PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees

Autores
Catalano, Santiago Andres; Escapa, Ignacio Hernán; Pugh, Kelsey D.; Hammond, Ashley S; Goloboff, Pablo Augusto; Almécija, Sergio
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In recent years, there has been a growing interest in using morphology to establish the placement of species on phylogenetic trees derived from molecular data. This is relevant in the case of recently extinct or fossil species, which are usually represented only by fragmentary morphology. In the latter case, constrained analyses using backbone trees have also proven helpful in evaluating the placement of fragmentary specimens on phylogenetic trees derived from morphological data. Consequently, several available phylogenetic programs now include functions to run constrained searches. However, a comprehensive evaluation of the obtained results is not readily available within existing analytical tools. Here, we present an integrated approach—PlaceMyFossils—specifically designed to (1) thoroughly evaluate the phylogenetic placement of given query species (especially fossils) on a reference tree, (2) determine which characters and character partitions are most relevant in defining the phylogenetic placement, (3) assess the confidence of the results, and (4) define the optimal analytical conditions to place the query species. PlaceMyFossils combines several analyses implemented as an interactive script for TNT (Tree Analysis Using New Technologies software), a popular—and free—phylogenetic software that is widely used in paleontological studies. Finally, we demonstrate the utility and investigate the performance of PlaceMyFossils compared to other available tools using two disparate empirical datasets drawn from conifers and dinosaurs. While primarily designed for working with fossils, this tool also holds great potential for advancing morphological and molecular systematics. It offers a powerful resource for empirical systematists aiming to integrate molecular and morphological data. This is particularly relevant given the growing interest in morphological evolution as a complementary perspective on evolutionary processes and the drivers of diversification.
Fil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentina. American Museum of Natural History; Estados Unidos
Fil: Escapa, Ignacio Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Museo Paleontológico Egidio Feruglio; Argentina
Fil: Pugh, Kelsey D.. American Museum of Natural History; Estados Unidos
Fil: Hammond, Ashley S. American Museum of Natural History; Estados Unidos
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina
Fil: Almécija, Sergio. American Museum of Natural History; Estados Unidos. Universitat Autònoma de Barcelona; España
Materia
Phylogeny
Scaffolds
Parsimony
Maximum Likelihood
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:11336/265152

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spelling PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone TreesCatalano, Santiago AndresEscapa, Ignacio HernánPugh, Kelsey D.Hammond, Ashley SGoloboff, Pablo AugustoAlmécija, SergioPhylogenyScaffoldsParsimonyMaximum Likelihoodhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1In recent years, there has been a growing interest in using morphology to establish the placement of species on phylogenetic trees derived from molecular data. This is relevant in the case of recently extinct or fossil species, which are usually represented only by fragmentary morphology. In the latter case, constrained analyses using backbone trees have also proven helpful in evaluating the placement of fragmentary specimens on phylogenetic trees derived from morphological data. Consequently, several available phylogenetic programs now include functions to run constrained searches. However, a comprehensive evaluation of the obtained results is not readily available within existing analytical tools. Here, we present an integrated approach—PlaceMyFossils—specifically designed to (1) thoroughly evaluate the phylogenetic placement of given query species (especially fossils) on a reference tree, (2) determine which characters and character partitions are most relevant in defining the phylogenetic placement, (3) assess the confidence of the results, and (4) define the optimal analytical conditions to place the query species. PlaceMyFossils combines several analyses implemented as an interactive script for TNT (Tree Analysis Using New Technologies software), a popular—and free—phylogenetic software that is widely used in paleontological studies. Finally, we demonstrate the utility and investigate the performance of PlaceMyFossils compared to other available tools using two disparate empirical datasets drawn from conifers and dinosaurs. While primarily designed for working with fossils, this tool also holds great potential for advancing morphological and molecular systematics. It offers a powerful resource for empirical systematists aiming to integrate molecular and morphological data. This is particularly relevant given the growing interest in morphological evolution as a complementary perspective on evolutionary processes and the drivers of diversification.Fil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentina. American Museum of Natural History; Estados UnidosFil: Escapa, Ignacio Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Museo Paleontológico Egidio Feruglio; ArgentinaFil: Pugh, Kelsey D.. American Museum of Natural History; Estados UnidosFil: Hammond, Ashley S. American Museum of Natural History; Estados UnidosFil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Almécija, Sergio. American Museum of Natural History; Estados Unidos. Universitat Autònoma de Barcelona; EspañaOxford University Press2025-04info: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/11336/265152Catalano, Santiago Andres; Escapa, Ignacio Hernán; Pugh, Kelsey D.; Hammond, Ashley S; Goloboff, Pablo Augusto; et al.; PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees; Oxford University Press; Systematic Biology; 2025; 4-2025; 1-291063-5157CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syaf025/8115461info:eu-repo/semantics/altIdentifier/doi/10.1093/sysbio/syaf025info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:17:36Zoai:ri.conicet.gov.ar:11336/265152instacron: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 10:17:37.161CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees
title PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees
spellingShingle PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees
Catalano, Santiago Andres
Phylogeny
Scaffolds
Parsimony
Maximum Likelihood
title_short PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees
title_full PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees
title_fullStr PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees
title_full_unstemmed PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees
title_sort PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees
dc.creator.none.fl_str_mv Catalano, Santiago Andres
Escapa, Ignacio Hernán
Pugh, Kelsey D.
Hammond, Ashley S
Goloboff, Pablo Augusto
Almécija, Sergio
author Catalano, Santiago Andres
author_facet Catalano, Santiago Andres
Escapa, Ignacio Hernán
Pugh, Kelsey D.
Hammond, Ashley S
Goloboff, Pablo Augusto
Almécija, Sergio
author_role author
author2 Escapa, Ignacio Hernán
Pugh, Kelsey D.
Hammond, Ashley S
Goloboff, Pablo Augusto
Almécija, Sergio
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Phylogeny
Scaffolds
Parsimony
Maximum Likelihood
topic Phylogeny
Scaffolds
Parsimony
Maximum Likelihood
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv In recent years, there has been a growing interest in using morphology to establish the placement of species on phylogenetic trees derived from molecular data. This is relevant in the case of recently extinct or fossil species, which are usually represented only by fragmentary morphology. In the latter case, constrained analyses using backbone trees have also proven helpful in evaluating the placement of fragmentary specimens on phylogenetic trees derived from morphological data. Consequently, several available phylogenetic programs now include functions to run constrained searches. However, a comprehensive evaluation of the obtained results is not readily available within existing analytical tools. Here, we present an integrated approach—PlaceMyFossils—specifically designed to (1) thoroughly evaluate the phylogenetic placement of given query species (especially fossils) on a reference tree, (2) determine which characters and character partitions are most relevant in defining the phylogenetic placement, (3) assess the confidence of the results, and (4) define the optimal analytical conditions to place the query species. PlaceMyFossils combines several analyses implemented as an interactive script for TNT (Tree Analysis Using New Technologies software), a popular—and free—phylogenetic software that is widely used in paleontological studies. Finally, we demonstrate the utility and investigate the performance of PlaceMyFossils compared to other available tools using two disparate empirical datasets drawn from conifers and dinosaurs. While primarily designed for working with fossils, this tool also holds great potential for advancing morphological and molecular systematics. It offers a powerful resource for empirical systematists aiming to integrate molecular and morphological data. This is particularly relevant given the growing interest in morphological evolution as a complementary perspective on evolutionary processes and the drivers of diversification.
Fil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentina. American Museum of Natural History; Estados Unidos
Fil: Escapa, Ignacio Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Museo Paleontológico Egidio Feruglio; Argentina
Fil: Pugh, Kelsey D.. American Museum of Natural History; Estados Unidos
Fil: Hammond, Ashley S. American Museum of Natural History; Estados Unidos
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina
Fil: Almécija, Sergio. American Museum of Natural History; Estados Unidos. Universitat Autònoma de Barcelona; España
description In recent years, there has been a growing interest in using morphology to establish the placement of species on phylogenetic trees derived from molecular data. This is relevant in the case of recently extinct or fossil species, which are usually represented only by fragmentary morphology. In the latter case, constrained analyses using backbone trees have also proven helpful in evaluating the placement of fragmentary specimens on phylogenetic trees derived from morphological data. Consequently, several available phylogenetic programs now include functions to run constrained searches. However, a comprehensive evaluation of the obtained results is not readily available within existing analytical tools. Here, we present an integrated approach—PlaceMyFossils—specifically designed to (1) thoroughly evaluate the phylogenetic placement of given query species (especially fossils) on a reference tree, (2) determine which characters and character partitions are most relevant in defining the phylogenetic placement, (3) assess the confidence of the results, and (4) define the optimal analytical conditions to place the query species. PlaceMyFossils combines several analyses implemented as an interactive script for TNT (Tree Analysis Using New Technologies software), a popular—and free—phylogenetic software that is widely used in paleontological studies. Finally, we demonstrate the utility and investigate the performance of PlaceMyFossils compared to other available tools using two disparate empirical datasets drawn from conifers and dinosaurs. While primarily designed for working with fossils, this tool also holds great potential for advancing morphological and molecular systematics. It offers a powerful resource for empirical systematists aiming to integrate molecular and morphological data. This is particularly relevant given the growing interest in morphological evolution as a complementary perspective on evolutionary processes and the drivers of diversification.
publishDate 2025
dc.date.none.fl_str_mv 2025-04
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/11336/265152
Catalano, Santiago Andres; Escapa, Ignacio Hernán; Pugh, Kelsey D.; Hammond, Ashley S; Goloboff, Pablo Augusto; et al.; PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees; Oxford University Press; Systematic Biology; 2025; 4-2025; 1-29
1063-5157
CONICET Digital
CONICET
url http://hdl.handle.net/11336/265152
identifier_str_mv Catalano, Santiago Andres; Escapa, Ignacio Hernán; Pugh, Kelsey D.; Hammond, Ashley S; Goloboff, Pablo Augusto; et al.; PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees; Oxford University Press; Systematic Biology; 2025; 4-2025; 1-29
1063-5157
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://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syaf025/8115461
info:eu-repo/semantics/altIdentifier/doi/10.1093/sysbio/syaf025
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 Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
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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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