Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
Abstract 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...
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ftdoajarticles:oai:doaj.org/article:c3e2b357c5d14293933e901d925b9425 2023-05-15T15:36:59+02:00 Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation Fritjof Lammers Moritz Blumer Cornelia Rücklé Maria A. Nilsson 2019-01-01T00:00:00Z https://doi.org/10.1186/s13100-018-0143-2 https://doaj.org/article/c3e2b357c5d14293933e901d925b9425 EN eng BMC http://link.springer.com/article/10.1186/s13100-018-0143-2 https://doaj.org/toc/1759-8753 doi:10.1186/s13100-018-0143-2 1759-8753 https://doaj.org/article/c3e2b357c5d14293933e901d925b9425 Mobile DNA, Vol 10, Iss 1, Pp 1-10 (2019) Evolution Phylogenetics Whales Transposable elements Retrotransposon Genetics QH426-470 article 2019 ftdoajarticles https://doi.org/10.1186/s13100-018-0143-2 2022-12-31T00:14:05Z Abstract 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. Article in Journal/Newspaper baleen whale baleen whales Directory of Open Access Journals: DOAJ Articles Rorqual ENVELOPE(-62.311,-62.311,-65.648,-65.648) Mobile DNA 10 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Evolution Phylogenetics Whales Transposable elements Retrotransposon Genetics QH426-470 |
spellingShingle |
Evolution Phylogenetics Whales Transposable elements Retrotransposon Genetics QH426-470 Fritjof Lammers Moritz Blumer Cornelia Rücklé Maria A. Nilsson Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation |
topic_facet |
Evolution Phylogenetics Whales Transposable elements Retrotransposon Genetics QH426-470 |
description |
Abstract 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. |
format |
Article in Journal/Newspaper |
author |
Fritjof Lammers Moritz Blumer Cornelia Rücklé Maria A. Nilsson |
author_facet |
Fritjof Lammers Moritz Blumer Cornelia Rücklé Maria A. Nilsson |
author_sort |
Fritjof Lammers |
title |
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_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_sort |
retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation |
publisher |
BMC |
publishDate |
2019 |
url |
https://doi.org/10.1186/s13100-018-0143-2 https://doaj.org/article/c3e2b357c5d14293933e901d925b9425 |
long_lat |
ENVELOPE(-62.311,-62.311,-65.648,-65.648) |
geographic |
Rorqual |
geographic_facet |
Rorqual |
genre |
baleen whale baleen whales |
genre_facet |
baleen whale baleen whales |
op_source |
Mobile DNA, Vol 10, Iss 1, Pp 1-10 (2019) |
op_relation |
http://link.springer.com/article/10.1186/s13100-018-0143-2 https://doaj.org/toc/1759-8753 doi:10.1186/s13100-018-0143-2 1759-8753 https://doaj.org/article/c3e2b357c5d14293933e901d925b9425 |
op_doi |
https://doi.org/10.1186/s13100-018-0143-2 |
container_title |
Mobile DNA |
container_volume |
10 |
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1 |
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1766367426581102592 |