Origin of Polyploidy, Phylogenetic Relationships, and Biogeography of Botiid Fishes (Teleostei: Cypriniformes)
Botiidae is a small family of freshwater fishes distributed across Southeast Asia, South Asia, and East Asia. It comprises two subfamilies: the diploid Leptobotiinae and the tetraploid Botiinae. Whether species in the Botiinae are autotetraploids or allotetraploids and how many polyploidization even...
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| author | Lei Yang Richard L. Mayden Gavin J. P. Naylor |
| author_facet | Lei Yang Richard L. Mayden Gavin J. P. Naylor |
| author_sort | Lei Yang |
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| description | Botiidae is a small family of freshwater fishes distributed across Southeast Asia, South Asia, and East Asia. It comprises two subfamilies: the diploid Leptobotiinae and the tetraploid Botiinae. Whether species in the Botiinae are autotetraploids or allotetraploids and how many polyploidization events occurred during the evolution of this subfamily remain open questions. The phylogenetic relationships and biogeography of the Botiidae also require further investigation. In the current study, we compared phylogenetic trees constructed using DNA sequences from the mitochondrial genome and five phased nuclear genes. We also performed whole genome sequencing for two tetraploid species: <i>Chromobotia macracanthus</i> and <i>Yasuhikotakia modesta</i>. Genome profiling of five botiine species suggests that they are likely of allotetraploid origin. Nuclear gene tree topologies indicate that the tetraploidization of the Botiinae occurred only once in the common ancestor of this subfamily. Although the possible maternal progenitor and paternal progenitor of the Botiinae cannot be determined, the subfamily Leptobotiinae can be excluded as a progenitor. The gene trees built in this study generally agree on the following sister group relationships: Leptobotiinae/Botiinae, <i>Leptobotia</i>/<i>Parabotia</i>, <i>Chromobotia</i>/<i>Botia</i>, <i>Yasuhikotakia</i>/<i>Syncrossus</i>, and <i>Sinibotia</i>/<i>Ambastaia</i>. Clades formed by the last two generic pairs are also sisters to each other. Timetree analyses and ancestral range reconstruction suggest that the family Botiidae might have originated in East Asia and Mainland Southeast Asia approximately 51 million years ago and later dispersed to South Asia and the islands of Southeast Asia. |
| format | Article |
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| spelling | doaj-art-8eeda820bf764a6b99e8f7f02e03ff512025-08-20T02:33:40ZengMDPI AGBiology2079-77372025-05-0114553110.3390/biology14050531Origin of Polyploidy, Phylogenetic Relationships, and Biogeography of Botiid Fishes (Teleostei: Cypriniformes)Lei Yang0Richard L. Mayden1Gavin J. P. Naylor2Florida Museum of Natural History, University of Florida, 1659 Museum Rd., Gainesville, FL 32611, USABiology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USAFlorida Museum of Natural History, University of Florida, 1659 Museum Rd., Gainesville, FL 32611, USABotiidae is a small family of freshwater fishes distributed across Southeast Asia, South Asia, and East Asia. It comprises two subfamilies: the diploid Leptobotiinae and the tetraploid Botiinae. Whether species in the Botiinae are autotetraploids or allotetraploids and how many polyploidization events occurred during the evolution of this subfamily remain open questions. The phylogenetic relationships and biogeography of the Botiidae also require further investigation. In the current study, we compared phylogenetic trees constructed using DNA sequences from the mitochondrial genome and five phased nuclear genes. We also performed whole genome sequencing for two tetraploid species: <i>Chromobotia macracanthus</i> and <i>Yasuhikotakia modesta</i>. Genome profiling of five botiine species suggests that they are likely of allotetraploid origin. Nuclear gene tree topologies indicate that the tetraploidization of the Botiinae occurred only once in the common ancestor of this subfamily. Although the possible maternal progenitor and paternal progenitor of the Botiinae cannot be determined, the subfamily Leptobotiinae can be excluded as a progenitor. The gene trees built in this study generally agree on the following sister group relationships: Leptobotiinae/Botiinae, <i>Leptobotia</i>/<i>Parabotia</i>, <i>Chromobotia</i>/<i>Botia</i>, <i>Yasuhikotakia</i>/<i>Syncrossus</i>, and <i>Sinibotia</i>/<i>Ambastaia</i>. Clades formed by the last two generic pairs are also sisters to each other. Timetree analyses and ancestral range reconstruction suggest that the family Botiidae might have originated in East Asia and Mainland Southeast Asia approximately 51 million years ago and later dispersed to South Asia and the islands of Southeast Asia.https://www.mdpi.com/2079-7737/14/5/531allopolyploidygenomeloachmitogenomenucleartimetree |
| spellingShingle | Lei Yang Richard L. Mayden Gavin J. P. Naylor Origin of Polyploidy, Phylogenetic Relationships, and Biogeography of Botiid Fishes (Teleostei: Cypriniformes) Biology allopolyploidy genome loach mitogenome nuclear timetree |
| title | Origin of Polyploidy, Phylogenetic Relationships, and Biogeography of Botiid Fishes (Teleostei: Cypriniformes) |
| title_full | Origin of Polyploidy, Phylogenetic Relationships, and Biogeography of Botiid Fishes (Teleostei: Cypriniformes) |
| title_fullStr | Origin of Polyploidy, Phylogenetic Relationships, and Biogeography of Botiid Fishes (Teleostei: Cypriniformes) |
| title_full_unstemmed | Origin of Polyploidy, Phylogenetic Relationships, and Biogeography of Botiid Fishes (Teleostei: Cypriniformes) |
| title_short | Origin of Polyploidy, Phylogenetic Relationships, and Biogeography of Botiid Fishes (Teleostei: Cypriniformes) |
| title_sort | origin of polyploidy phylogenetic relationships and biogeography of botiid fishes teleostei cypriniformes |
| topic | allopolyploidy genome loach mitogenome nuclear timetree |
| url | https://www.mdpi.com/2079-7737/14/5/531 |
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