Building and Visualising Ordinations of Shape Data in R With Morphospace

Autores
Milla Carmona, Pablo Sebastián; Lehmann, Oscar Emilio Rodrigo; Deakin, William J.; Soto, Eduardo Maria; Soto, Ignacio Maria
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Ordination is a critical step of geometric morphometrics that allows simplification of high-dimensional shape spaces into lowdimensional representations summarising shape variation. While this is routinely used to visualise the main patterns of morphometric data, the lack of a unified approach curbs researchers' ability to make the most of available ordination and visualisation methods. Here we introduce morphospace, an R package providing a streamlined approach to shape ordination and visualisation, intended to enhance the biological relevance of the analysis. This package integrates a series of tools into a workflow including (1) filtering variation associated with nuisance factors out from shape data; (2) building ordinations emphasising different types of biological signal and mapping shape variation into them; (3) projecting elements onto this morphospace, including empirical or theoretical shapes, shape clusters, morphometric axes, phylogenetic trees or performance landscapes; and (4) combining shape variation with non-shape information to create alternative visualisations. We describe the basic mechanics and capabilities of morphospace, as well as its integration with other R packages, and briefly discuss the patterns it can help expose. Then, we showcase its applications by working three examples focused on phenomena commonly targeted in palaeontological and evolutionary research. The tools and workflow provided by morphospace facilitate the creation of publication-ready visualisations to accompany results of dedicated statistical tests and enhance heuristic exploration of the patterns present in shape data and the underlying processes that generated them.
Fil: Milla Carmona, Pablo Sebastián. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Lehmann, Oscar Emilio Rodrigo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
Fil: Deakin, William J.. University Of Bristol;
Fil: Soto, Eduardo Maria. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina
Fil: Soto, Ignacio Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina
Materia
GEOMETRIC MORPHOMETRICS
MULTIVARIATE ORDINATION METHODS
SHAPE VARIATION
MORPHOSPACE
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:11336/281250
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/281250
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Building and Visualising Ordinations of Shape Data in R With MorphospaceMilla Carmona, Pablo SebastiánLehmann, Oscar Emilio RodrigoDeakin, William J.Soto, Eduardo MariaSoto, Ignacio MariaGEOMETRIC MORPHOMETRICSMULTIVARIATE ORDINATION METHODSSHAPE VARIATIONMORPHOSPACEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Ordination is a critical step of geometric morphometrics that allows simplification of high-dimensional shape spaces into lowdimensional representations summarising shape variation. While this is routinely used to visualise the main patterns of morphometric data, the lack of a unified approach curbs researchers' ability to make the most of available ordination and visualisation methods. Here we introduce morphospace, an R package providing a streamlined approach to shape ordination and visualisation, intended to enhance the biological relevance of the analysis. This package integrates a series of tools into a workflow including (1) filtering variation associated with nuisance factors out from shape data; (2) building ordinations emphasising different types of biological signal and mapping shape variation into them; (3) projecting elements onto this morphospace, including empirical or theoretical shapes, shape clusters, morphometric axes, phylogenetic trees or performance landscapes; and (4) combining shape variation with non-shape information to create alternative visualisations. We describe the basic mechanics and capabilities of morphospace, as well as its integration with other R packages, and briefly discuss the patterns it can help expose. Then, we showcase its applications by working three examples focused on phenomena commonly targeted in palaeontological and evolutionary research. The tools and workflow provided by morphospace facilitate the creation of publication-ready visualisations to accompany results of dedicated statistical tests and enhance heuristic exploration of the patterns present in shape data and the underlying processes that generated them.Fil: Milla Carmona, Pablo Sebastián. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Lehmann, Oscar Emilio Rodrigo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Deakin, William J.. University Of Bristol;Fil: Soto, Eduardo Maria. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; ArgentinaFil: Soto, Ignacio Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; ArgentinaWiley2025-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/vnd.openxmlformats-officedocument.wordprocessingml.documentapplication/pdfhttp://hdl.handle.net/11336/281250Milla Carmona, Pablo Sebastián; Lehmann, Oscar Emilio Rodrigo; Deakin, William J.; Soto, Eduardo Maria; Soto, Ignacio Maria; Building and Visualising Ordinations of Shape Data in R With Morphospace; Wiley; Ecology and Evolution; 15; 6; 6-2025; 1-132045-7758CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1002/ece3.71503info:eu-repo/semantics/altIdentifier/doi/10.1002/ece3.71503info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-02-26T10:10:45Zoai:ri.conicet.gov.ar:11336/281250instacron: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:34982026-02-26 10:10:45.431CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Building and Visualising Ordinations of Shape Data in R With Morphospace
title Building and Visualising Ordinations of Shape Data in R With Morphospace
spellingShingle Building and Visualising Ordinations of Shape Data in R With Morphospace
Milla Carmona, Pablo Sebastián
GEOMETRIC MORPHOMETRICS
MULTIVARIATE ORDINATION METHODS
SHAPE VARIATION
MORPHOSPACE
title_short Building and Visualising Ordinations of Shape Data in R With Morphospace
title_full Building and Visualising Ordinations of Shape Data in R With Morphospace
title_fullStr Building and Visualising Ordinations of Shape Data in R With Morphospace
title_full_unstemmed Building and Visualising Ordinations of Shape Data in R With Morphospace
title_sort Building and Visualising Ordinations of Shape Data in R With Morphospace
dc.creator.none.fl_str_mv Milla Carmona, Pablo Sebastián
Lehmann, Oscar Emilio Rodrigo
Deakin, William J.
Soto, Eduardo Maria
Soto, Ignacio Maria
author Milla Carmona, Pablo Sebastián
author_facet Milla Carmona, Pablo Sebastián
Lehmann, Oscar Emilio Rodrigo
Deakin, William J.
Soto, Eduardo Maria
Soto, Ignacio Maria
author_role author
author2 Lehmann, Oscar Emilio Rodrigo
Deakin, William J.
Soto, Eduardo Maria
Soto, Ignacio Maria
author2_role author
author
author
author
dc.subject.none.fl_str_mv GEOMETRIC MORPHOMETRICS
MULTIVARIATE ORDINATION METHODS
SHAPE VARIATION
MORPHOSPACE
topic GEOMETRIC MORPHOMETRICS
MULTIVARIATE ORDINATION METHODS
SHAPE VARIATION
MORPHOSPACE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Ordination is a critical step of geometric morphometrics that allows simplification of high-dimensional shape spaces into lowdimensional representations summarising shape variation. While this is routinely used to visualise the main patterns of morphometric data, the lack of a unified approach curbs researchers' ability to make the most of available ordination and visualisation methods. Here we introduce morphospace, an R package providing a streamlined approach to shape ordination and visualisation, intended to enhance the biological relevance of the analysis. This package integrates a series of tools into a workflow including (1) filtering variation associated with nuisance factors out from shape data; (2) building ordinations emphasising different types of biological signal and mapping shape variation into them; (3) projecting elements onto this morphospace, including empirical or theoretical shapes, shape clusters, morphometric axes, phylogenetic trees or performance landscapes; and (4) combining shape variation with non-shape information to create alternative visualisations. We describe the basic mechanics and capabilities of morphospace, as well as its integration with other R packages, and briefly discuss the patterns it can help expose. Then, we showcase its applications by working three examples focused on phenomena commonly targeted in palaeontological and evolutionary research. The tools and workflow provided by morphospace facilitate the creation of publication-ready visualisations to accompany results of dedicated statistical tests and enhance heuristic exploration of the patterns present in shape data and the underlying processes that generated them.
Fil: Milla Carmona, Pablo Sebastián. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Lehmann, Oscar Emilio Rodrigo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
Fil: Deakin, William J.. University Of Bristol;
Fil: Soto, Eduardo Maria. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina
Fil: Soto, Ignacio Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina
description Ordination is a critical step of geometric morphometrics that allows simplification of high-dimensional shape spaces into lowdimensional representations summarising shape variation. While this is routinely used to visualise the main patterns of morphometric data, the lack of a unified approach curbs researchers' ability to make the most of available ordination and visualisation methods. Here we introduce morphospace, an R package providing a streamlined approach to shape ordination and visualisation, intended to enhance the biological relevance of the analysis. This package integrates a series of tools into a workflow including (1) filtering variation associated with nuisance factors out from shape data; (2) building ordinations emphasising different types of biological signal and mapping shape variation into them; (3) projecting elements onto this morphospace, including empirical or theoretical shapes, shape clusters, morphometric axes, phylogenetic trees or performance landscapes; and (4) combining shape variation with non-shape information to create alternative visualisations. We describe the basic mechanics and capabilities of morphospace, as well as its integration with other R packages, and briefly discuss the patterns it can help expose. Then, we showcase its applications by working three examples focused on phenomena commonly targeted in palaeontological and evolutionary research. The tools and workflow provided by morphospace facilitate the creation of publication-ready visualisations to accompany results of dedicated statistical tests and enhance heuristic exploration of the patterns present in shape data and the underlying processes that generated them.
publishDate 2025
dc.date.none.fl_str_mv 2025-06
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/11336/281250
Milla Carmona, Pablo Sebastián; Lehmann, Oscar Emilio Rodrigo; Deakin, William J.; Soto, Eduardo Maria; Soto, Ignacio Maria; Building and Visualising Ordinations of Shape Data in R With Morphospace; Wiley; Ecology and Evolution; 15; 6; 6-2025; 1-13
2045-7758
CONICET Digital
CONICET
url http://hdl.handle.net/11336/281250
identifier_str_mv Milla Carmona, Pablo Sebastián; Lehmann, Oscar Emilio Rodrigo; Deakin, William J.; Soto, Eduardo Maria; Soto, Ignacio Maria; Building and Visualising Ordinations of Shape Data in R With Morphospace; Wiley; Ecology and Evolution; 15; 6; 6-2025; 1-13
2045-7758
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/10.1002/ece3.71503
info:eu-repo/semantics/altIdentifier/doi/10.1002/ece3.71503
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/vnd.openxmlformats-officedocument.wordprocessingml.document
application/pdf
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
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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