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Effects of Taxon Sampling in Reconstructions of Intron Evolution

Introns comprise a considerable portion of eukaryotic genomes; however, their evolution is understudied. Numerous works of the last years largely disagree on many aspects of intron evolution. Interpretation of these differences is hindered because different algorithms and taxon sampling strategies w...

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Detalles Bibliográficos
Autores principales: Nikitin, Mikhail A., Aleoshin, Vladimir V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3647540/
https://www.ncbi.nlm.nih.gov/pubmed/23671844
http://dx.doi.org/10.1155/2013/671316
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author Nikitin, Mikhail A.
Aleoshin, Vladimir V.
author_facet Nikitin, Mikhail A.
Aleoshin, Vladimir V.
author_sort Nikitin, Mikhail A.
collection PubMed
description Introns comprise a considerable portion of eukaryotic genomes; however, their evolution is understudied. Numerous works of the last years largely disagree on many aspects of intron evolution. Interpretation of these differences is hindered because different algorithms and taxon sampling strategies were used. Here, we present the first attempt of a systematic evaluation of the effects of taxon sampling on popular intron evolution estimation algorithms. Using the “taxon jackknife” method, we compared the effect of taxon sampling on the behavior of intron evolution inferring algorithms. We show that taxon sampling can dramatically affect the inferences and identify conditions where algorithms are prone to systematic errors. Presence or absence of some key species is often more important than the taxon sampling size alone. Criteria of representativeness of the taxonomic sampling for reliable reconstructions are outlined. Presence of the deep-branching species with relatively high intron density is more important than sheer number of species. According to these criteria, currently available genomic databases are representative enough to provide reliable inferences of the intron evolution in animals, land plants, and fungi, but they underrepresent many groups of unicellular eukaryotes, including the well-studied Alveolata.
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spelling pubmed-36475402013-05-13 Effects of Taxon Sampling in Reconstructions of Intron Evolution Nikitin, Mikhail A. Aleoshin, Vladimir V. Int J Genomics Research Article Introns comprise a considerable portion of eukaryotic genomes; however, their evolution is understudied. Numerous works of the last years largely disagree on many aspects of intron evolution. Interpretation of these differences is hindered because different algorithms and taxon sampling strategies were used. Here, we present the first attempt of a systematic evaluation of the effects of taxon sampling on popular intron evolution estimation algorithms. Using the “taxon jackknife” method, we compared the effect of taxon sampling on the behavior of intron evolution inferring algorithms. We show that taxon sampling can dramatically affect the inferences and identify conditions where algorithms are prone to systematic errors. Presence or absence of some key species is often more important than the taxon sampling size alone. Criteria of representativeness of the taxonomic sampling for reliable reconstructions are outlined. Presence of the deep-branching species with relatively high intron density is more important than sheer number of species. According to these criteria, currently available genomic databases are representative enough to provide reliable inferences of the intron evolution in animals, land plants, and fungi, but they underrepresent many groups of unicellular eukaryotes, including the well-studied Alveolata. Hindawi Publishing Corporation 2013 2013-03-03 /pmc/articles/PMC3647540/ /pubmed/23671844 http://dx.doi.org/10.1155/2013/671316 Text en Copyright © 2013 M. A. Nikitin and V. V. Aleoshin. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Nikitin, Mikhail A.
Aleoshin, Vladimir V.
Effects of Taxon Sampling in Reconstructions of Intron Evolution
title Effects of Taxon Sampling in Reconstructions of Intron Evolution
title_full Effects of Taxon Sampling in Reconstructions of Intron Evolution
title_fullStr Effects of Taxon Sampling in Reconstructions of Intron Evolution
title_full_unstemmed Effects of Taxon Sampling in Reconstructions of Intron Evolution
title_short Effects of Taxon Sampling in Reconstructions of Intron Evolution
title_sort effects of taxon sampling in reconstructions of intron evolution
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3647540/
https://www.ncbi.nlm.nih.gov/pubmed/23671844
http://dx.doi.org/10.1155/2013/671316
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