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Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida

Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI) from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency...

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Autores principales: Young, Monica R, Hebert, Paul D. N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550450/
https://www.ncbi.nlm.nih.gov/pubmed/26308206
http://dx.doi.org/10.1371/journal.pone.0135053
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author Young, Monica R
Hebert, Paul D. N.
author_facet Young, Monica R
Hebert, Paul D. N.
author_sort Young, Monica R
collection PubMed
description Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI) from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids, including representatives from all 16 orders and 43% of its families (267/625). It examines divergences at three taxonomic levels—among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10–0.39), while the mean of the Family Distances for the ten orders ranges fivefold (0.07–0.35). BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration. Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is ‘locked down’ in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in ‘locked down’ taxa.
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spelling pubmed-45504502015-09-01 Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida Young, Monica R Hebert, Paul D. N. PLoS One Research Article Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI) from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids, including representatives from all 16 orders and 43% of its families (267/625). It examines divergences at three taxonomic levels—among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10–0.39), while the mean of the Family Distances for the ten orders ranges fivefold (0.07–0.35). BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration. Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is ‘locked down’ in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in ‘locked down’ taxa. Public Library of Science 2015-08-26 /pmc/articles/PMC4550450/ /pubmed/26308206 http://dx.doi.org/10.1371/journal.pone.0135053 Text en © 2015 Young, Hebert http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Young, Monica R
Hebert, Paul D. N.
Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida
title Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida
title_full Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida
title_fullStr Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida
title_full_unstemmed Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida
title_short Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida
title_sort patterns of protein evolution in cytochrome c oxidase 1 (coi) from the class arachnida
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550450/
https://www.ncbi.nlm.nih.gov/pubmed/26308206
http://dx.doi.org/10.1371/journal.pone.0135053
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