Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)

It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explo...

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Autores principales:	Xiaoyan Sun, Jinhui Cheng
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	concerted evolution secondary structure heterogeneity Bayesian spinicaudata Genetics QH426-470
Acceso en línea:	https://doaj.org/article/ac74ef0ca2c44b1e8d69ff33bbba27f3
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id	oai:doaj.org-article:ac74ef0ca2c44b1e8d69ff33bbba27f3
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spelling	oai:doaj.org-article:ac74ef0ca2c44b1e8d69ff33bbba27f32021-11-25T17:41:01ZPhylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)10.3390/genes121117052073-4425https://doaj.org/article/ac74ef0ca2c44b1e8d69ff33bbba27f32021-10-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1705https://doaj.org/toc/2073-4425It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the <i>28S rRNA</i> gene. The Bayesian analyses were performed on nuclear (<i>28S rRNA</i>, <i>EF1α</i>) and mitochondrial (<i>16S rRNA</i>, <i>COI</i>) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.Xiaoyan SunJinhui ChengMDPI AGarticleconcerted evolutionsecondary structureheterogeneityBayesianspinicaudataGeneticsQH426-470ENGenes, Vol 12, Iss 1705, p 1705 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	concerted evolution secondary structure heterogeneity Bayesian spinicaudata Genetics QH426-470
spellingShingle	concerted evolution secondary structure heterogeneity Bayesian spinicaudata Genetics QH426-470 Xiaoyan Sun Jinhui Cheng Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)
description	It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the <i>28S rRNA</i> gene. The Bayesian analyses were performed on nuclear (<i>28S rRNA</i>, <i>EF1α</i>) and mitochondrial (<i>16S rRNA</i>, <i>COI</i>) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.
format	article
author	Xiaoyan Sun Jinhui Cheng
author_facet	Xiaoyan Sun Jinhui Cheng
author_sort	Xiaoyan Sun
title	Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)
title_short	Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)
title_full	Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)
title_fullStr	Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)
title_full_unstemmed	Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)
title_sort	phylogenetic signal dissection of heterogeneous 28s and 16s rrna genes in spinicaudata (branchiopoda, diplostraca)
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/ac74ef0ca2c44b1e8d69ff33bbba27f3
work_keys_str_mv	AT xiaoyansun phylogeneticsignaldissectionofheterogeneous28sand16srrnagenesinspinicaudatabranchiopodadiplostraca AT jinhuicheng phylogeneticsignaldissectionofheterogeneous28sand16srrnagenesinspinicaudatabranchiopodadiplostraca
_version_	1718412124556886016

Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)

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