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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/82003
Ver los metadatos del registro completo
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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 |
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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1844613131024728064 |
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13.070432 |