A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates

Abstract Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Ramp sequences were compared from 247 vertebrates (114 Mamm...

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Autores principales:	Lauren M. McKinnon, Justin B. Miller, Michael F. Whiting, John S. K. Kauwe, Perry G. Ridge
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5fae049b1040431db2516aa2eae4067f
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spelling	oai:doaj.org-article:5fae049b1040431db2516aa2eae4067f2021-12-02T15:23:01ZA comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates10.1038/s41598-020-78803-32045-2322https://doaj.org/article/5fae049b1040431db2516aa2eae4067f2021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-78803-3https://doaj.org/toc/2045-2322Abstract Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Ramp sequences were compared from 247 vertebrates (114 Mammalian and 133 non-mammalian), where the presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life synthetic tree to determine the number of parallelisms and reversals that occurred, and those results were compared to random permutations. Parsimony and maximum likelihood analyses of the presence and absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, 81% of vertebrate mammalian ramps and 81.2% of other vertebrate ramps had less parallelisms and reversals than the mean from 1000 randomly permuted trees. A chi-square analysis of completely orthologous ramp sequences resulted in a p-value < 0.001 as compared to random chance. Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches if many orthologs are taken into account. However, phylogenomic methods utilizing few orthologs should be cautious in incorporating ramp sequences because individual ramp sequences may provide conflicting signals.Lauren M. McKinnonJustin B. MillerMichael F. WhitingJohn S. K. KauwePerry G. RidgeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lauren M. McKinnon Justin B. Miller Michael F. Whiting John S. K. Kauwe Perry G. Ridge A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates
description	Abstract Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Ramp sequences were compared from 247 vertebrates (114 Mammalian and 133 non-mammalian), where the presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life synthetic tree to determine the number of parallelisms and reversals that occurred, and those results were compared to random permutations. Parsimony and maximum likelihood analyses of the presence and absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, 81% of vertebrate mammalian ramps and 81.2% of other vertebrate ramps had less parallelisms and reversals than the mean from 1000 randomly permuted trees. A chi-square analysis of completely orthologous ramp sequences resulted in a p-value < 0.001 as compared to random chance. Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches if many orthologs are taken into account. However, phylogenomic methods utilizing few orthologs should be cautious in incorporating ramp sequences because individual ramp sequences may provide conflicting signals.
format	article
author	Lauren M. McKinnon Justin B. Miller Michael F. Whiting John S. K. Kauwe Perry G. Ridge
author_facet	Lauren M. McKinnon Justin B. Miller Michael F. Whiting John S. K. Kauwe Perry G. Ridge
author_sort	Lauren M. McKinnon
title	A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates
title_short	A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates
title_full	A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates
title_fullStr	A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates
title_full_unstemmed	A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates
title_sort	comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/5fae049b1040431db2516aa2eae4067f
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A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates

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