Cargando…

Phylogenetic congruence, conflict and consilience between molecular and morphological data

Morphology and molecules are important data sources for estimating evolutionary relationships. Modern studies often utilise morphological and molecular partitions alongside each other in combined analyses. However, the effect of combining phenomic and genomic partitions is unclear. This is exacerbat...

Descripción completa

Detalles Bibliográficos
Autores principales: Keating, Joseph N, Garwood, Russell J, Sansom, Robert S
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10321016/
https://www.ncbi.nlm.nih.gov/pubmed/37403037
http://dx.doi.org/10.1186/s12862-023-02131-z
_version_ 1785068552093433856
author Keating, Joseph N
Garwood, Russell J
Sansom, Robert S
author_facet Keating, Joseph N
Garwood, Russell J
Sansom, Robert S
author_sort Keating, Joseph N
collection PubMed
description Morphology and molecules are important data sources for estimating evolutionary relationships. Modern studies often utilise morphological and molecular partitions alongside each other in combined analyses. However, the effect of combining phenomic and genomic partitions is unclear. This is exacerbated by their size imbalance, and conflict over the efficacy of different inference methods when using morphological characters. To systematically address the effect of topological incongruence, size imbalance, and tree inference methods, we conduct a meta-analysis of 32 combined (molecular + morphology) datasets across metazoa. Our results reveal that morphological-molecular topological incongruence is pervasive: these data partitions yield very different trees, irrespective of which method is used for morphology inference. Analysis of the combined data often yields unique trees that are not sampled by either partition individually, even with the inclusion of relatively small quantities of morphological characters. Differences between morphology inference methods in terms of resolution and congruence largely relate to consensus methods. Furthermore, stepping stone Bayes factor analyses reveal that morphological and molecular partitions are not consistently combinable, i.e. data partitions are not always best explained under a single evolutionary process. In light of these results, we advise that the congruence between morphological and molecular data partitions needs to be considered in combined analyses. Nonetheless, our results reveal that, for most datasets, morphology and molecules can, and should, be combined in order to best estimate evolutionary history and reveal hidden support for novel relationships. Studies that analyse only phenomic or genomic data in isolation are unlikely to provide the full evolutionary picture. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-023-02131-z.
format Online
Article
Text
id pubmed-10321016
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-103210162023-07-06 Phylogenetic congruence, conflict and consilience between molecular and morphological data Keating, Joseph N Garwood, Russell J Sansom, Robert S BMC Ecol Evol Research Morphology and molecules are important data sources for estimating evolutionary relationships. Modern studies often utilise morphological and molecular partitions alongside each other in combined analyses. However, the effect of combining phenomic and genomic partitions is unclear. This is exacerbated by their size imbalance, and conflict over the efficacy of different inference methods when using morphological characters. To systematically address the effect of topological incongruence, size imbalance, and tree inference methods, we conduct a meta-analysis of 32 combined (molecular + morphology) datasets across metazoa. Our results reveal that morphological-molecular topological incongruence is pervasive: these data partitions yield very different trees, irrespective of which method is used for morphology inference. Analysis of the combined data often yields unique trees that are not sampled by either partition individually, even with the inclusion of relatively small quantities of morphological characters. Differences between morphology inference methods in terms of resolution and congruence largely relate to consensus methods. Furthermore, stepping stone Bayes factor analyses reveal that morphological and molecular partitions are not consistently combinable, i.e. data partitions are not always best explained under a single evolutionary process. In light of these results, we advise that the congruence between morphological and molecular data partitions needs to be considered in combined analyses. Nonetheless, our results reveal that, for most datasets, morphology and molecules can, and should, be combined in order to best estimate evolutionary history and reveal hidden support for novel relationships. Studies that analyse only phenomic or genomic data in isolation are unlikely to provide the full evolutionary picture. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-023-02131-z. BioMed Central 2023-07-05 /pmc/articles/PMC10321016/ /pubmed/37403037 http://dx.doi.org/10.1186/s12862-023-02131-z Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Keating, Joseph N
Garwood, Russell J
Sansom, Robert S
Phylogenetic congruence, conflict and consilience between molecular and morphological data
title Phylogenetic congruence, conflict and consilience between molecular and morphological data
title_full Phylogenetic congruence, conflict and consilience between molecular and morphological data
title_fullStr Phylogenetic congruence, conflict and consilience between molecular and morphological data
title_full_unstemmed Phylogenetic congruence, conflict and consilience between molecular and morphological data
title_short Phylogenetic congruence, conflict and consilience between molecular and morphological data
title_sort phylogenetic congruence, conflict and consilience between molecular and morphological data
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10321016/
https://www.ncbi.nlm.nih.gov/pubmed/37403037
http://dx.doi.org/10.1186/s12862-023-02131-z
work_keys_str_mv AT keatingjosephn phylogeneticcongruenceconflictandconsiliencebetweenmolecularandmorphologicaldata
AT garwoodrussellj phylogeneticcongruenceconflictandconsiliencebetweenmolecularandmorphologicaldata
AT sansomroberts phylogeneticcongruenceconflictandconsiliencebetweenmolecularandmorphologicaldata