Homoplasy of Retrotransposon Insertions in Toothed Whales
Retrotransposon insertion patterns facilitate a virtually homoplasy-free picture of phylogenetic history. Still, a few most likely random parallel insertions or deletions result in rare cases of homoplasy in primates. The following question arises: how frequent is retrotransposon homoplasy in other...
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ftpubmed:oai:pubmedcentral.nih.gov:10531181 2023-10-29T02:40:42+01:00 Homoplasy of Retrotransposon Insertions in Toothed Whales Doronina, Liliya Ogoniak, Lynn Schmitz, Jürgen 2023-09-21 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10531181/ https://doi.org/10.3390/genes14091830 en eng MDPI http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10531181/ http://dx.doi.org/10.3390/genes14091830 © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Genes (Basel) Article Text 2023 ftpubmed https://doi.org/10.3390/genes14091830 2023-10-01T01:11:04Z Retrotransposon insertion patterns facilitate a virtually homoplasy-free picture of phylogenetic history. Still, a few most likely random parallel insertions or deletions result in rare cases of homoplasy in primates. The following question arises: how frequent is retrotransposon homoplasy in other phylogenetic clades? Here, we derived genome insertion data of toothed whales to evaluate the extension of homoplasy in a representative laurasiatherian group. Among more than a thousand extracted and aligned retrotransposon loci, we detected 37 cases of precise parallel insertions in species that are separated by over more than 10 million years, a time frame which minimizes the effects of incomplete lineage sorting. We compared the phylogenetic signal of insertions with the flanking sequences of these loci to further exclude potential polymorphic loci derived by incomplete lineage sorting. We found that the phylogenetic signals of retrotransposon insertion patterns exhibiting true homoplasy differ from the signals of their flanking sequences. In toothed whales, precise parallel insertions account for around 0.18–0.29% of insertion cases, which is about 12.5 times the frequency of such insertions among Alus in primates. We also detected five specific deletions of retrotransposons on various lineages of toothed whale evolution, a frequency of 0.003%, which is slightly higher than such occurrences in primates. Overall, the level of retrotransposon homoplasy in toothed whales is still marginal compared to the phylogenetic diagnostic retrotransposon presence/absence signal. Text toothed whale toothed whales PubMed Central (PMC) Genes 14 9 1830 |
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Article Doronina, Liliya Ogoniak, Lynn Schmitz, Jürgen Homoplasy of Retrotransposon Insertions in Toothed Whales |
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Retrotransposon insertion patterns facilitate a virtually homoplasy-free picture of phylogenetic history. Still, a few most likely random parallel insertions or deletions result in rare cases of homoplasy in primates. The following question arises: how frequent is retrotransposon homoplasy in other phylogenetic clades? Here, we derived genome insertion data of toothed whales to evaluate the extension of homoplasy in a representative laurasiatherian group. Among more than a thousand extracted and aligned retrotransposon loci, we detected 37 cases of precise parallel insertions in species that are separated by over more than 10 million years, a time frame which minimizes the effects of incomplete lineage sorting. We compared the phylogenetic signal of insertions with the flanking sequences of these loci to further exclude potential polymorphic loci derived by incomplete lineage sorting. We found that the phylogenetic signals of retrotransposon insertion patterns exhibiting true homoplasy differ from the signals of their flanking sequences. In toothed whales, precise parallel insertions account for around 0.18–0.29% of insertion cases, which is about 12.5 times the frequency of such insertions among Alus in primates. We also detected five specific deletions of retrotransposons on various lineages of toothed whale evolution, a frequency of 0.003%, which is slightly higher than such occurrences in primates. Overall, the level of retrotransposon homoplasy in toothed whales is still marginal compared to the phylogenetic diagnostic retrotransposon presence/absence signal. |
format |
Text |
author |
Doronina, Liliya Ogoniak, Lynn Schmitz, Jürgen |
author_facet |
Doronina, Liliya Ogoniak, Lynn Schmitz, Jürgen |
author_sort |
Doronina, Liliya |
title |
Homoplasy of Retrotransposon Insertions in Toothed Whales |
title_short |
Homoplasy of Retrotransposon Insertions in Toothed Whales |
title_full |
Homoplasy of Retrotransposon Insertions in Toothed Whales |
title_fullStr |
Homoplasy of Retrotransposon Insertions in Toothed Whales |
title_full_unstemmed |
Homoplasy of Retrotransposon Insertions in Toothed Whales |
title_sort |
homoplasy of retrotransposon insertions in toothed whales |
publisher |
MDPI |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10531181/ https://doi.org/10.3390/genes14091830 |
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toothed whale toothed whales |
genre_facet |
toothed whale toothed whales |
op_source |
Genes (Basel) |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10531181/ http://dx.doi.org/10.3390/genes14091830 |
op_rights |
© 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
op_doi |
https://doi.org/10.3390/genes14091830 |
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Genes |
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14 |
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9 |
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1830 |
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1781069106578980864 |