Phylogenetic inference based on landmark data in 41 empirical data sets

The inference of phylogenetic hypotheses from landmark data has been questioned during the last two decades. Besides theoretical concerns, one of the limitations pointed out for the use of landmark data in phylogenetics is its (supposed) lack of information relevant to the inference of phylogenetic...

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Detalles Bibliográficos
Autores: Catalano, Santiago Andres, Torres Galvis, Ambrosio
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:Argentina
Institución:Consejo Nacional de Investigaciones Científicas y Técnicas
Repositorio:CONICET Digital (CONICET)
Idioma:inglés
OAI Identifier:oai:ri.conicet.gov.ar:11336/56630
Acceso en línea:http://hdl.handle.net/11336/56630
Access Level:acceso abierto
Palabra clave:Landmarks
Phylogeny
Morphology
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
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spelling Phylogenetic inference based on landmark data in 41 empirical data setsCatalano, Santiago AndresTorres Galvis, AmbrosioLandmarksPhylogenyMorphologyhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The inference of phylogenetic hypotheses from landmark data has been questioned during the last two decades. Besides theoretical concerns, one of the limitations pointed out for the use of landmark data in phylogenetics is its (supposed) lack of information relevant to the inference of phylogenetic relationships. However, empirical analyses are scarce; there exists no previous study that systematically evaluates the phylogenetic performance of landmark data in a series of data sets. In the present study, we analysed 41 published data sets in order to assess the correspondence between the phylogenetic trees derived from landmark data and those obtained with alternative and independent sources of evidence, and determined the main factors that might affect this inference. The data sets presented a variable number of terminals (5–200) and configurations (1–14), belonging to different taxonomic groups. The results showed that for most of the data sets analysed, the trees derived from landmark data presented a low correspondence with the reference phylogenies. The results were similar irrespective of the phylogenetic method considered. Complementary analyses strongly suggested that the limited amount of evidence included in each data set (one or a few landmark configurations) is the main cause for that low correspondence: the phylogenetic analysis of eight data sets that presented three or more configurations clearly showed that the inclusion of several landmark configurations improves the results. In addition, the analyses indicated that the inclusion of landmark data from different configurations is more important than the inclusion of more landmarks from the same configuration. Based on the results presented here, we consider that the poor results previously obtained in phylogenetic analyses based on landmark data were not caused by methodological limitations, but rather due to the limited amount of evidence included in the data sets.Fil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Torres Galvis, Ambrosio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaWiley Blackwell Publishing, Inc2017-01info: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/11336/56630Catalano, Santiago Andres; Torres Galvis, Ambrosio; Phylogenetic inference based on landmark data in 41 empirical data sets; Wiley Blackwell Publishing, Inc; Zoologica Scripta; 46; 1; 1-2017; 1-110300-3256CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1111/zsc.12186info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/zsc.12186info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2024-05-08T13:33:36Zoai:ri.conicet.gov.ar:11336/56630instacron: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:34982024-05-08 13:33:36.654CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Phylogenetic inference based on landmark data in 41 empirical data sets
title Phylogenetic inference based on landmark data in 41 empirical data sets
spellingShingle Phylogenetic inference based on landmark data in 41 empirical data sets
Catalano, Santiago Andres
Landmarks
Phylogeny
Morphology
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
title_short Phylogenetic inference based on landmark data in 41 empirical data sets
title_full Phylogenetic inference based on landmark data in 41 empirical data sets
title_fullStr Phylogenetic inference based on landmark data in 41 empirical data sets
title_full_unstemmed Phylogenetic inference based on landmark data in 41 empirical data sets
title_sort Phylogenetic inference based on landmark data in 41 empirical data sets
dc.creator.none.fl_str_mv Catalano, Santiago Andres
Torres Galvis, Ambrosio
author Catalano, Santiago Andres
author_facet Catalano, Santiago Andres
Torres Galvis, Ambrosio
author_role author
author2 Torres Galvis, Ambrosio
author2_role author
dc.subject.none.fl_str_mv Landmarks
Phylogeny
Morphology
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
topic Landmarks
Phylogeny
Morphology
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
description The inference of phylogenetic hypotheses from landmark data has been questioned during the last two decades. Besides theoretical concerns, one of the limitations pointed out for the use of landmark data in phylogenetics is its (supposed) lack of information relevant to the inference of phylogenetic relationships. However, empirical analyses are scarce; there exists no previous study that systematically evaluates the phylogenetic performance of landmark data in a series of data sets. In the present study, we analysed 41 published data sets in order to assess the correspondence between the phylogenetic trees derived from landmark data and those obtained with alternative and independent sources of evidence, and determined the main factors that might affect this inference. The data sets presented a variable number of terminals (5–200) and configurations (1–14), belonging to different taxonomic groups. The results showed that for most of the data sets analysed, the trees derived from landmark data presented a low correspondence with the reference phylogenies. The results were similar irrespective of the phylogenetic method considered. Complementary analyses strongly suggested that the limited amount of evidence included in each data set (one or a few landmark configurations) is the main cause for that low correspondence: the phylogenetic analysis of eight data sets that presented three or more configurations clearly showed that the inclusion of several landmark configurations improves the results. In addition, the analyses indicated that the inclusion of landmark data from different configurations is more important than the inclusion of more landmarks from the same configuration. Based on the results presented here, we consider that the poor results previously obtained in phylogenetic analyses based on landmark data were not caused by methodological limitations, but rather due to the limited amount of evidence included in the data sets.
publishDate 2017
dc.date.none.fl_str_mv 2017-01
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/11336/56630
Catalano, Santiago Andres; Torres Galvis, Ambrosio; Phylogenetic inference based on landmark data in 41 empirical data sets; Wiley Blackwell Publishing, Inc; Zoologica Scripta; 46; 1; 1-2017; 1-11
0300-3256
CONICET Digital
CONICET
url http://hdl.handle.net/11336/56630
identifier_str_mv Catalano, Santiago Andres; Torres Galvis, Ambrosio; Phylogenetic inference based on landmark data in 41 empirical data sets; Wiley Blackwell Publishing, Inc; Zoologica Scripta; 46; 1; 1-2017; 1-11
0300-3256
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/zsc.12186
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/zsc.12186
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
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
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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score 15,811543

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