Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.

<h4>Background</h4>Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. Howe...

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Autores principales:	John J Wiens, Jonathan Tiu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ec3fa515e98d45c1a4485790fd2d771c
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spelling	oai:doaj.org-article:ec3fa515e98d45c1a4485790fd2d771c2021-11-18T07:09:05ZHighly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.1932-620310.1371/journal.pone.0042925https://doaj.org/article/ec3fa515e98d45c1a4485790fd2d771c2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22900065/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study).<h4>Methodology/principal findings</h4>We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial.<h4>Conclusions</h4>We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems.John J WiensJonathan TiuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e42925 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q John J Wiens Jonathan Tiu Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.
description	<h4>Background</h4>Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study).<h4>Methodology/principal findings</h4>We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial.<h4>Conclusions</h4>We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems.
format	article
author	John J Wiens Jonathan Tiu
author_facet	John J Wiens Jonathan Tiu
author_sort	John J Wiens
title	Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.
title_short	Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.
title_full	Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.
title_fullStr	Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.
title_full_unstemmed	Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.
title_sort	highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/ec3fa515e98d45c1a4485790fd2d771c
work_keys_str_mv	AT johnjwiens highlyincompletetaxacanrescuephylogeneticanalysesfromthenegativeimpactsoflimitedtaxonsampling AT jonathantiu highlyincompletetaxacanrescuephylogeneticanalysesfromthenegativeimpactsoflimitedtaxonsampling
_version_	1718423888999743488

Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling.

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