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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/265152
Ver los metadatos del registro completo
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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 |
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CONICET Digital (CONICET) |
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CONICET Digital (CONICET) |
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Consejo Nacional de Investigaciones Científicas y Técnicas |
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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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1844614130761203712 |
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13.070432 |