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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/258754
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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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1844613605462376448 |
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13.070432 |