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Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms

Ancestral state reconstruction is an important tool to study morphological evolution and often involves estimating transition rates among character states. However, various factors, including taxonomic scale and sampling density, may impact transition rate estimation and indirectly also the probabil...

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Autores principales: Reyes, Elisabeth, Nadot, Sophie, von Balthazar, Maria, Schönenberger, Jürg, Sauquet, Hervé
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013437/
https://www.ncbi.nlm.nih.gov/pubmed/29930308
http://dx.doi.org/10.1038/s41598-018-27750-1
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author Reyes, Elisabeth
Nadot, Sophie
von Balthazar, Maria
Schönenberger, Jürg
Sauquet, Hervé
author_facet Reyes, Elisabeth
Nadot, Sophie
von Balthazar, Maria
Schönenberger, Jürg
Sauquet, Hervé
author_sort Reyes, Elisabeth
collection PubMed
description Ancestral state reconstruction is an important tool to study morphological evolution and often involves estimating transition rates among character states. However, various factors, including taxonomic scale and sampling density, may impact transition rate estimation and indirectly also the probability of the state at a given node. Here, we test the influence of rate heterogeneity using maximum likelihood methods on five binary perianth characters, optimized on a phylogenetic tree of angiosperms including 1230 species sampled from all families. We compare the states reconstructed by an equal-rate (Mk1) and a two-rate model (Mk2) fitted either with a single set of rates for the whole tree or as a partitioned model, allowing for different rates on five partitions of the tree. We find strong signal for rate heterogeneity among the five subdivisions for all five characters, but little overall impact of the choice of model on reconstructed ancestral states, which indicates that most of our inferred ancestral states are the same whether heterogeneity is accounted for or not.
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spelling pubmed-60134372018-06-27 Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms Reyes, Elisabeth Nadot, Sophie von Balthazar, Maria Schönenberger, Jürg Sauquet, Hervé Sci Rep Article Ancestral state reconstruction is an important tool to study morphological evolution and often involves estimating transition rates among character states. However, various factors, including taxonomic scale and sampling density, may impact transition rate estimation and indirectly also the probability of the state at a given node. Here, we test the influence of rate heterogeneity using maximum likelihood methods on five binary perianth characters, optimized on a phylogenetic tree of angiosperms including 1230 species sampled from all families. We compare the states reconstructed by an equal-rate (Mk1) and a two-rate model (Mk2) fitted either with a single set of rates for the whole tree or as a partitioned model, allowing for different rates on five partitions of the tree. We find strong signal for rate heterogeneity among the five subdivisions for all five characters, but little overall impact of the choice of model on reconstructed ancestral states, which indicates that most of our inferred ancestral states are the same whether heterogeneity is accounted for or not. Nature Publishing Group UK 2018-06-21 /pmc/articles/PMC6013437/ /pubmed/29930308 http://dx.doi.org/10.1038/s41598-018-27750-1 Text en © The Author(s) 2018 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Reyes, Elisabeth
Nadot, Sophie
von Balthazar, Maria
Schönenberger, Jürg
Sauquet, Hervé
Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms
title Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms
title_full Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms
title_fullStr Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms
title_full_unstemmed Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms
title_short Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms
title_sort testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013437/
https://www.ncbi.nlm.nih.gov/pubmed/29930308
http://dx.doi.org/10.1038/s41598-018-27750-1
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