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Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation

BACKGROUND: Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolu...

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Autores principales: Lammers, Fritjof, Blumer, Moritz, Rücklé, Cornelia, Nilsson, Maria A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6340175/
https://www.ncbi.nlm.nih.gov/pubmed/30679961
http://dx.doi.org/10.1186/s13100-018-0143-2
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author Lammers, Fritjof
Blumer, Moritz
Rücklé, Cornelia
Nilsson, Maria A.
author_facet Lammers, Fritjof
Blumer, Moritz
Rücklé, Cornelia
Nilsson, Maria A.
author_sort Lammers, Fritjof
collection PubMed
description BACKGROUND: Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolutionary processes such as gene flow and incomplete lineage sorting (ILS). Here, whole-genome sequencing data of the extant baleen whale radiation allowed us to identify transposable element (TE) insertions in order to perform phylogenomic analyses and measure germline insertion rates of TEs. Baleen whales exhibit the slowest nucleotide substitution rate among mammals, hence we additionally examined the evolutionary insertion rates of TE insertions across the genomes. RESULTS: In eleven whole-genome sequences representing the extant radiation of baleen whales, we identified 91,859 CHR-SINE insertions that were used to reconstruct the phylogeny with different approaches as well as perform evolutionary network analyses and a quantification of conflicting phylogenetic signals. Our results indicate that the radiation of rorquals and gray whales might not be bifurcating. The morphologically derived gray whales are placed inside the rorqual group, as the sister-species to humpback and fin whales. Detailed investigation of TE insertion rates confirm that a mutational slow down in the whale lineage is present but less pronounced for TEs than for nucleotide substitutions. CONCLUSIONS: Whole genome sequencing based detection of TE insertions showed that the speciation processes in baleen whales represent a rapid radiation. Large genome-scale TE data sets in addition allow to understand retrotransposition rates in non-model organisms and show the potential for TE calling methods to study the evolutionary history of species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13100-018-0143-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-63401752019-01-24 Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation Lammers, Fritjof Blumer, Moritz Rücklé, Cornelia Nilsson, Maria A. Mob DNA Research BACKGROUND: Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolutionary processes such as gene flow and incomplete lineage sorting (ILS). Here, whole-genome sequencing data of the extant baleen whale radiation allowed us to identify transposable element (TE) insertions in order to perform phylogenomic analyses and measure germline insertion rates of TEs. Baleen whales exhibit the slowest nucleotide substitution rate among mammals, hence we additionally examined the evolutionary insertion rates of TE insertions across the genomes. RESULTS: In eleven whole-genome sequences representing the extant radiation of baleen whales, we identified 91,859 CHR-SINE insertions that were used to reconstruct the phylogeny with different approaches as well as perform evolutionary network analyses and a quantification of conflicting phylogenetic signals. Our results indicate that the radiation of rorquals and gray whales might not be bifurcating. The morphologically derived gray whales are placed inside the rorqual group, as the sister-species to humpback and fin whales. Detailed investigation of TE insertion rates confirm that a mutational slow down in the whale lineage is present but less pronounced for TEs than for nucleotide substitutions. CONCLUSIONS: Whole genome sequencing based detection of TE insertions showed that the speciation processes in baleen whales represent a rapid radiation. Large genome-scale TE data sets in addition allow to understand retrotransposition rates in non-model organisms and show the potential for TE calling methods to study the evolutionary history of species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13100-018-0143-2) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-21 /pmc/articles/PMC6340175/ /pubmed/30679961 http://dx.doi.org/10.1186/s13100-018-0143-2 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Lammers, Fritjof
Blumer, Moritz
Rücklé, Cornelia
Nilsson, Maria A.
Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
title Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
title_full Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
title_fullStr Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
title_full_unstemmed Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
title_short Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
title_sort retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6340175/
https://www.ncbi.nlm.nih.gov/pubmed/30679961
http://dx.doi.org/10.1186/s13100-018-0143-2
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