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Jeena NS, Sajikumar KK, Rahuman S, Ragesh N, Koya KPS, Chinnadurai S, Sasikumar G, Mohamed KS. Insights into the divergent evolution of the oceanic squid Sthenoteuthis oualaniensis (Cephalopoda: Ommastrephidae) from the Indian Ocean. Integr Zool 2023; 18:924-948. [PMID: 36610009 DOI: 10.1111/1749-4877.12705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms (viz. middle-sized, dwarf, and giant forms) whose taxonomic status has been disputed for decades. This integrated taxonomic study examines these prevenient morphotypes gathered on cruises in the Indian Ocean to ascertain their status in the evolutionary history of the species. Molecular analyses employing mitochondrial (COI, ND2) and nuclear (H3) markers revealed four genetically distinct and novel lineages of the species in the Indian Ocean, representing three morphotypes from the Arabian Sea and one from the Southern Indian Ocean. The mitochondrial-based phylograms revealed two distinct clades in the species: "dwarf forms + giant form" and "middle-sized forms," which further branch into geographically structured evolutionary units. Species delimitation analyses recovered five distinct clades, namely, the Arabian Sea giant and dwarf forms, Equatorial, Eastern Typical, and Other Middle-sized forms, representing the consensus molecular operational taxonomic units. H3 being heterozygous could not resolve the phylogeny. Haplotype network and AMOVA analysis of mtDNA genes indicated explicit phylogeographic structuring of haplotypes, whereas these outputs and PCA results were incongruent with the morphological grouping. Phenetic features distinguishing the morphotypes were sometimes plastic and mismatched with the genotypes. The giant form was genetically close to the dwarf forms, contradicting the earlier notion that it descended from the middle-sized form. It may be assumed that the dwarf form evolved following sympatric speciation and adaptation to warm equatorial waters, while the focal features of the Western Arabian Sea guide toward allopatric speciation of the giant form.
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Affiliation(s)
- Nikarthil S Jeena
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | | | - Summaya Rahuman
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - Nadakkal Ragesh
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - K P Said Koya
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - Shunmugavel Chinnadurai
- Fishing Technology Division, Veraval Research Centre of ICAR-Central Institute of Fisheries Technology, Matsyabhavan, Bhidia, Veraval, Gujarat, India
| | - Geetha Sasikumar
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
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Yan W, Wang Z, Zhou B. Population evolution of seagrasses returning to the ocean. Heliyon 2023; 9:e20231. [PMID: 37809433 PMCID: PMC10559988 DOI: 10.1016/j.heliyon.2023.e20231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/05/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Seagrasses are higher flowering plants that live entirely in marine environments, with the greatest habitat variation occurring from land to sea. Genetic structure or population differentiation history is a hot topic in evolutionary biology, which is of great significance for understanding speciation. Genetic information is obtained from geographically distributed subpopulations, different subspecies, or strains of the same species using next-generation sequencing techniques. Genetic variation is identified by comparison with reference genomes. Genetic diversity is explored using population structure, principal component analysis (PCA), and phylogenetic relationships. Patterns of population genetic differentiation are elucidated by combining the isolation by distance (IBD) model, linkage disequilibrium levels, and genetic statistical analysis. Demographic history is simulated using effective population size, divergence time, and site frequency spectrum (SFS). Through various population genetic analyses, the genetic structure and historical population dynamics of seagrass can be clarified, and their evolutionary processes can be further explored at the molecular level to understand how evolutionary processes contributed to the formation of early ecological species and provide data support for seagrass conservation.
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Affiliation(s)
- Wenjie Yan
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Zhaohua Wang
- First Institute of Oceanography, MNR, Qingdao, 266061, China
| | - Bin Zhou
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
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Sukumaran S, Sebastian W, Gopalakrishnan A, Mathew OK, Vysakh VG, Rohit P, Jena JK. The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps. Sci Data 2023; 10:565. [PMID: 37626109 PMCID: PMC10457283 DOI: 10.1038/s41597-023-02481-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The Indian oil sardine, Sardinella longiceps, is a widely distributed and commercially important small pelagic fish of the Northern Indian Ocean. The genome of the Indian oil sardine has been characterized using Illumina and Nanopore platforms. The assembly is 1.077 Gb (31.86 Mb Scaffold N50) in size with a repeat content of 23.24%. The BUSCO (Benchmarking Universal Single Copy Orthologues) completeness of the assembly is 93.5% when compared with Actinopterygii (ray finned fishes) data set. A total of 46316 protein coding genes were predicted. Sardinella longiceps is nutritionally rich with high levels of omega-3 polyunsaturated fatty acids (PUFA). The core genes for omega-3 PUFA biosynthesis, such as Elovl 1a and 1b,Elovl 2, Elovl 4a and 4b,Elovl 8a and 8b,and Fads 2, were observed in Sardinella longiceps. The presence of these genes may indicate the PUFA biosynthetic capability of Indian oil sardine, which needs to be confirmed functionally.
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Affiliation(s)
- Sandhya Sukumaran
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
| | - Wilson Sebastian
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - Oommen K Mathew
- Agrigenome Labs Pvt. Ltd., Kakkanad, Kochi, Kerala, 682042, India
| | - V G Vysakh
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - Prathibha Rohit
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - J K Jena
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
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van der Reis AL, Norrie CR, Jeffs AG, Lavery SD, Carroll EL. Genetic and particle modelling approaches to assessing population connectivity in a deep sea lobster. Sci Rep 2022; 12:16783. [PMID: 36202873 PMCID: PMC9537507 DOI: 10.1038/s41598-022-19790-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/05/2022] [Indexed: 11/11/2022] Open
Abstract
The emergence of high resolution population genetic techniques, such as genotyping-by-sequencing (GBS), in combination with recent advances in particle modelling of larval dispersal in marine organisms, can deliver powerful new insights to support fisheries conservation and management. In this study, we used this combination to investigate the population connectivity of a commercial deep sea lobster species, the New Zealand scampi, Metanephrops challengeri, which ranges across a vast area of seafloor around New Zealand. This species has limited dispersal capabilities, including larvae with weak swimming abilities and short pelagic duration, while the reptant juvenile/adult stages of the lifecycle are obligate burrow dwellers with limited home ranges. Ninety-one individuals, collected from five scampi fishery management areas around New Zealand, were genotyped using GBS. Using 983 haplotypic genomic loci, three genetically distinct groups were identified: eastern, southern and western. These groups showed significant genetic differentiation with clear source-sink dynamics. The direction of gene flow inferred from the genomic data largely reflected the hydrodynamic particle modelling of ocean current flow around New Zealand. The modelled dispersal during pelagic larval phase highlights the strong connectivity among eastern sampling locations and explains the low genetic differentiation detected among these sampled areas. Our results highlight the value of using a transdisciplinary approach in the inference of connectivity among populations for informing conservation and fishery management.
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Affiliation(s)
- Aimee L van der Reis
- Institute of Marine Science, University of Auckland, Auckland, New Zealand. .,School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Craig R Norrie
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, USA
| | - Andrew G Jeffs
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Shane D Lavery
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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