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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ftdatacite:10.6084/m9.figshare.c.4373432.v1 2023-05-15T15:36:59+02:00 Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation Fritjof Lammers Blumer, Moritz RĂźcklĂŠ, Cornelia Nilsson, Maria 2019 https://dx.doi.org/10.6084/m9.figshare.c.4373432.v1 https://springernature.figshare.com/collections/Retrophylogenomics_in_rorquals_indicate_large_ancestral_population_sizes_and_a_rapid_radiation/4373432/1 unknown Figshare https://dx.doi.org/10.1186/s13100-018-0143-2 https://dx.doi.org/10.6084/m9.figshare.c.4373432 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Cell Biology Genetics FOS Biological sciences Evolutionary Biology Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Cancer Inorganic Chemistry FOS Chemical sciences Collection article 2019 ftdatacite https://doi.org/10.6084/m9.figshare.c.4373432.v1 https://doi.org/10.1186/s13100-018-0143-2 https://doi.org/10.6084/m9.figshare.c.4373432 2021-11-05T12:55:41Z 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 DataCite Metadata Store (German National Library of Science and Technology) Rorqual ENVELOPE(-62.311,-62.311,-65.648,-65.648) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Cell Biology Genetics FOS Biological sciences Evolutionary Biology Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Cancer Inorganic Chemistry FOS Chemical sciences |
spellingShingle |
Cell Biology Genetics FOS Biological sciences Evolutionary Biology Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Cancer Inorganic Chemistry FOS Chemical sciences Fritjof Lammers Blumer, Moritz RĂźcklĂŠ, Cornelia Nilsson, Maria Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation |
topic_facet |
Cell Biology Genetics FOS Biological sciences Evolutionary Biology Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Cancer Inorganic Chemistry FOS Chemical sciences |
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 Blumer, Moritz RĂźcklĂŠ, Cornelia Nilsson, Maria |
author_facet |
Fritjof Lammers Blumer, Moritz RĂźcklĂŠ, Cornelia Nilsson, Maria |
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 |
Figshare |
publishDate |
2019 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.4373432.v1 https://springernature.figshare.com/collections/Retrophylogenomics_in_rorquals_indicate_large_ancestral_population_sizes_and_a_rapid_radiation/4373432/1 |
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_relation |
https://dx.doi.org/10.1186/s13100-018-0143-2 https://dx.doi.org/10.6084/m9.figshare.c.4373432 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.4373432.v1 https://doi.org/10.1186/s13100-018-0143-2 https://doi.org/10.6084/m9.figshare.c.4373432 |
_version_ |
1766367421390651392 |