SINEs as Credible Signs to Prove Common Ancestry in the Tree of Life: A Brief Review of Pioneering Case Studies in Retroposon Systematics
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- Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
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- Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
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- Norihiro Okada
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
書誌事項
- 公開日
- 2022-05-31
- 資源種別
- journal article
- 権利情報
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- https://creativecommons.org/licenses/by/4.0/
- DOI
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- 10.3390/genes13060989
- 公開者
- MDPI AG
説明
<jats:p>Currently, the insertions of SINEs (and other retrotransposed elements) are regarded as one of the most reliable synapomorphies in molecular systematics. The methodological mainstream of molecular systematics is the calculation of nucleotide (or amino acid) sequence divergences under a suitable substitution model. In contrast, SINE insertion analysis does not require any complex model because SINE insertions are unidirectional and irreversible. This straightforward methodology was named the “SINE method,” which resolved various taxonomic issues that could not be settled by sequence comparison alone. The SINE method has challenged several traditional hypotheses proposed based on the fossil record and anatomy, prompting constructive discussions in the Evo/Devo era. Here, we review our pioneering SINE studies on salmon, cichlids, cetaceans, Afrotherian mammals, and birds. We emphasize the power of the SINE method in detecting incomplete lineage sorting by tracing the genealogy of specific genomic loci with minimal noise. Finally, in the context of the whole-genome era, we discuss how the SINE method can be applied to further our understanding of the tree of life.</jats:p>
収録刊行物
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- Genes
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Genes 13 (6), 989-, 2022-05-31
MDPI AG
