Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on <i>Paphiopedilum</i> Pfitz. (Orchidaceae)

The phylogeny of the genus <i>Paphiopedilum</i> based on the plastome is consistent with morphological analysis. However, to date, none of the analyzed nuclear markers has confirmed this. Topology incongruence among the trees of different nuclear markers concerns entire sections of the s...

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Autores principales:	Marcin Górniak, Dariusz L. Szlachetko, Natalia Olędrzyńska, Aleksandra M. Naczk, Agata Mieszkowska, Lidia Boss, Marek S. Ziętara
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	homoploid hybridization nuclear genes concatenation molecular dating Orchidaceae <i>Paphiopedilum</i> Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/d57c7a6ce3084606aa8bf039bc1c2f7c
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spelling	oai:doaj.org-article:d57c7a6ce3084606aa8bf039bc1c2f7c2021-11-11T16:52:06ZSpecies Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on <i>Paphiopedilum</i> Pfitz. (Orchidaceae)10.3390/ijms2221113931422-00671661-6596https://doaj.org/article/d57c7a6ce3084606aa8bf039bc1c2f7c2021-10-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/21/11393https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067The phylogeny of the genus <i>Paphiopedilum</i> based on the plastome is consistent with morphological analysis. However, to date, none of the analyzed nuclear markers has confirmed this. Topology incongruence among the trees of different nuclear markers concerns entire sections of the subgenus <i>Paphiopedilum</i>. The low-copy nuclear protein-coding gene <i>PHYC</i> was obtained for 22 species representing all sections and subgenera of <i>Paphiopedilum</i>. The nuclear-based phylogeny is supported by morphological characteristics and plastid data analysis. We assumed that an incongruence in nuclear gene trees is caused by ancestral homoploid hybridization. We present a model for inferring the phylogeny of the species despite the incongruence of the different tree topologies. Our analysis, based on six low-copy nuclear genes, is congruent with plastome phylogeny and has been confirmed by phylogenetic network analysis.Marcin GórniakDariusz L. SzlachetkoNatalia OlędrzyńskaAleksandra M. NaczkAgata MieszkowskaLidia BossMarek S. ZiętaraMDPI AGarticlehomoploid hybridizationnuclear genesconcatenationmolecular datingOrchidaceae<i>Paphiopedilum</i>Biology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 11393, p 11393 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	homoploid hybridization nuclear genes concatenation molecular dating Orchidaceae <i>Paphiopedilum</i> Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	homoploid hybridization nuclear genes concatenation molecular dating Orchidaceae <i>Paphiopedilum</i> Biology (General) QH301-705.5 Chemistry QD1-999 Marcin Górniak Dariusz L. Szlachetko Natalia Olędrzyńska Aleksandra M. Naczk Agata Mieszkowska Lidia Boss Marek S. Ziętara Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on <i>Paphiopedilum</i> Pfitz. (Orchidaceae)
description	The phylogeny of the genus <i>Paphiopedilum</i> based on the plastome is consistent with morphological analysis. However, to date, none of the analyzed nuclear markers has confirmed this. Topology incongruence among the trees of different nuclear markers concerns entire sections of the subgenus <i>Paphiopedilum</i>. The low-copy nuclear protein-coding gene <i>PHYC</i> was obtained for 22 species representing all sections and subgenera of <i>Paphiopedilum</i>. The nuclear-based phylogeny is supported by morphological characteristics and plastid data analysis. We assumed that an incongruence in nuclear gene trees is caused by ancestral homoploid hybridization. We present a model for inferring the phylogeny of the species despite the incongruence of the different tree topologies. Our analysis, based on six low-copy nuclear genes, is congruent with plastome phylogeny and has been confirmed by phylogenetic network analysis.
format	article
author	Marcin Górniak Dariusz L. Szlachetko Natalia Olędrzyńska Aleksandra M. Naczk Agata Mieszkowska Lidia Boss Marek S. Ziętara
author_facet	Marcin Górniak Dariusz L. Szlachetko Natalia Olędrzyńska Aleksandra M. Naczk Agata Mieszkowska Lidia Boss Marek S. Ziętara
author_sort	Marcin Górniak
title	Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on <i>Paphiopedilum</i> Pfitz. (Orchidaceae)
title_short	Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on <i>Paphiopedilum</i> Pfitz. (Orchidaceae)
title_full	Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on <i>Paphiopedilum</i> Pfitz. (Orchidaceae)
title_fullStr	Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on <i>Paphiopedilum</i> Pfitz. (Orchidaceae)
title_full_unstemmed	Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on <i>Paphiopedilum</i> Pfitz. (Orchidaceae)
title_sort	species phylogeny versus gene trees: a case study of an incongruent data matrix based on <i>paphiopedilum</i> pfitz. (orchidaceae)
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/d57c7a6ce3084606aa8bf039bc1c2f7c
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Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on <i>Paphiopedilum</i> Pfitz. (Orchidaceae)

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