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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2023
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ftdoajarticles:oai:doaj.org/article:c64d284115834c03afc7f2d3ad72babb 2023-10-29T02:40:42+01:00 Homoplasy of Retrotransposon Insertions in Toothed Whales Liliya Doronina Lynn Ogoniak Jürgen Schmitz 2023-09-01T00:00:00Z https://doi.org/10.3390/genes14091830 https://doaj.org/article/c64d284115834c03afc7f2d3ad72babb EN eng MDPI AG https://www.mdpi.com/2073-4425/14/9/1830 https://doaj.org/toc/2073-4425 doi:10.3390/genes14091830 2073-4425 https://doaj.org/article/c64d284115834c03afc7f2d3ad72babb Genes, Vol 14, Iss 1830, p 1830 (2023) retrotransposons homoplasy parallel insertions retrotransposon deletions whales Odontoceti Genetics QH426-470 article 2023 ftdoajarticles https://doi.org/10.3390/genes14091830 2023-10-01T00:38:14Z 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 Alu s 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. Article in Journal/Newspaper toothed whale toothed whales Directory of Open Access Journals: DOAJ Articles Genes 14 9 1830 |
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Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
retrotransposons homoplasy parallel insertions retrotransposon deletions whales Odontoceti Genetics QH426-470 |
spellingShingle |
retrotransposons homoplasy parallel insertions retrotransposon deletions whales Odontoceti Genetics QH426-470 Liliya Doronina Lynn Ogoniak Jürgen Schmitz Homoplasy of Retrotransposon Insertions in Toothed Whales |
topic_facet |
retrotransposons homoplasy parallel insertions retrotransposon deletions whales Odontoceti Genetics QH426-470 |
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 Alu s 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 |
Article in Journal/Newspaper |
author |
Liliya Doronina Lynn Ogoniak Jürgen Schmitz |
author_facet |
Liliya Doronina Lynn Ogoniak Jürgen Schmitz |
author_sort |
Liliya Doronina |
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 AG |
publishDate |
2023 |
url |
https://doi.org/10.3390/genes14091830 https://doaj.org/article/c64d284115834c03afc7f2d3ad72babb |
genre |
toothed whale toothed whales |
genre_facet |
toothed whale toothed whales |
op_source |
Genes, Vol 14, Iss 1830, p 1830 (2023) |
op_relation |
https://www.mdpi.com/2073-4425/14/9/1830 https://doaj.org/toc/2073-4425 doi:10.3390/genes14091830 2073-4425 https://doaj.org/article/c64d284115834c03afc7f2d3ad72babb |
op_doi |
https://doi.org/10.3390/genes14091830 |
container_title |
Genes |
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14 |
container_issue |
9 |
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1830 |
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1781069106378702848 |