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Pancoro A, Indriatmoko, Wijaya D, Karima E. Sea surface temperature and current-related parameters affecting local adaptation of scalloped spiny lobster population in Indonesia's archipelagic system. Sci Rep 2024; 14:18403. [PMID: 39117785 PMCID: PMC11310395 DOI: 10.1038/s41598-024-68923-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/29/2024] [Indexed: 08/10/2024] Open
Abstract
The Scalloped Spiny lobster (Panulirus homarus, Linnaeus 1758) known as one of the commercially harvested Panilurid lobster. This species was distributed widely across continents. Indonesia, as one of the largest archipelagic systems in the world, was also distribution area of the Scalloped Spiny lobster. These facts have led to questions regarding spiny lobster harvest and culture management by considering population differentiation and habitat fragmentation on complex and distinct archipelagic islands. Our investigation was conducted using high-density SNPs datasets from several spiny lobsters harvested from five locations in Indonesia. We found strong differentiation among spiny lobster populations clustered into 3 sub-populations. Environment association analysis and Fst analysis revealed outlier loci significantly associated with Sea Surface Temperature variation and potentially correlated with Sea Current-related parameters. The evidence of a structured population of scalloped spiny lobsters in Indonesia can serve as a consideration in the management of spiny lobsters.
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Affiliation(s)
- Adi Pancoro
- School of Life Science and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia.
| | - Indriatmoko
- Research Institute for Fisheries Enhancement, Indonesian Ministry of Marine Affairs and Fisheries, Purwakarta, 51151, Indonesia
| | - Danu Wijaya
- Research Institute for Fisheries Enhancement, Indonesian Ministry of Marine Affairs and Fisheries, Purwakarta, 51151, Indonesia
| | - Elfina Karima
- School of Life Science and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
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2
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Bertram A, Bell J, Brauer C, Fairclough D, Hamer P, Sandoval‐Castillo J, Wellenreuther M, Beheregaray LB. Estimation of effective number of breeders and effective population size in an abundant and heavily exploited marine teleost. Evol Appl 2024; 17:e13758. [PMID: 39040813 PMCID: PMC11261160 DOI: 10.1111/eva.13758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/16/2024] [Accepted: 07/03/2024] [Indexed: 07/24/2024] Open
Abstract
Obtaining reliable estimates of the effective number of breeders (N b) and generational effective population size (N e) for fishery-important species is challenging because they are often iteroparous and highly abundant, which can lead to bias and imprecision. However, recent advances in understanding of these parameters, as well as the development of bias correction methods, have improved the capacity to generate reliable estimates. We utilized samples of both single-cohort young of the year and mixed-age adults from two geographically and genetically isolated stocks of the Australasian snapper (Chrysophrys auratus) to investigate the feasibility of generating reliable N b and N e estimates for a fishery species. Snapper is an abundant, iteroparous broadcast spawning teleost that is heavily exploited by recreational and commercial fisheries. Employing neutral genome-wide SNPs and the linkage-disequilibrium method, we determined that the most reliable N b and N e estimates could be derived by genotyping at least 200 individuals from a single cohort. Although our estimates made from the mixed-age adult samples were generally lower and less precise than those based on a single cohort, they still proved useful for understanding relative differences in genetic effective size between stocks. The correction formulas applied to adjust for biases due to physical linkage of loci and age structure resulted in substantial upward modifications of our estimates, demonstrating the importance of applying these bias corrections. Our findings provide important guidelines for estimating N b and N e for iteroparous species with large populations. This work also highlights the utility of samples originally collected for stock structure and stock assessment work for investigating genetic effective size in fishery-important species.
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Affiliation(s)
- Andrea Bertram
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Justin Bell
- Victorian Fisheries AuthorityQueenscliffVictoriaAustralia
| | - Chris Brauer
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - David Fairclough
- Department of Primary Industries and Regional DevelopmentAquatic Sciences and AssessmentHillarysWestern AustraliaAustralia
| | | | - Jonathan Sandoval‐Castillo
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research LimitedNelsonNew Zealand
- The School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
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Friis G, Smith EG, Lovelock CE, Ortega A, Marshell A, Duarte CM, Burt JA. Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula. Mol Ecol 2024; 33:e17260. [PMID: 38197286 DOI: 10.1111/mec.17260] [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: 12/07/2022] [Revised: 11/13/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The grey mangroves (Avicennia marina) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyse fully sequenced genomes sampled from 19 locations across the Red Sea, the Arabian Sea and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Population structure and phylogenetic analyses revealed marked genetic structure correlating with geographic distance and highly supported clades among and within the seas surrounding the Arabian Peninsula. Demographic modelling showed times of divergence consistent with recent periods of geographic isolation and low marine connectivity during glaciations, suggesting the presence of (cryptic) glacial refugia in the Red Sea and the PAG. Significant migration was detected within the Red Sea and the PAG, and across the Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary contact among populations. Genetic-environment association analyses revealed high levels of adaptive divergence and detected signs of multi-loci local adaptation driven by temperature extremes and hypersalinity. These results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.
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Affiliation(s)
- Guillermo Friis
- Center for Genomics and Systems Biology (CGSB) and Mubadala ACCESS Center, New York University - Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Catherine E Lovelock
- School of Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Alejandra Ortega
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alyssa Marshell
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - John A Burt
- Center for Genomics and Systems Biology (CGSB) and Mubadala ACCESS Center, New York University - Abu Dhabi, Abu Dhabi, United Arab Emirates
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Haye PA, Segovia NI, Vera R, Acuña E. Phylogeography reveals a panmictic population of the Chilean nylon shrimp along its exploitation range in the southeast Pacific Ocean. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00589-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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5
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Graham CF, Boreham DR, Manzon RG, Wilson JY, Somers CM. Population structure of lake whitefish ( Coregonus clupeaformis) from the Mississippian lineage in North America. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The lake whitefish ( Coregonus clupeaformis) is a commercially valuable freshwater species with a broad distribution in North America. Some phylogeographic work has been done on this species, but little is known about genetic population subdivision among populations of the widely dispersed Mississippian lineage. We used 3,173 single nucleotide polymorphisms in 508 lake whitefish from 22 different lakes to examine population structure across central Canada and the United States. Bayesian clustering, ordination, and fixation indices identified population subdivision that largely reflected geographic distance and hydrological connectivity, with greater differentiation between lakes that are farther apart. Population subdivision was hierarchical, with greater differentiation between Canadian provinces and less differentiation based on river basins within provincial boundaries. Interestingly, isolation by distance alone was not sufficient to account for all of the observed genetic differentiation among populations. We conclude that important components of lake whitefish genetic diversity are present at different spatial scales, and that populations within the Mississippian lineage have differentiated widely across their range.
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Affiliation(s)
- Carly F. Graham
- Department of Biology, University of Regina, Regina, SK, Canada
| | - Douglas R. Boreham
- Medical Sciences, Northern Ontario School of Medicine, Greater Sudbury, ON, Canada
| | | | - Joanna Y. Wilson
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Vu NTT, Zenger KR, Silva CNS, Guppy JL, Jerry DR. Population Structure, Genetic Connectivity, and Signatures of Local Adaptation of the Giant Black Tiger Shrimp (Penaeus monodon) throughout the Indo-Pacific Region. Genome Biol Evol 2021; 13:evab214. [PMID: 34529049 PMCID: PMC8495139 DOI: 10.1093/gbe/evab214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2021] [Indexed: 12/04/2022] Open
Abstract
The giant black tiger shrimp (Penaeus monodon) is native to the Indo-Pacific and is the second most farmed penaeid shrimp species globally. Understanding genetic structure, connectivity, and local adaptation among Indo-Pacific black tiger shrimp populations is important for informing sustainable fisheries management and aquaculture breeding programs. Population genetic and outlier detection analyses were undertaken using 10,593 genome-wide single nucleotide polymorphisms (SNPs) from 16 geographically disparate Indo-Pacific P. monodon populations. Levels of genetic diversity were highest for Southeast Asian populations and were lowest for Western Indian Ocean (WIO) populations. Both neutral (n = 9,930) and outlier (n = 663) loci datasets revealed a pattern of strong genetic structure of P. monodon corresponding with broad geographical regions and clear genetic breaks among samples within regions. Neutral loci revealed seven genetic clusters and the separation of Fiji and WIO clusters from all other clusters, whereas outlier loci revealed six genetic clusters and high genetic differentiation among populations. The neutral loci dataset estimated five migration events that indicated migration to Southeast Asia from the WIO, with partial connectivity to populations in both oceans. We also identified 26 putatively adaptive SNPs that exhibited significant Pearson correlation (P < 0.05) between minor allele frequency and maximum or minimum sea surface temperature. Matched transcriptome contig annotations suggest putatively adaptive SNPs involvement in cellular and metabolic processes, pigmentation, immune response, and currently unknown functions. This study provides novel genome-level insights that have direct implications for P. monodon aquaculture and fishery management practices.
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Affiliation(s)
- Nga T T Vu
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Kyall R Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Catarina N S Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Jarrod L Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Dean R Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Tropical Futures Institute, James Cook University, Singapore
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Vu NTT, Zenger KR, Guppy JL, Sellars MJ, Silva CNS, Kjeldsen SR, Jerry DR. Correction to: Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis. BMC Genomics 2021; 22:559. [PMID: 34284725 PMCID: PMC8293502 DOI: 10.1186/s12864-021-07794-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Nga T T Vu
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia. .,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.
| | - Kyall R Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Jarrod L Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Melony J Sellars
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,CSIRO Agriculture & Food, Integrated Sustainable Aquaculture Production Program, Queensland Bioscience Precinct, St Lucia, 4067, Australia.,Present address: Genics Pty Ltd, Level 5, Gehrmann Building. 60 Research Road, St Lucia, QLD, 4067, Australia
| | - Catarina N S Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Shannon R Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Dean R Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.,Tropical Futures Institute, James Cook University, Singapore, Singapore
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