as a component of statistical analyses. In his example, each of the four datasets yielded identical regression coefficients and model fits, and yet when visualized revealed strikingly different patterns of covariation between x and y. Phylogenetic comparative methods (the set of methodologies that use phylogenies, often combined with phenotypic trait data, to make inferences about evolution) are statistical methods too; yet visualizing the data and phylogeny in a sensible way that would permit us to detect unexpected patterns or unanticipated deviations from model assumptions is not a routine component of phylogenetic comparative analyses. Here, we use a quartet of phylogenetic datasets to illustrate that the same estimated parameters and model fits can be obtained from data that were generated using markedly different procedures—including pure Brownian motion evolution and randomly selected data uncorrelated with the tree. Just as in the case of Anscombe's quartet, when graphed the differences between the four datasets are quickly revealed. The intent of this article is to help build the general case that phylogenetic comparative methods are statistical methods and consequently that graphing or visualization should invariably be included as an essential step in our standard data analytical pipelines. Phylogenies are complex data structures and thus visualizing data on trees in a meaningful and useful way is a challenging endeavour. We recommend that the development of graphical methods for simultaneously visualizing data and tree should continue to be an important goal in phylogenetic comparative biology.
publishDate 2020
dc.date.accessioned.none.fl_str_mv 2020-07-30T17:15:53Z
dc.date.available.none.fl_str_mv 2020-07-30T17:15:53Z
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dc.identifier.issn.none.fl_str_mv 2041-210X
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dc.identifier.doi.none.fl_str_mv https://doi.org/10.1111/2041-210X.13067
dc.identifier.instname.spa.fl_str_mv instname:Universidad El Bosque
dc.identifier.reponame.spa.fl_str_mv reponame:Repositorio Institucional Universidad El Bosque
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https://doi.org/10.1111/2041-210X.13067
https://repositorio.unbosque.edu.co
dc.language.iso.none.fl_str_mv eng
language eng
dc.relation.ispartofseries.spa.fl_str_mv Methods in Ecology and Evolution, 2041-210X, Vol 9, Nro. 10, 2018, p. 2145-2154
dc.relation.uri.none.fl_str_mv https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13067
dc.rights.local.spa.fl_str_mv Acceso abierto
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eu_rights_str_mv openAccess
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dc.publisher.spa.fl_str_mv Wiley
dc.publisher.journal.spa.fl_str_mv Methods in Ecology and Evolution
institution Universidad El Bosque
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spelling Revell, Liam J.Schliep, KlausValderrama, EugenioRichardson, James E.2020-07-30T17:15:53Z2020-07-30T17:15:53Z2041-210Xhttp://hdl.handle.net/20.500.12495/3625https://doi.org/10.1111/2041-210X.13067instname:Universidad El Bosquereponame:Repositorio Institucional Universidad El Bosquehttps://repositorio.unbosque.edu.coapplication/pdfengWileyMethods in Ecology and EvolutionMethods in Ecology and Evolution, 2041-210X, Vol 9, Nro. 10, 2018, p. 2145-2154https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13067Graphs in phylogenetic comparative analysis: Anscombe's quartet revisitedGraphs in phylogenetic comparative analysis: Anscombe's quartet revisitedArtículo de revistahttp://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1info:eu-repo/semantics/articlehttp://purl.org/coar/version/c_970fb48d4fbd8a85Comparative methodsMacroevolutionPhylogenyPlottingVisualizationIn 1973, the statistician Francis Anscombe used a clever set of bivariate datasets (now known as Anscombe's quartet) to illustrate the importance of graphing data as a component of statistical analyses. In his example, each of the four datasets yielded identical regression coefficients and model fits, and yet when visualized revealed strikingly different patterns of covariation between x and y. Phylogenetic comparative methods (the set of methodologies that use phylogenies, often combined with phenotypic trait data, to make inferences about evolution) are statistical methods too; yet visualizing the data and phylogeny in a sensible way that would permit us to detect unexpected patterns or unanticipated deviations from model assumptions is not a routine component of phylogenetic comparative analyses. Here, we use a quartet of phylogenetic datasets to illustrate that the same estimated parameters and model fits can be obtained from data that were generated using markedly different procedures—including pure Brownian motion evolution and randomly selected data uncorrelated with the tree. Just as in the case of Anscombe's quartet, when graphed the differences between the four datasets are quickly revealed. The intent of this article is to help build the general case that phylogenetic comparative methods are statistical methods and consequently that graphing or visualization should invariably be included as an essential step in our standard data analytical pipelines. Phylogenies are complex data structures and thus visualizing data on trees in a meaningful and useful way is a challenging endeavour. We recommend that the development of graphical methods for simultaneously visualizing data and tree should continue to be an important goal in phylogenetic comparative biology.Acceso abiertohttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessAcceso abierto2018-07-16LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://repositorio.unbosque.edu.co/bitstreams/fcf3f284-8f6d-44af-b395-cc9866ba73d2/download8a4605be74aa9ea9d79846c1fba20a33MD53ORIGINALRevell, Liam J..pdfRevell, Liam J..pdfapplication/pdf308883https://repositorio.unbosque.edu.co/bitstreams/3d525b8e-ee32-435a-ae16-f73150afb08b/downloadc1ba75c3bd20ae4cbda6ab693b778bcfMD54THUMBNAILRevell, Liam J..pdf.jpgRevell, Liam J..pdf.jpgIM Thumbnailimage/jpeg8775https://repositorio.unbosque.edu.co/bitstreams/feb4fe7e-ea22-4d8e-b870-25c131cad2ff/download755653d73e11732b14f0e6ce985f6e8bMD55TEXTRevell, Liam J..pdf.txtRevell, Liam J..pdf.txtExtracted texttext/plain44832https://repositorio.unbosque.edu.co/bitstreams/d555a99f-6b0b-41f0-b90a-1b39a52c9183/downloada82f0a2ea9f0c10d427530d8654b2aacMD5620.500.12495/3625oai:repositorio.unbosque.edu.co:20.500.12495/36252024-02-07 08:56:53.115restrictedhttps://repositorio.unbosque.edu.coRepositorio Institucional Universidad El Bosquebibliotecas@biteca.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