Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.

Reconciling traditional classifications, morphology, and the phylogenetic relationships of brown-spored agaric mushrooms has proven difficult in many groups, due to extensive convergence in morphological features. Here, we address the monophyly of the Bolbitiaceae, a family with over 700 described s...

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Autores principales:	Annamária Tóth, Anton Hausknecht, Irmgard Krisai-Greilhuber, Tamás Papp, Csaba Vágvölgyi, László G Nagy
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9556075a91944521a57944f467b629c4
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spelling	oai:doaj.org-article:9556075a91944521a57944f467b629c42021-11-18T07:57:41ZIteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.1932-620310.1371/journal.pone.0056143https://doaj.org/article/9556075a91944521a57944f467b629c42013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23418526/?tool=EBIhttps://doaj.org/toc/1932-6203Reconciling traditional classifications, morphology, and the phylogenetic relationships of brown-spored agaric mushrooms has proven difficult in many groups, due to extensive convergence in morphological features. Here, we address the monophyly of the Bolbitiaceae, a family with over 700 described species and examine the higher-level relationships within the family using a newly constructed multilocus dataset (ITS, nrLSU rDNA and EF1-alpha). We tested whether the fast-evolving Internal Transcribed Spacer (ITS) sequences can be accurately aligned across the family, by comparing the outcome of two iterative alignment refining approaches (an automated and a manual) and various indel-treatment strategies. We used PRANK to align sequences in both cases. Our results suggest that--although PRANK successfully evades overmatching of gapped sites, referred previously to as alignment overmatching--it infers an unrealistically high number of indel events with natively generated guide-trees. This 'alignment undermatching' could be avoided by using more rigorous (e.g. ML) guide trees. The trees inferred in this study support the monophyly of the core Bolbitiaceae, with the exclusion of Panaeolus, Agrocybe, and some of the genera formerly placed in the family. Bolbitius and Conocybe were found monophyletic, however, Pholiotina and Galerella require redefinition. The phylogeny revealed that stipe coverage type is a poor predictor of phylogenetic relationships, indicating the need for a revision of the intrageneric relationships within Conocybe.Annamária TóthAnton HausknechtIrmgard Krisai-GreilhuberTamás PappCsaba VágvölgyiLászló G NagyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 2, p e56143 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Annamária Tóth Anton Hausknecht Irmgard Krisai-Greilhuber Tamás Papp Csaba Vágvölgyi László G Nagy Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.
description	Reconciling traditional classifications, morphology, and the phylogenetic relationships of brown-spored agaric mushrooms has proven difficult in many groups, due to extensive convergence in morphological features. Here, we address the monophyly of the Bolbitiaceae, a family with over 700 described species and examine the higher-level relationships within the family using a newly constructed multilocus dataset (ITS, nrLSU rDNA and EF1-alpha). We tested whether the fast-evolving Internal Transcribed Spacer (ITS) sequences can be accurately aligned across the family, by comparing the outcome of two iterative alignment refining approaches (an automated and a manual) and various indel-treatment strategies. We used PRANK to align sequences in both cases. Our results suggest that--although PRANK successfully evades overmatching of gapped sites, referred previously to as alignment overmatching--it infers an unrealistically high number of indel events with natively generated guide-trees. This 'alignment undermatching' could be avoided by using more rigorous (e.g. ML) guide trees. The trees inferred in this study support the monophyly of the core Bolbitiaceae, with the exclusion of Panaeolus, Agrocybe, and some of the genera formerly placed in the family. Bolbitius and Conocybe were found monophyletic, however, Pholiotina and Galerella require redefinition. The phylogeny revealed that stipe coverage type is a poor predictor of phylogenetic relationships, indicating the need for a revision of the intrageneric relationships within Conocybe.
format	article
author	Annamária Tóth Anton Hausknecht Irmgard Krisai-Greilhuber Tamás Papp Csaba Vágvölgyi László G Nagy
author_facet	Annamária Tóth Anton Hausknecht Irmgard Krisai-Greilhuber Tamás Papp Csaba Vágvölgyi László G Nagy
author_sort	Annamária Tóth
title	Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.
title_short	Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.
title_full	Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.
title_fullStr	Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.
title_full_unstemmed	Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.
title_sort	iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family bolbitiaceae.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/9556075a91944521a57944f467b629c4
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Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.

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