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The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads

Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) m...

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Autores principales: Doronina, Liliya, Matzke, Andreas, Churakov, Gennady, Stoll, Monika, Huge, Andreas, Schmitz, Jürgen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335264/
https://www.ncbi.nlm.nih.gov/pubmed/28256552
http://dx.doi.org/10.1038/srep43562
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author Doronina, Liliya
Matzke, Andreas
Churakov, Gennady
Stoll, Monika
Huge, Andreas
Schmitz, Jürgen
author_facet Doronina, Liliya
Matzke, Andreas
Churakov, Gennady
Stoll, Monika
Huge, Andreas
Schmitz, Jürgen
author_sort Doronina, Liliya
collection PubMed
description Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data).
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spelling pubmed-53352642017-03-07 The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads Doronina, Liliya Matzke, Andreas Churakov, Gennady Stoll, Monika Huge, Andreas Schmitz, Jürgen Sci Rep Article Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data). Nature Publishing Group 2017-03-03 /pmc/articles/PMC5335264/ /pubmed/28256552 http://dx.doi.org/10.1038/srep43562 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Doronina, Liliya
Matzke, Andreas
Churakov, Gennady
Stoll, Monika
Huge, Andreas
Schmitz, Jürgen
The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads
title The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads
title_full The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads
title_fullStr The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads
title_full_unstemmed The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads
title_short The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads
title_sort beaver’s phylogenetic lineage illuminated by retroposon reads
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335264/
https://www.ncbi.nlm.nih.gov/pubmed/28256552
http://dx.doi.org/10.1038/srep43562
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