Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices

Autores
Ezcurra, Martin Daniel
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Although simulations have shown that implied weighting (IW) outperforms equal weighting (EW) in phylogenetic parsimonyanalyses, weighting against homoplasy lacks extensive usage in palaeontology. Iterative modifications of several phylogeneticmatrices in the last decades resulted in extensive genealogies of datasets that allow the evaluation of differences in the stabilityof results for alternative character weighting methods directly on empirical data. Each generation was compared against themost recent generation in each genealogy because it is assumed that it is the most comprehensive (higher sampling), revised(fewer misscorings) and complete (lower amount of missing data) matrix of the genealogy. The analyses were conducted on sixdifferent genealogies under EW and IW and extended implied weighting (EIW) with a range of concavity constant values (k)between 3 and 30. Pairwise comparisons between trees were conducted using Robinson–Foulds distances normalized by the totalnumber of groups, distortion coefficient, subtree pruning and regrafting moves, and the proportional sum of group dissimilarities.The results consistently show that IW and EIW produce results more similar to those of the last dataset than EW in thevast majority of genealogies and for all comparative measures. This is significant because almost all of these matrices were originallyanalysed only under EW. Implied weighting and EIW do not outperform each other unambiguously. Euclidean distancesbased on a principal components analysis of the comparative measures show that different ranges of k-values retrieve the mostsimilar results to the last generation in different genealogies. There is a significant positive linear correlation between the optimalk-values and the number of terminals of the last generations. This could be employed to inform about the range of k-values tobe used in phylogenetic analyses based on matrix size but with the caveat that this emergent relationship still relies on a lowsample size of genealogies.
Fil: Ezcurra, Martin Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
Materia
Cladistics
phylogeny
implied weights
homoplasy
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/258754

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spelling Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matricesEzcurra, Martin DanielCladisticsphylogenyimplied weightshomoplasyhttps://purl.org/becyt/ford/1.5https://purl.org/becyt/ford/1Although simulations have shown that implied weighting (IW) outperforms equal weighting (EW) in phylogenetic parsimonyanalyses, weighting against homoplasy lacks extensive usage in palaeontology. Iterative modifications of several phylogeneticmatrices in the last decades resulted in extensive genealogies of datasets that allow the evaluation of differences in the stabilityof results for alternative character weighting methods directly on empirical data. Each generation was compared against themost recent generation in each genealogy because it is assumed that it is the most comprehensive (higher sampling), revised(fewer misscorings) and complete (lower amount of missing data) matrix of the genealogy. The analyses were conducted on sixdifferent genealogies under EW and IW and extended implied weighting (EIW) with a range of concavity constant values (k)between 3 and 30. Pairwise comparisons between trees were conducted using Robinson–Foulds distances normalized by the totalnumber of groups, distortion coefficient, subtree pruning and regrafting moves, and the proportional sum of group dissimilarities.The results consistently show that IW and EIW produce results more similar to those of the last dataset than EW in thevast majority of genealogies and for all comparative measures. This is significant because almost all of these matrices were originallyanalysed only under EW. Implied weighting and EIW do not outperform each other unambiguously. Euclidean distancesbased on a principal components analysis of the comparative measures show that different ranges of k-values retrieve the mostsimilar results to the last generation in different genealogies. There is a significant positive linear correlation between the optimalk-values and the number of terminals of the last generations. This could be employed to inform about the range of k-values tobe used in phylogenetic analyses based on matrix size but with the caveat that this emergent relationship still relies on a lowsample size of genealogies.Fil: Ezcurra, Martin Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaWiley Blackwell Publishing, Inc2024-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/258754Ezcurra, Martin Daniel; Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices; Wiley Blackwell Publishing, Inc; Cladistics; 40; 3; 5-2024; 242-2810748-3007CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1111/cla.12581info:eu-repo/semantics/altIdentifier/doi/10.1111/cla.12581info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:52:19Zoai:ri.conicet.gov.ar:11336/258754instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:52:19.299CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices
title Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices
spellingShingle Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices
Ezcurra, Martin Daniel
Cladistics
phylogeny
implied weights
homoplasy
title_short Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices
title_full Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices
title_fullStr Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices
title_full_unstemmed Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices
title_sort Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices
dc.creator.none.fl_str_mv Ezcurra, Martin Daniel
author Ezcurra, Martin Daniel
author_facet Ezcurra, Martin Daniel
author_role author
dc.subject.none.fl_str_mv Cladistics
phylogeny
implied weights
homoplasy
topic Cladistics
phylogeny
implied weights
homoplasy
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.5
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Although simulations have shown that implied weighting (IW) outperforms equal weighting (EW) in phylogenetic parsimonyanalyses, weighting against homoplasy lacks extensive usage in palaeontology. Iterative modifications of several phylogeneticmatrices in the last decades resulted in extensive genealogies of datasets that allow the evaluation of differences in the stabilityof results for alternative character weighting methods directly on empirical data. Each generation was compared against themost recent generation in each genealogy because it is assumed that it is the most comprehensive (higher sampling), revised(fewer misscorings) and complete (lower amount of missing data) matrix of the genealogy. The analyses were conducted on sixdifferent genealogies under EW and IW and extended implied weighting (EIW) with a range of concavity constant values (k)between 3 and 30. Pairwise comparisons between trees were conducted using Robinson–Foulds distances normalized by the totalnumber of groups, distortion coefficient, subtree pruning and regrafting moves, and the proportional sum of group dissimilarities.The results consistently show that IW and EIW produce results more similar to those of the last dataset than EW in thevast majority of genealogies and for all comparative measures. This is significant because almost all of these matrices were originallyanalysed only under EW. Implied weighting and EIW do not outperform each other unambiguously. Euclidean distancesbased on a principal components analysis of the comparative measures show that different ranges of k-values retrieve the mostsimilar results to the last generation in different genealogies. There is a significant positive linear correlation between the optimalk-values and the number of terminals of the last generations. This could be employed to inform about the range of k-values tobe used in phylogenetic analyses based on matrix size but with the caveat that this emergent relationship still relies on a lowsample size of genealogies.
Fil: Ezcurra, Martin Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
description Although simulations have shown that implied weighting (IW) outperforms equal weighting (EW) in phylogenetic parsimonyanalyses, weighting against homoplasy lacks extensive usage in palaeontology. Iterative modifications of several phylogeneticmatrices in the last decades resulted in extensive genealogies of datasets that allow the evaluation of differences in the stabilityof results for alternative character weighting methods directly on empirical data. Each generation was compared against themost recent generation in each genealogy because it is assumed that it is the most comprehensive (higher sampling), revised(fewer misscorings) and complete (lower amount of missing data) matrix of the genealogy. The analyses were conducted on sixdifferent genealogies under EW and IW and extended implied weighting (EIW) with a range of concavity constant values (k)between 3 and 30. Pairwise comparisons between trees were conducted using Robinson–Foulds distances normalized by the totalnumber of groups, distortion coefficient, subtree pruning and regrafting moves, and the proportional sum of group dissimilarities.The results consistently show that IW and EIW produce results more similar to those of the last dataset than EW in thevast majority of genealogies and for all comparative measures. This is significant because almost all of these matrices were originallyanalysed only under EW. Implied weighting and EIW do not outperform each other unambiguously. Euclidean distancesbased on a principal components analysis of the comparative measures show that different ranges of k-values retrieve the mostsimilar results to the last generation in different genealogies. There is a significant positive linear correlation between the optimalk-values and the number of terminals of the last generations. This could be employed to inform about the range of k-values tobe used in phylogenetic analyses based on matrix size but with the caveat that this emergent relationship still relies on a lowsample size of genealogies.
publishDate 2024
dc.date.none.fl_str_mv 2024-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/258754
Ezcurra, Martin Daniel; Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices; Wiley Blackwell Publishing, Inc; Cladistics; 40; 3; 5-2024; 242-281
0748-3007
CONICET Digital
CONICET
url http://hdl.handle.net/11336/258754
identifier_str_mv Ezcurra, Martin Daniel; Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices; Wiley Blackwell Publishing, Inc; Cladistics; 40; 3; 5-2024; 242-281
0748-3007
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1111/cla.12581
info:eu-repo/semantics/altIdentifier/doi/10.1111/cla.12581
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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