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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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Autores principales: Doronina, Liliya, Ogoniak, Lynn, Schmitz, Jürgen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10531181/
https://www.ncbi.nlm.nih.gov/pubmed/37761970
http://dx.doi.org/10.3390/genes14091830
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author Doronina, Liliya
Ogoniak, Lynn
Schmitz, Jürgen
author_facet Doronina, Liliya
Ogoniak, Lynn
Schmitz, Jürgen
author_sort Doronina, Liliya
collection PubMed
description 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.
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spelling pubmed-105311812023-09-28 Homoplasy of Retrotransposon Insertions in Toothed Whales Doronina, Liliya Ogoniak, Lynn Schmitz, Jürgen Genes (Basel) Article 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. MDPI 2023-09-21 /pmc/articles/PMC10531181/ /pubmed/37761970 http://dx.doi.org/10.3390/genes14091830 Text en © 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/).
spellingShingle Article
Doronina, Liliya
Ogoniak, Lynn
Schmitz, Jürgen
Homoplasy of Retrotransposon Insertions in Toothed Whales
title 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_short Homoplasy of Retrotransposon Insertions in Toothed Whales
title_sort homoplasy of retrotransposon insertions in toothed whales
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10531181/
https://www.ncbi.nlm.nih.gov/pubmed/37761970
http://dx.doi.org/10.3390/genes14091830
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