Weighting against homoplasy improves phylogenetic analysis of morphological data sets

Autores
Goloboff, Pablo Augusto; Carpeneter, James M.; Arias Becerra, Joan Salvador; Miranda Esquivel, Daniel Rafael
Año de publicación
2008
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are advanced. Characters that collectively determine few well-supported groups may be highly reliable when taken individually (as shown by specific examples), so that inferring greater reliability for sets of characters that lead to an increase in jackknife frequencies may not always be warranted. But even if changes in jackknife frequencies can be used to infer reliability, we demonstrate that jackknife frequencies in large molecular data sets are actually improved when downweighting characters according to their homoplasy but using properly rescaled functions (instead of the very strong standard functions, or the extreme of inclusion ⁄ exclusion); this further weakens the argument that downweighting homoplastic characters is undesirable. Last, we show that downweighting characters according to their homoplasy (using standard homoplasy-weighting methods) on 70 morphological data sets (with 50?170 taxa), produces clear increases in jackknife frequencies. The results obtained under homoplasy weighting also appear more stable than results under equal weights: adding either taxa or characters, when weighting against homoplasy, produced results more similar to original analyses (i.e., with larger numbers of groups that continue being supported after addition of taxa or characters), with similar or lower error rates (i.e., proportion of groups recovered that subsequently turn out to be incorrect). Therefore, the same argument that had been advanced against homoplasy weighting in the case of large molecular data sets is an argument in favor of such weighting in the case of morphological data sets.
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina
Fil: Carpeneter, James M.. The American Museum of Natural History; Estados Unidos
Fil: Arias Becerra, Joan Salvador. Universidad Industrial de Santander; Colombia. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentina
Fil: Miranda Esquivel, Daniel Rafael. Universidad Industrial de Santander; Colombia
Materia
Phylogenetics
Character Weighting
Methodology
Parsimony
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/82003

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spelling Weighting against homoplasy improves phylogenetic analysis of morphological data setsGoloboff, Pablo AugustoCarpeneter, James M.Arias Becerra, Joan SalvadorMiranda Esquivel, Daniel RafaelPhylogeneticsCharacter WeightingMethodologyParsimonyhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are advanced. Characters that collectively determine few well-supported groups may be highly reliable when taken individually (as shown by specific examples), so that inferring greater reliability for sets of characters that lead to an increase in jackknife frequencies may not always be warranted. But even if changes in jackknife frequencies can be used to infer reliability, we demonstrate that jackknife frequencies in large molecular data sets are actually improved when downweighting characters according to their homoplasy but using properly rescaled functions (instead of the very strong standard functions, or the extreme of inclusion ⁄ exclusion); this further weakens the argument that downweighting homoplastic characters is undesirable. Last, we show that downweighting characters according to their homoplasy (using standard homoplasy-weighting methods) on 70 morphological data sets (with 50?170 taxa), produces clear increases in jackknife frequencies. The results obtained under homoplasy weighting also appear more stable than results under equal weights: adding either taxa or characters, when weighting against homoplasy, produced results more similar to original analyses (i.e., with larger numbers of groups that continue being supported after addition of taxa or characters), with similar or lower error rates (i.e., proportion of groups recovered that subsequently turn out to be incorrect). Therefore, the same argument that had been advanced against homoplasy weighting in the case of large molecular data sets is an argument in favor of such weighting in the case of morphological data sets.Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Carpeneter, James M.. The American Museum of Natural History; Estados UnidosFil: Arias Becerra, Joan Salvador. Universidad Industrial de Santander; Colombia. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaFil: Miranda Esquivel, Daniel Rafael. Universidad Industrial de Santander; ColombiaWiley Blackwell Publishing, Inc2008-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/82003Goloboff, Pablo Augusto; Carpeneter, James M.; Arias Becerra, Joan Salvador; Miranda Esquivel, Daniel Rafael; Weighting against homoplasy improves phylogenetic analysis of morphological data sets; Wiley Blackwell Publishing, Inc; Cladistics; 24; 5; 10-2008; 758-7730748-3007CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1111/j.1096-0031.2008.00209.xinfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2008.00209.xinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:36:08Zoai:ri.conicet.gov.ar:11336/82003instacron: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 09:36:08.818CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Weighting against homoplasy improves phylogenetic analysis of morphological data sets
title Weighting against homoplasy improves phylogenetic analysis of morphological data sets
spellingShingle Weighting against homoplasy improves phylogenetic analysis of morphological data sets
Goloboff, Pablo Augusto
Phylogenetics
Character Weighting
Methodology
Parsimony
title_short Weighting against homoplasy improves phylogenetic analysis of morphological data sets
title_full Weighting against homoplasy improves phylogenetic analysis of morphological data sets
title_fullStr Weighting against homoplasy improves phylogenetic analysis of morphological data sets
title_full_unstemmed Weighting against homoplasy improves phylogenetic analysis of morphological data sets
title_sort Weighting against homoplasy improves phylogenetic analysis of morphological data sets
dc.creator.none.fl_str_mv Goloboff, Pablo Augusto
Carpeneter, James M.
Arias Becerra, Joan Salvador
Miranda Esquivel, Daniel Rafael
author Goloboff, Pablo Augusto
author_facet Goloboff, Pablo Augusto
Carpeneter, James M.
Arias Becerra, Joan Salvador
Miranda Esquivel, Daniel Rafael
author_role author
author2 Carpeneter, James M.
Arias Becerra, Joan Salvador
Miranda Esquivel, Daniel Rafael
author2_role author
author
author
dc.subject.none.fl_str_mv Phylogenetics
Character Weighting
Methodology
Parsimony
topic Phylogenetics
Character Weighting
Methodology
Parsimony
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are advanced. Characters that collectively determine few well-supported groups may be highly reliable when taken individually (as shown by specific examples), so that inferring greater reliability for sets of characters that lead to an increase in jackknife frequencies may not always be warranted. But even if changes in jackknife frequencies can be used to infer reliability, we demonstrate that jackknife frequencies in large molecular data sets are actually improved when downweighting characters according to their homoplasy but using properly rescaled functions (instead of the very strong standard functions, or the extreme of inclusion ⁄ exclusion); this further weakens the argument that downweighting homoplastic characters is undesirable. Last, we show that downweighting characters according to their homoplasy (using standard homoplasy-weighting methods) on 70 morphological data sets (with 50?170 taxa), produces clear increases in jackknife frequencies. The results obtained under homoplasy weighting also appear more stable than results under equal weights: adding either taxa or characters, when weighting against homoplasy, produced results more similar to original analyses (i.e., with larger numbers of groups that continue being supported after addition of taxa or characters), with similar or lower error rates (i.e., proportion of groups recovered that subsequently turn out to be incorrect). Therefore, the same argument that had been advanced against homoplasy weighting in the case of large molecular data sets is an argument in favor of such weighting in the case of morphological data sets.
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina
Fil: Carpeneter, James M.. The American Museum of Natural History; Estados Unidos
Fil: Arias Becerra, Joan Salvador. Universidad Industrial de Santander; Colombia. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentina
Fil: Miranda Esquivel, Daniel Rafael. Universidad Industrial de Santander; Colombia
description The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are advanced. Characters that collectively determine few well-supported groups may be highly reliable when taken individually (as shown by specific examples), so that inferring greater reliability for sets of characters that lead to an increase in jackknife frequencies may not always be warranted. But even if changes in jackknife frequencies can be used to infer reliability, we demonstrate that jackknife frequencies in large molecular data sets are actually improved when downweighting characters according to their homoplasy but using properly rescaled functions (instead of the very strong standard functions, or the extreme of inclusion ⁄ exclusion); this further weakens the argument that downweighting homoplastic characters is undesirable. Last, we show that downweighting characters according to their homoplasy (using standard homoplasy-weighting methods) on 70 morphological data sets (with 50?170 taxa), produces clear increases in jackknife frequencies. The results obtained under homoplasy weighting also appear more stable than results under equal weights: adding either taxa or characters, when weighting against homoplasy, produced results more similar to original analyses (i.e., with larger numbers of groups that continue being supported after addition of taxa or characters), with similar or lower error rates (i.e., proportion of groups recovered that subsequently turn out to be incorrect). Therefore, the same argument that had been advanced against homoplasy weighting in the case of large molecular data sets is an argument in favor of such weighting in the case of morphological data sets.
publishDate 2008
dc.date.none.fl_str_mv 2008-10
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/11336/82003
Goloboff, Pablo Augusto; Carpeneter, James M.; Arias Becerra, Joan Salvador; Miranda Esquivel, Daniel Rafael; Weighting against homoplasy improves phylogenetic analysis of morphological data sets; Wiley Blackwell Publishing, Inc; Cladistics; 24; 5; 10-2008; 758-773
0748-3007
CONICET Digital
CONICET
url http://hdl.handle.net/11336/82003
identifier_str_mv Goloboff, Pablo Augusto; Carpeneter, James M.; Arias Becerra, Joan Salvador; Miranda Esquivel, Daniel Rafael; Weighting against homoplasy improves phylogenetic analysis of morphological data sets; Wiley Blackwell Publishing, Inc; Cladistics; 24; 5; 10-2008; 758-773
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/doi/10.1111/j.1096-0031.2008.00209.x
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2008.00209.x
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
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
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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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