A Practical Guide to Design and Assess a Phylogenomic Study

Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of “big data” molecular phylogenetics provided a battery of new tools for biologists bu...

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Autor: Lozano Fernández, Jesús
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/304287
Acceso en línea:http://hdl.handle.net/10261/304287
Access Level:acceso abierto
Palabra clave:Systematics
Systematic error
High-throughput sequencing
Models of sequence evolution
Phylogenetics
Genomics
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spelling A Practical Guide to Design and Assess a Phylogenomic StudyLozano Fernández, JesúsSystematicsSystematic errorHigh-throughput sequencingModels of sequence evolutionPhylogeneticsGenomicsOver the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of “big data” molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phylogenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of “more genes, more robustness” often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when planning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the technical robustness of phylogenomic studies or improve the experimental design of a project.J.L.-F. was supported by a Juan de la Cierva Incorporación fellowship (Ministerio de Ciencia e Innovación, IJC2018-035237-I).Oxford University PressMinisterio de Ciencia e Innovación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2023202320222023info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/304287reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/IJC2018-035237-I/https://doi.org/10.1093/gbe/evac129Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3042872026-05-22T06:33:51Z
dc.title.none.fl_str_mv A Practical Guide to Design and Assess a Phylogenomic Study
title A Practical Guide to Design and Assess a Phylogenomic Study
spellingShingle A Practical Guide to Design and Assess a Phylogenomic Study
Lozano Fernández, Jesús
Systematics
Systematic error
High-throughput sequencing
Models of sequence evolution
Phylogenetics
Genomics
title_short A Practical Guide to Design and Assess a Phylogenomic Study
title_full A Practical Guide to Design and Assess a Phylogenomic Study
title_fullStr A Practical Guide to Design and Assess a Phylogenomic Study
title_full_unstemmed A Practical Guide to Design and Assess a Phylogenomic Study
title_sort A Practical Guide to Design and Assess a Phylogenomic Study
dc.creator.none.fl_str_mv Lozano Fernández, Jesús
author Lozano Fernández, Jesús
author_facet Lozano Fernández, Jesús
author_role author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Systematics
Systematic error
High-throughput sequencing
Models of sequence evolution
Phylogenetics
Genomics
topic Systematics
Systematic error
High-throughput sequencing
Models of sequence evolution
Phylogenetics
Genomics
description Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of “big data” molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phylogenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of “more genes, more robustness” often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when planning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the technical robustness of phylogenomic studies or improve the experimental design of a project.
publishDate 2022
dc.date.none.fl_str_mv 2022
2023
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/304287
url http://hdl.handle.net/10261/304287
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/IJC2018-035237-I/
https://doi.org/10.1093/gbe/evac129
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 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:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
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