Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal
DNA repeat composition of low coverage (0.1–0.5) genomic libraries of four amphipods species endemic to Lake Baikal (East Siberia) and four endemic gastropod species of the fam. Baicaliidae have been compared to each other. In order to do so, a neighbor joining tree was inferred for each quartet of...
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2023-07-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/3777 |
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| author | Wang Yuxiang T. E. Peretolchina E. V. Romanova D. Y. Sherbakov |
| author_facet | Wang Yuxiang T. E. Peretolchina E. V. Romanova D. Y. Sherbakov |
| author_sort | Wang Yuxiang |
| collection | DOAJ |
| description | DNA repeat composition of low coverage (0.1–0.5) genomic libraries of four amphipods species endemic to Lake Baikal (East Siberia) and four endemic gastropod species of the fam. Baicaliidae have been compared to each other. In order to do so, a neighbor joining tree was inferred for each quartet of species (amphipods and mollusks) based on the ratio of repeat classes shared in each pair of species. The topology of this tree was compared to the phylogenies inferred for the same species from the concatenated protein-coding mitochondrial nucleotide sequences. In all species analyzed, the fraction of DNA repeats involved circa half of the genome. In relatively more ancient amphipods (most recent common ancestor, MRCA, existed approximately sixty millions years ago), the most abundant were species-specific repeats, while in much younger Baicaliidae (MRCA equal to ca. three millions years) most of the DNA repeats were shared among all four species. If the presence/absence of a repeat is regarded as a separate independent trait, and the ratio of shared to total numbers of repeats in a species pair is used as the measure of distance, the topology of the NJ tree is the same as the quartet phylogeny inferred for the mitogenomes protein coding nucleotide sequences. Meanwhile, in each group of species, a substantial number of repeats were detected pointing to the possibility of non-neutral evolution or a horizontal transfer between species occupying the same biotope. These repeats were shared by non-sister groups while being absent in the sister genomes. On the other hand, in such cases some traits of ecological significance were also shared. |
| format | Article |
| id | doaj-art-3b35c4163b10461cb43adf28aa4c332b |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2023-07-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-3b35c4163b10461cb43adf28aa4c332b2025-02-01T09:58:12ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592023-07-0127434935610.18699/VJGB-23-421360Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake BaikalWang Yuxiang0T. E. Peretolchina1E. V. Romanova2D. Y. Sherbakov3Limnological institute of the Siberian Branch of the Russian Academy of SciencesLimnological institute of the Siberian Branch of the Russian Academy of SciencesLimnological institute of the Siberian Branch of the Russian Academy of SciencesLimnological institute of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University; Irkutsk State UniversityDNA repeat composition of low coverage (0.1–0.5) genomic libraries of four amphipods species endemic to Lake Baikal (East Siberia) and four endemic gastropod species of the fam. Baicaliidae have been compared to each other. In order to do so, a neighbor joining tree was inferred for each quartet of species (amphipods and mollusks) based on the ratio of repeat classes shared in each pair of species. The topology of this tree was compared to the phylogenies inferred for the same species from the concatenated protein-coding mitochondrial nucleotide sequences. In all species analyzed, the fraction of DNA repeats involved circa half of the genome. In relatively more ancient amphipods (most recent common ancestor, MRCA, existed approximately sixty millions years ago), the most abundant were species-specific repeats, while in much younger Baicaliidae (MRCA equal to ca. three millions years) most of the DNA repeats were shared among all four species. If the presence/absence of a repeat is regarded as a separate independent trait, and the ratio of shared to total numbers of repeats in a species pair is used as the measure of distance, the topology of the NJ tree is the same as the quartet phylogeny inferred for the mitogenomes protein coding nucleotide sequences. Meanwhile, in each group of species, a substantial number of repeats were detected pointing to the possibility of non-neutral evolution or a horizontal transfer between species occupying the same biotope. These repeats were shared by non-sister groups while being absent in the sister genomes. On the other hand, in such cases some traits of ecological significance were also shared.https://vavilov.elpub.ru/jour/article/view/3777dna repeatslake baikalphylogenybaicaliidaeamphipodsevolution of repeatsrepeatome |
| spellingShingle | Wang Yuxiang T. E. Peretolchina E. V. Romanova D. Y. Sherbakov Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal Вавиловский журнал генетики и селекции dna repeats lake baikal phylogeny baicaliidae amphipods evolution of repeats repeatome |
| title | Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal |
| title_full | Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal |
| title_fullStr | Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal |
| title_full_unstemmed | Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal |
| title_short | Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal |
| title_sort | comparison of the evolutionary patterns of dna repeats in ancient and young invertebrate species flocks of lake baikal |
| topic | dna repeats lake baikal phylogeny baicaliidae amphipods evolution of repeats repeatome |
| url | https://vavilov.elpub.ru/jour/article/view/3777 |
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