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Jeena NS, Rahuman S, Sebastian W, Kumar R, Sajeela KA, Kizhakudan JK, Menon KK, Roul SK, Gopalakrishnan A, Radhakrishnan EV. Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification. Int J Biol Macromol 2024; 277:134327. [PMID: 39098694 DOI: 10.1016/j.ijbiomac.2024.134327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685-15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analysis revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource.
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Affiliation(s)
- N S Jeena
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India.
| | - Summaya Rahuman
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - Wilson Sebastian
- Centre for Marine Living Resources and Ecology (CMLRE), Kochi, Kerala, India
| | - Rajan Kumar
- Shellfish Fisheries Division, Regional Station of CMFRI, Veraval, Gujarat, India
| | - K A Sajeela
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - Joe K Kizhakudan
- Mariculture Division, Regional Centre of CMFRI, Visakhapatnam, Andhra Pradesh, India
| | | | - Subal Kumar Roul
- Finfish Fisheries Division, Regional Station of CMFRI, Digha, West Bengal, India
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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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3
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Farhadi A, Jeffs AG, Lavery SD. Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies. BMC Genomics 2022; 23:750. [DOI: 10.1186/s12864-022-08984-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Evolutionary divergence and speciation often occur at a slower rate in the marine realm due to the higher potential for long-distance reproductive interaction through larval dispersal. One common evolutionary pattern in the Indo-Pacific, is divergence of populations and species at the peripheries of widely-distributed organisms. However, the evolutionary and demographic histories of such divergence are yet to be well understood. Here we address these issues by coupling genome-wide SNP data with mitochondrial DNA sequences to test the patterns of genetic divergence and possible secondary contact among geographically distant populations of the highly valuable spiny lobster Panulirus homarus species complex, distributed widely through the Indo-Pacific, from South Africa to the Marquesas Islands.
Result
After stringent filtering, 2020 SNPs were used for population genetic and demographic analyses, revealing strong regional structure (FST = 0.148, P < 0001), superficially in accordance with previous analyses. However, detailed demographic analyses supported a much more complex evolutionary history of these populations, including a hybrid origin of a North-West Indian Ocean (NWIO) population, which has previously been discriminated morphologically, but not genetically. The best-supported demographic models suggested that the current genetic relationships among populations were due to a complex series of past divergences followed by asymmetric migration in more recent times.
Conclusion
Overall, this study suggests that alternating periods of marine divergence and gene flow have driven the current genetic patterns observed in this lobster and may help explain the observed wider patterns of marine species diversity in the Indo-Pacific.
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Hettiarachchi SA, Hyeon JY, Mahardini A, Kim HS, Byun JH, Kim HJ, Jeong JG, Yeo JK, Kim SK, Kim SJ, Heo YS, Sathyadith J, Kang DH, Hur SP. DNA barcoding and morphological identification of spiny lobsters in South Korean waters: a new record of Panulirus longipes and Panulirus homarus homarus. PeerJ 2022; 10:e12744. [PMID: 35047236 PMCID: PMC8757375 DOI: 10.7717/peerj.12744] [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: 07/17/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023] Open
Abstract
To date, 19 species of spiny lobsters from the genus Panulirus have been discovered, of which only P. japonicus, P. penicilatus, P. stimpsoni, and P. versicolor have been documented in South Korean waters. In this study, we aimed to identify and update the current list of spiny lobster species that inhabit South Korean waters based on the morphological features and the phylogenetic profile of cytochrome oxidase I (COI) of mitochondrial DNA (mtDNA). Spiny lobsters were collected from the southern and eastern coasts of Jeju Island, South Korea. Phylogenetic analyses were performed using neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. The ML tree was used to determine the spiny lobster lineages, thereby clustering the 17 specimens collected in this study into clades A, B, C, and D, which were reciprocally monophyletic with P. japonicus, P. homarus homarus, P. longipes, and P. stimpsoni, respectively. These clades were also supported by morphological examinations. Interestingly, morphological variations, including the connected pleural and transverse groove at the third abdominal somite, were observed in four specimens that were genetically confirmed as P. japonicus. This finding is novel within the P. japonicus taxonomical reports. Additionally, this study updates the documentation of spiny lobsters inhabiting South Korean waters as P. longipes and P. homarus homarus were recorded for the first time in this region.
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Affiliation(s)
- Sachithra Amarin Hettiarachchi
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences & Technology, University of Ruhuna, Matara, Sri Lanka,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Ji-Yeon Hyeon
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Biology, Jeju National University, Jeju, Republic of Korea
| | - Angka Mahardini
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea
| | - Hyung-Suk Kim
- Department of Kinesiology, Jeju National University, Jeju, Republic of Korea
| | - Jun-Hwan Byun
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea
| | - Han-Jun Kim
- Marine Ecosystem Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Jong-Gyun Jeong
- LED-Marine Biology Convergence Technology Research Center, Pukyong National University, Busan, Republic of Korea
| | - Jung-Kyu Yeo
- LED-Marine Biology Convergence Technology Research Center, Pukyong National University, Busan, Republic of Korea
| | - Shin-Kwon Kim
- Aquaculture Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Se-Jae Kim
- Department of Biology, Jeju National University, Jeju, Republic of Korea
| | - Youn-Seong Heo
- LED-Marine Biology Convergence Technology Research Center, Pukyong National University, Busan, Republic of Korea
| | - Jonathan Sathyadith
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Do-Hyung Kang
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Sung-Pyo Hur
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
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5
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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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Amaral AR, Chanfana C, Smith BD, Mansur R, Collins T, Baldwin R, Minton G, Parra GJ, Krützen M, Jefferson TA, Karczmarski L, Guissamulo A, Brownell RL, Rosenbaum HC. Genomics of Population Differentiation in Humpback Dolphins, Sousa spp. in the Indo-Pacific Ocean. J Hered 2020; 111:652-660. [PMID: 33475708 DOI: 10.1093/jhered/esaa055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Speciation is a fundamental process in evolution and crucial to the formation of biodiversity. It is a continuous and complex process, which can involve multiple interacting barriers leading to heterogeneous genomic landscapes with various peaks of divergence among populations. In this study, we used a population genomics approach to gain insights on the speciation process and to understand the population structure within the genus Sousa across its distribution in the Indo-Pacific region. We found 5 distinct clusters, corresponding to S. plumbea along the eastern African coast and the Arabian Sea, the Bangladesh population, S. chinensis off Thailand and S. sahulensis off Australian waters. We suggest that the high level of differentiation found, even across geographically close areas, is likely determined by different oceanographic features such as sea surface temperature and primary productivity.
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Affiliation(s)
- Ana R Amaral
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY.,Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Cátia Chanfana
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Brian D Smith
- Wildlife Conservation Society, Ocean Giants Program, Bronx, NY
| | - Rubaiyat Mansur
- Wildlife Conservation Society, Ocean Giants Program, Bronx, NY
| | - Tim Collins
- Wildlife Conservation Society, Ocean Giants Program, Bronx, NY
| | | | - Gianna Minton
- Megaptera Marine Conservation, The Hague, The Netherlands
| | - Guido J Parra
- Cetacean Ecology, Behaviour and Evolution Lab, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, CH Zurich, Switzerland
| | | | - Leszek Karczmarski
- Division of Cetacean Ecology and Division of Comparative Behavioural Ecology, Cetacea Research Institute, Lantau, Hong Kong.,Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Almeida Guissamulo
- Universidade Eduardo Mondlane, Museu de Historia Natural, Praca Travessia do Zambeze, Maputo, Mozambique
| | - Robert L Brownell
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla Shores Drive, La Jolla, CA
| | - Howard C Rosenbaum
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY.,Wildlife Conservation Society, Ocean Giants Program, Bronx, NY
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Singh SP, Groeneveld JC, Willows‐Munro S. Genetic structure and life history are key factors in species distribution models of spiny lobsters. Ecol Evol 2020; 10:14394-14410. [PMID: 33391723 PMCID: PMC7771135 DOI: 10.1002/ece3.7043] [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: 07/30/2020] [Revised: 10/08/2020] [Accepted: 10/23/2020] [Indexed: 11/06/2022] Open
Abstract
AIM We incorporated genetic structure and life history phase in species distribution models (SDMs) constructed for a widespread spiny lobster, to reveal local adaptations specific to individual subspecies and predict future range shifts under the RCP 8.5 climate change scenario. LOCATION Indo-West Pacific. METHODS MaxEnt was used to construct present-day SDMs for the spiny lobster Panulirus homarus and individually for the three genetically distinct subspecies of which it comprises. SDMs incorporated both sea surface and benthic (seafloor) climate layers to recreate discrete influences of these habitats during the drifting larval and benthic juvenile and adult life history phases. Principle component analysis (PCA) was used to infer environmental variables to which individual subspecies were adapted. SDM projections of present-day habitat suitability were compared with predictions for the year 2,100, under the RCP 8.5 climate change scenario. RESULTS In the PCA, salinity best explained P. h. megasculptus habitat suitability, compared with current velocity in P. h. rubellus and sea surface temperature in P. h. homarus. Drifting and benthic life history phases were adapted to different combinations of sea surface and benthic environmental variables considered. Highly suitable habitats for benthic phases were spatially enveloped within more extensive sea surface habitats suitable for drifting larvae. SDMs predicted that present-day highly suitable habitats for P. homarus will decrease by the year 2,100. MAIN CONCLUSIONS Incorporating genetic structure in SDMs showed that individual spiny lobster subspecies had unique adaptations, which could not be resolved in species-level models. The use of sea surface and benthic climate layers revealed the relative importance of environmental variables during drifting and benthic life history phases. SDMs that included genetic structure and life history were more informative in predictive models of climate change effects.
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Affiliation(s)
| | - Johan C. Groeneveld
- Oceanographic Research InstituteDurbanSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalPietermaritzburgSouth Africa
| | - Sandi Willows‐Munro
- School of Life SciencesUniversity of KwaZulu‐NatalPietermaritzburgSouth Africa
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Plön S, Thakur V, Parr L, Lavery SD. Phylogeography of the dugong (Dugong dugon) based on historical samples identifies vulnerable Indian Ocean populations. PLoS One 2019; 14:e0219350. [PMID: 31509531 PMCID: PMC6738584 DOI: 10.1371/journal.pone.0219350] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/22/2019] [Indexed: 12/15/2022] Open
Abstract
We investigated the phylogeography of the dugong (Dugong dugon) across its original range using museum material from 14 natural history museum and university collections. The mitochondrial DNA control region was successfully amplified from samples of bone or tooth powder from 162 individuals. These samples range from 1827 to 1996 and span the historical distribution range of the dugong. We were able to successfully amplify overlapping fragments of the D-loop region of the mitochondrial DNA (mtDNA) resulting in sequences of a 355 bp fragment for 162 individuals for the final analyses. This included a new sequence (189 bp) from a previously unidentified piece of skin of the extinct Steller’s sea cow (Hydrodamalis gigas), as an outgroup. The resulting dugong sequences match those from previous studies of dugongs from Australia and Indonesia, but revealed several new and divergent mtDNA lineages in the Indian Ocean. One mtDNA lineage includes most specimens from the Western Indian Ocean, with another distinct lineage isolated to nearby Madagascar and Comores. There is little geographic structuring detectable among other populations in the Western Indian Ocean and all populations from that region appear to have historically contained comparatively low levels of genetic diversity. The genetic diversity of several Indian Ocean samples collected after 1950 was lower than that of the samples collected earlier from similar locations, a result coincident with the anecdotal reductions in population size. The new lineages and potential loss of diversity highlight the particular conservation importance and vulnerability of dugong populations in the Western Indian Ocean.
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Affiliation(s)
- Stephanie Plön
- African Earth Observation Network (AEON)- Earth Stewardship Science Research Institute (ESSRI), Nelson Mandela University, Port Elizabeth, South Africa
- * E-mail:
| | - Vibha Thakur
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Leslee Parr
- Department of Biological Sciences, San José State University, San José, California, United States of America
| | - Shane D. Lavery
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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Roycroft EJ, Le Port A, Lavery SD. Population structure and male-biased dispersal in the short-tail stingray Bathytoshia brevicaudata (Myliobatoidei: Dasyatidae). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01167-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Singh SP, Groeneveld JC, Hart‐Davis MG, Backeberg BC, Willows‐Munro S. Seascape genetics of the spiny lobster Panulirus homarus in the Western Indian Ocean: Understanding how oceanographic features shape the genetic structure of species with high larval dispersal potential. Ecol Evol 2018; 8:12221-12237. [PMID: 30598813 PMCID: PMC6303728 DOI: 10.1002/ece3.4684] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/03/2023] Open
Abstract
This study examines the fine-scale population genetic structure and phylogeography of the spiny lobster Panulirus homarus in the Western Indian Ocean. A seascape genetics approach was used to relate the observed genetic structure based on 21 microsatellite loci to ocean circulation patterns, and to determine the influence of latitude, sea surface temperature (SST), and ocean turbidity (KD490) on population-level processes. At a geospatial level, the genetic clusters recovered corresponded to three putative subspecies, P. h. rubellus from the SW Indian Ocean, P. h. megasculptus from the NW Indian Ocean, and P. h. homarus from the tropical region in-between. Virtual passive Lagrangian particles advected using satellite-derived ocean surface currents were used to simulate larval dispersal. In the SW Indian Ocean, the dispersion of particles tracked over a 4-month period provided insight into a steep genetic gradient observed at the Delagoa Bight, which separates P. h. rubellus and P. h. homarus. South of the contact zone, particles were advected southwestwards by prevailing boundary currents or were retained in nearshore eddies close to release locations. Some particles released in southeast Madagascar dispersed across the Mozambique Channel and reached the African shelf. Dispersal was characterized by high seasonal and inter-annual variability, and a large proportion of particles were dispersed far offshore and presumably lost. In the NW Indian Ocean, particles were retained within the Arabian Sea. Larval retention and self-recruitment in the Arabian Sea could explain the recent genetic divergence between P. h. megasculptus and P. h. homarus. Geographic distance and minimum SST were significantly associated with genetic differentiation in multivariate analysis, suggesting that larval tolerance to SST plays a role in shaping the population structure of P. homarus.
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Affiliation(s)
- Sohana P. Singh
- Oceanographic Research InstituteMarine ParadeSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalPietermaritzburgSouth Africa
| | - Johan C. Groeneveld
- Oceanographic Research InstituteMarine ParadeSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalPietermaritzburgSouth Africa
| | - Michael G. Hart‐Davis
- Institute for Coastal and Marine ResearchNelson Mandela UniversityPort ElizabethSouth Africa
- Department of Oceanography, Nansen‐Tutu Centre for Marine Environmental ResearchUniversity of Cape TownSouth Africa
- Egagasini NodeSouth African Environmental Observation NetworkCape TownSouth Africa
| | - Björn C. Backeberg
- Department of Oceanography, Nansen‐Tutu Centre for Marine Environmental ResearchUniversity of Cape TownSouth Africa
- Council for Scientific and Industrial Research, Natural Resources and the EnvironmentCoastal Systems Research GroupStellenboschSouth Africa
- Nansen Environmental and Remote Sensing CenterBergenNorway
| | - Sandi Willows‐Munro
- School of Life SciencesUniversity of KwaZulu‐NatalPietermaritzburgSouth Africa
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11
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Al-Breiki RD, Kjeldsen SR, Afzal H, Al Hinai MS, Zenger KR, Jerry DR, Al-Abri MA, Delghandi M. Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline. BMC Genomics 2018; 19:690. [PMID: 30231936 PMCID: PMC6146514 DOI: 10.1186/s12864-018-5044-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species. RESULTS After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = - 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus. CONCLUSIONS Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.
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Affiliation(s)
- Rufaida Dhuhai Al-Breiki
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
- College of Agriculture and Marine Sciences, Department of Marine Sciences and Fisheries, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Shannon R. Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Hasifa Afzal
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Manal Saif Al Hinai
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Mohammed Ali Al-Abri
- College of Agriculture and Marine Sciences, Department of Animal and Veterinary Sciences and Technology, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Madjid Delghandi
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
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