Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences
Abstract Nemipterus randalli, commonly known as Randall’s threadfin bream, is a commercially important marine finfish. Understanding its genetic structure is critical to effective management and conservation efforts. Previous investigations on population structure in this species were limited by geo...
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| Format: | Article |
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Nature Portfolio
2024-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-024-58047-1 |
| _version_ | 1797233649809096704 |
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| author | Neenu Raj Sandhya Sukumaran Anjaly Jose K. Nisha Subal Kumar Roul Shikha Rahangdale Shoba Joe Kizhakudan A. Gopalakrishnan |
| author_facet | Neenu Raj Sandhya Sukumaran Anjaly Jose K. Nisha Subal Kumar Roul Shikha Rahangdale Shoba Joe Kizhakudan A. Gopalakrishnan |
| author_sort | Neenu Raj |
| collection | DOAJ |
| description | Abstract Nemipterus randalli, commonly known as Randall’s threadfin bream, is a commercially important marine finfish. Understanding its genetic structure is critical to effective management and conservation efforts. Previous investigations on population structure in this species were limited by geographic coverage. In this study, we utilized the mitochondrial Cytochrome b gene and nuclear Ribosomal protein gene intron Rp S7 sequences to investigate the population genetic structure, demography and genetic diversity of N. randalli along Indian waters. Our results revealed high haplotype diversity but low nucleotide diversity. AMOVA revealed that the variation among the population was highly significant. Hierarchical AMOVA provided further evidence of significant genetic differentiation between the west and east coasts, which was corroborated by the Bayesian tree and the median-joining network diagram. The mtDNA sequences revealed significant genetic structure between populations based on fixation index analysis following the isolation-by-distance model. Furthermore, the neutrality test and mismatch analysis suggest that N. randalli populations may have experienced a population expansion. However, nuclear marker RpS7, showed a high level of polymorphism, which obscured the population structuring observed with the mitochondrial marker. Consequently, concordant results were not obtained when comparing the mitochondrial and nuclear DNA sequences. The strong genetic differentiation between the east and west coast observed using mitochondrial marker could be attributed to a combination of geographic and environmental factors. These findings lay the groundwork for developing effective conservation and management strategies for N. randalli, considering its genetic structure. |
| first_indexed | 2024-04-24T16:19:32Z |
| format | Article |
| id | doaj.art-31ce68156e1b4b079ffd1df01be829e6 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-24T16:19:32Z |
| publishDate | 2024-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-31ce68156e1b4b079ffd1df01be829e62024-03-31T11:14:55ZengNature PortfolioScientific Reports2045-23222024-03-0114111310.1038/s41598-024-58047-1Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequencesNeenu Raj0Sandhya Sukumaran1Anjaly Jose2K. Nisha3Subal Kumar Roul4Shikha Rahangdale5Shoba Joe Kizhakudan6A. Gopalakrishnan7Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research InstituteMarine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research InstituteMarine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research InstituteMarine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research InstituteMarine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research InstituteMarine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research InstituteMarine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research InstituteMarine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research InstituteAbstract Nemipterus randalli, commonly known as Randall’s threadfin bream, is a commercially important marine finfish. Understanding its genetic structure is critical to effective management and conservation efforts. Previous investigations on population structure in this species were limited by geographic coverage. In this study, we utilized the mitochondrial Cytochrome b gene and nuclear Ribosomal protein gene intron Rp S7 sequences to investigate the population genetic structure, demography and genetic diversity of N. randalli along Indian waters. Our results revealed high haplotype diversity but low nucleotide diversity. AMOVA revealed that the variation among the population was highly significant. Hierarchical AMOVA provided further evidence of significant genetic differentiation between the west and east coasts, which was corroborated by the Bayesian tree and the median-joining network diagram. The mtDNA sequences revealed significant genetic structure between populations based on fixation index analysis following the isolation-by-distance model. Furthermore, the neutrality test and mismatch analysis suggest that N. randalli populations may have experienced a population expansion. However, nuclear marker RpS7, showed a high level of polymorphism, which obscured the population structuring observed with the mitochondrial marker. Consequently, concordant results were not obtained when comparing the mitochondrial and nuclear DNA sequences. The strong genetic differentiation between the east and west coast observed using mitochondrial marker could be attributed to a combination of geographic and environmental factors. These findings lay the groundwork for developing effective conservation and management strategies for N. randalli, considering its genetic structure.https://doi.org/10.1038/s41598-024-58047-1 |
| spellingShingle | Neenu Raj Sandhya Sukumaran Anjaly Jose K. Nisha Subal Kumar Roul Shikha Rahangdale Shoba Joe Kizhakudan A. Gopalakrishnan Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences Scientific Reports |
| title | Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences |
| title_full | Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences |
| title_fullStr | Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences |
| title_full_unstemmed | Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences |
| title_short | Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences |
| title_sort | population genetic structure of randall s threadfin bream nemipterus randalli in indian waters based on mitochondrial and nuclear gene sequences |
| url | https://doi.org/10.1038/s41598-024-58047-1 |
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