Mitogenomic characterization and phylogenetic placement of the Red pandora Pagellus bellottii from the Eastern Atlantic Ocean within the family Sparidae
Abstract The systematics and conservation management of the Red pandora (Pagellus bellottii) remain challenging due to the overlapping morphology and distributions with closely related congeners in the Eastern Atlantic Ocean and Mediterranean Sea. These challenges are further exacerbated by populati...
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Nature Portfolio
2025-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-025-16187-y |
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| author | Arief Wujdi Emmanuel Ofosu Mireku Ewusi Sinar Pagi Sektiana Muhammad Hilman Fu’adil Amin Estuardo López-Vera Hyun-Woo Kim Hye-Eun Kang Shantanu Kundu |
| author_facet | Arief Wujdi Emmanuel Ofosu Mireku Ewusi Sinar Pagi Sektiana Muhammad Hilman Fu’adil Amin Estuardo López-Vera Hyun-Woo Kim Hye-Eun Kang Shantanu Kundu |
| author_sort | Arief Wujdi |
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| description | Abstract The systematics and conservation management of the Red pandora (Pagellus bellottii) remain challenging due to the overlapping morphology and distributions with closely related congeners in the Eastern Atlantic Ocean and Mediterranean Sea. These challenges are further exacerbated by population declines driven by intensive coastal fisheries and a paucity of molecular data. In this study, high-throughput sequencing was utilized to assemble the first complete mitogenome of P. bellottii from its native range. The mitogenome (16,666 bp) comprises the typical set of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a non-coding control region (CR). The analysis of PCGs revealed a predominance of hydrophobic and neutral amino acids and strong purifying selection. Unlike P. bogaraveo, no evidence of heteroplasmy was observed in the WANCY tRNA gene cluster of P. bellottii. Notably, nucleotide polymorphisms were identified within conserved motifs of the CR. The Bayesian inference and Maximum Likelihood phylogenetic analyses revealed non-monophyly among several Sparidae genera (Pagellus, Dentex, and Pagrus), with P. bellottii clustering most closely with P. erythrinus. Molecular dating estimated the divergence between P. bellottii and P. erythrinus at approximately 6.1 million years ago (MYA), during the Miocene, a period more recent than the divergence of P. bogaraveo and P. acarne (~ 10.5 MYA). These divergence times coincide with major geological events, such as the formation of the Gibraltar Arc and the opening of the Atlantic–Mediterranean gateway, which likely facilitated speciation and lineage diversification of Pagellus. Additionally, the asymmetric biogeographic distribution of P. bellottii and related species may be influenced by hydrographic barriers, climatic gradients across the North and South Atlantic, and historical events such as the Messinian salinity crisis. Overall, this study provides the first comprehensive mitogenomic insights into P. bellottii and underscores the importance of further genome-wide research to elucidate adaptive evolution and phylogeographic history for developing effective conservation and management strategies for all Sparidae in marine ecosystems. |
| format | Article |
| id | doaj-art-138efa4d5406457c92d8067f9f660d80 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-08-01 |
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| spelling | doaj-art-138efa4d5406457c92d8067f9f660d802025-08-24T11:24:06ZengNature PortfolioScientific Reports2045-23222025-08-0115111610.1038/s41598-025-16187-yMitogenomic characterization and phylogenetic placement of the Red pandora Pagellus bellottii from the Eastern Atlantic Ocean within the family SparidaeArief Wujdi0Emmanuel Ofosu Mireku Ewusi1Sinar Pagi Sektiana2Muhammad Hilman Fu’adil Amin3Estuardo López-Vera4Hyun-Woo Kim5Hye-Eun Kang6Shantanu Kundu7Interdisciplinary Program of Marine and Fisheries Sciences and Convergent Technology, Pukyong National UniversityFisheries Commission, Fisheries Scientific Survey Division, Ministry of Fisheries and Aquaculture DevelopmentJakarta Technical University of Fisheries, Ministry of Marine Affairs and FisheriesAdvance Tropical Biodiversity, Genomics, and Conservation Research Group, Department of Biology, Faculty of Science and Technology, Airlangga UniversityLaboratorio de Toxinología Marina, Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoAdvance Tropical Biodiversity, Genomics, and Conservation Research Group, Department of Biology, Faculty of Science and Technology, Airlangga UniversityInstitute of Marine Life Science, Pukyong National UniversityOcean and Fisheries Development International Cooperation Institute, College of Fisheries Science, Pukyong National UniversityAbstract The systematics and conservation management of the Red pandora (Pagellus bellottii) remain challenging due to the overlapping morphology and distributions with closely related congeners in the Eastern Atlantic Ocean and Mediterranean Sea. These challenges are further exacerbated by population declines driven by intensive coastal fisheries and a paucity of molecular data. In this study, high-throughput sequencing was utilized to assemble the first complete mitogenome of P. bellottii from its native range. The mitogenome (16,666 bp) comprises the typical set of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a non-coding control region (CR). The analysis of PCGs revealed a predominance of hydrophobic and neutral amino acids and strong purifying selection. Unlike P. bogaraveo, no evidence of heteroplasmy was observed in the WANCY tRNA gene cluster of P. bellottii. Notably, nucleotide polymorphisms were identified within conserved motifs of the CR. The Bayesian inference and Maximum Likelihood phylogenetic analyses revealed non-monophyly among several Sparidae genera (Pagellus, Dentex, and Pagrus), with P. bellottii clustering most closely with P. erythrinus. Molecular dating estimated the divergence between P. bellottii and P. erythrinus at approximately 6.1 million years ago (MYA), during the Miocene, a period more recent than the divergence of P. bogaraveo and P. acarne (~ 10.5 MYA). These divergence times coincide with major geological events, such as the formation of the Gibraltar Arc and the opening of the Atlantic–Mediterranean gateway, which likely facilitated speciation and lineage diversification of Pagellus. Additionally, the asymmetric biogeographic distribution of P. bellottii and related species may be influenced by hydrographic barriers, climatic gradients across the North and South Atlantic, and historical events such as the Messinian salinity crisis. Overall, this study provides the first comprehensive mitogenomic insights into P. bellottii and underscores the importance of further genome-wide research to elucidate adaptive evolution and phylogeographic history for developing effective conservation and management strategies for all Sparidae in marine ecosystems.https://doi.org/10.1038/s41598-025-16187-y |
| spellingShingle | Arief Wujdi Emmanuel Ofosu Mireku Ewusi Sinar Pagi Sektiana Muhammad Hilman Fu’adil Amin Estuardo López-Vera Hyun-Woo Kim Hye-Eun Kang Shantanu Kundu Mitogenomic characterization and phylogenetic placement of the Red pandora Pagellus bellottii from the Eastern Atlantic Ocean within the family Sparidae Scientific Reports |
| title | Mitogenomic characterization and phylogenetic placement of the Red pandora Pagellus bellottii from the Eastern Atlantic Ocean within the family Sparidae |
| title_full | Mitogenomic characterization and phylogenetic placement of the Red pandora Pagellus bellottii from the Eastern Atlantic Ocean within the family Sparidae |
| title_fullStr | Mitogenomic characterization and phylogenetic placement of the Red pandora Pagellus bellottii from the Eastern Atlantic Ocean within the family Sparidae |
| title_full_unstemmed | Mitogenomic characterization and phylogenetic placement of the Red pandora Pagellus bellottii from the Eastern Atlantic Ocean within the family Sparidae |
| title_short | Mitogenomic characterization and phylogenetic placement of the Red pandora Pagellus bellottii from the Eastern Atlantic Ocean within the family Sparidae |
| title_sort | mitogenomic characterization and phylogenetic placement of the red pandora pagellus bellottii from the eastern atlantic ocean within the family sparidae |
| url | https://doi.org/10.1038/s41598-025-16187-y |
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