Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.

Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the...

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Autores principales:	Adina J Renz, Axel Meyer, Shigehiro Kuraku
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/be316a792f1c48c48d891866e747dfb0
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spelling	oai:doaj.org-article:be316a792f1c48c48d891866e747dfb02021-11-18T07:40:11ZRevealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.1932-620310.1371/journal.pone.0066400https://doaj.org/article/be316a792f1c48c48d891866e747dfb02013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23825540/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon.Adina J RenzAxel MeyerShigehiro KurakuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 6, p e66400 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Adina J Renz Axel Meyer Shigehiro Kuraku Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.
description	Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon.
format	article
author	Adina J Renz Axel Meyer Shigehiro Kuraku
author_facet	Adina J Renz Axel Meyer Shigehiro Kuraku
author_sort	Adina J Renz
title	Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.
title_short	Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.
title_full	Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.
title_fullStr	Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.
title_full_unstemmed	Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.
title_sort	revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/be316a792f1c48c48d891866e747dfb0
work_keys_str_mv	AT adinajrenz revealinglessderivednatureofcartilaginousfishgenomeswiththeirevolutionarytimescaleinferredwithnucleargenes AT axelmeyer revealinglessderivednatureofcartilaginousfishgenomeswiththeirevolutionarytimescaleinferredwithnucleargenes AT shigehirokuraku revealinglessderivednatureofcartilaginousfishgenomeswiththeirevolutionarytimescaleinferredwithnucleargenes
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Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.

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