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Li CYJ, Tsai WP, Ranatunga RRMKP, Samidon M, Liu SYV. Genetic stock structure of the silky shark Carcharhinus falciformis in the Indo-Pacific Ocean. PLoS One 2023; 18:e0292743. [PMID: 37824585 PMCID: PMC10569576 DOI: 10.1371/journal.pone.0292743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
The silky shark, Carcharhinus falciformis, is a cosmopolitan species commonly caught as a bycatch for longline fisheries. However, the genetic stock structure for the Indo-Pacific Ocean is not well-defined yet. Here, we used eight microsatellite loci to examine the genetic stock structure and effective population size of 307 silky sharks across 5 Indo-Pacific sampling locations. A major genetic break was found between Aceh and the remaining locations (FST = 0.0505-0.0828, p = 0.001). The Indian Ocean displayed a slightly lower effective population estimate (Ne) compared to the Pacific Ocean, potentially due to the higher fishing pressure in the Indian Ocean region. The lowest Ne was found in the Aceh population (Ne = 2.3), suggesting it might be a small and endemic population. These findings offer valuable information for the conservation and management of the silky shark. We suggest that the population around Aceh waters constitutes a distinct stock and should be managed independently. Further investigations into migratory and movement patterns are needed to define the boundaries of different stocks, ensuring effective management the silky shark across the Indo-Pacific region.
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Affiliation(s)
- Chia-Yun Joanne Li
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wen-Pei Tsai
- Department of Fisheries Production and Management, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - R. R. M. K. P. Ranatunga
- Centre for Marine Science and Technology, Department of Zoology, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Munandar Samidon
- Department of Marine Science, Teuku Umar University, Aceh Barat, Indonesia
| | - Shang Yin Vanson Liu
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
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2
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Whitney JL, Coleman RR, Deakos MH. Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian reef Manta Rays. BMC Ecol Evol 2023; 23:31. [PMID: 37422622 PMCID: PMC10329317 DOI: 10.1186/s12862-023-02130-0] [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: 11/19/2022] [Accepted: 06/07/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Reef manta rays (Mobula alfredi) are globally distributed in tropical and subtropical seas. Their life history traits (slow growth, late maturity, low reproductive output) make them vulnerable to perturbations and therefore require informed management strategies. Previous studies have reported wide-spread genetic connectivity along continental shelves suggesting high gene flow along continuous habitats spanning hundreds of kilometers. However, in the Hawaiian Islands, tagging and photo-identification evidence suggest island populations are isolated despite proximity, a hypothesis that has not yet been evaluated with genetic data. RESULTS This island-resident hypothesis was tested by analyzing whole mitogenome haplotypes and 2048 nuclear single nucleotide polymorphisms (SNPs) between M. alfredi (n = 38) on Hawai'i Island and Maui Nui (the 4-island complex of Maui, Moloka'i, Lāna'i and Kaho'olawe). Strong divergence in the mitogenome (ΦST = 0.488) relative to nuclear genome-wide SNPs (neutral FST = 0.003; outlier FST = 0.186), and clustering of mitochondrial haplotypes among islands provides robust evidence that female reef manta rays are strongly philopatric and do not migrate between these two island groups. Combined with restricted male-mediated migration, equivalent to a single male moving between islands every 2.2 generations (~ 64 years), we provide evidence these populations are significantly demographically isolated. Estimates of contemporary effective population size (Ne) are 104 (95% CI: 99-110) in Hawai'i Island and 129 (95% CI: 122-136) in Maui Nui. CONCLUSIONS Concordant with evidence from photo identification and tagging studies, these genetic results indicate reef manta rays in Hawai'i have small, genetically-isolated resident island populations. We hypothesize that due to the Island Mass Effect, large islands provide sufficient resources to support resident populations, thereby making crossing deep channels separating island groups unnecessary. Small effective population size, low genetic diversity, and k-selected life history traits make these isolated populations vulnerable to region-specific anthropogenic threats, which include entanglement, boat strikes, and habitat degradation. The long-term persistence of reef manta rays in the Hawaiian Islands will require island-specific management strategies.
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Affiliation(s)
- Jonathan L Whitney
- National Oceanic and Atmospheric Administration, Pacific Islands Fisheries Science Center, Honolulu, Hawai'i, USA.
| | - Richard R Coleman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Sciences, University of Miami, Miami, FL, USA
| | - Mark H Deakos
- Hawai'i Association for Marine Education and Research, Lahaina, Maui, Hawai'i, USA
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3
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Scacco U, Di Crescenzo S, Sbrana A. Exploring fishing threat at fleet segment and subregional scale: Least expert knowledge and a resilience versus disturbance-based approach as conservation's tools for cartilaginous fish. Ecol Evol 2023; 13:e9881. [PMID: 36950373 PMCID: PMC10025082 DOI: 10.1002/ece3.9881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 02/09/2023] [Accepted: 02/16/2023] [Indexed: 03/21/2023] Open
Abstract
Based on an explorative but rigorous elicitation framework, we obtained the bycatch fishing probability at the fishing fleet segment level using expert estimates. Based on the knowledge of three scientific experts, we developed a new and creative structured method for smart and fast fishery-related risk assessments for species of high conservation concern. In order to test the method here propose, we applied it to 76 cartilaginous fish species (included in the IUCN Red Lists) and on five different fishing segments at both Italian and Mediterranean scale. The method produced qualitative results specific to the threat posed by fishing for each species and each segment with information between and within the segments. Based on the interpretation of resilience-disturbance interactions developed for ecological systems, the quantitative results provided reliable cumulative metrics, measuring the extinction risk due to fishing and the response to overfishing for the species considered. Additionally, the results highlight that the method perform best on a small geographic scale. Therefore, the application of this new method on other subregional or local scales where very few data are available (e.g., fishing effort) could be a valuable tool for the preliminary assessment for species of conservation concern. In fact, despite the absence of detailed catch data at local geographic scales, the flexibility of this method could help to highlight potential fishery-related conservation problems and thus redirect conservation strategies for threatened marine species such as many sharks and rays species.
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Affiliation(s)
- Umberto Scacco
- National Centre of Laboratories‐BiologyItalian Institute for Environmental Protection and Research (ISPRA)RomeItaly
- Department of Bio Ecological SciencesUniversity of TusciaViterboItaly
| | - Simone Di Crescenzo
- Department of Life and Environmental SciencesUniversity of CagliariCagliariItaly
| | - Alice Sbrana
- Department of BiologyUniversity of Rome Tor VergataRomeItaly
- PhD program in Evolutionary Biology and EcologyUniversity of Rome Tor VergataRomeItaly
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4
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Characterization of 35 new microsatellite markers for the blacktip reef shark (Carcharhinus melanopterus) and cross-species amplification in eight other shark species. Mol Biol Rep 2023; 50:3205-3215. [PMID: 36707491 DOI: 10.1007/s11033-022-08209-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/13/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND Shark species are overfished at a global scale, as they are poached for the finning industry or are caught as bycatch. Efficient conservation measures require fine-scale spatial and temporal studies to characterize shark habitat use, infer migratory habits, analyze relatedness, and detect population genetic differentiation. Gathering these types of data is costly and time-consuming, especially when it requires collection of shark tissue samples. METHODS AND RESULTS Genetic tools, such as microsatellite markers, are the most economical sampling method for collecting genetic data, as they enable the estimation of genetic diversity, population structure and parentage relationships and are thus an efficient way to inform conservation strategies. Here, a set of 45 microsatellite loci was tested on three blacktip reef shark (Carcharhinus melanopterus) populations from three Polynesian islands: Moorea, Morane and Tenararo. The set was composed of 10 previously published microsatellite markers and 35 microsatellite markers that were developed specifically for C. melanopterus as part of the present study. The 35 novel and 10 existing loci were cross-amplified on eight additional shark species (Carcharhinus amblyrhynchos, C. longimanus, C. sorrah, Galeocerdo cuvier, Negaprion acutidens, Prionacea glauca, Rhincodon typus and Sphyrna lewini). These species had an average of 69% of successful amplification, considered if at least 50% of the individual samples being successfully amplified per species and per locus. CONCLUSIONS This novel microsatellite marker set will help address numerous knowledge gaps that remain, concerning genetic stock identification, shark behavior and reproduction via parentage analysis.
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5
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Smith KL, Feldheim K, Carlson JK, Wiley TR, Taylor SS. Female philopatry in smalltooth sawfish Pristis pectinata: conservation and management implications. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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6
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Papa Y, Oosting T, Valenza-Troubat N, Wellenreuther M, Ritchie PA. Genetic stock structure of New Zealand fish and the use of genomics in fisheries management: an overview and outlook. NEW ZEALAND JOURNAL OF ZOOLOGY 2020. [DOI: 10.1080/03014223.2020.1788612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yvan Papa
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Tom Oosting
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Noemie Valenza-Troubat
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand
| | - Maren Wellenreuther
- New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Peter A. Ritchie
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Pirog A, Ravigné V, Fontaine MC, Rieux A, Gilabert A, Cliff G, Clua E, Daly R, Heithaus MR, Kiszka JJ, Matich P, Nevill JEG, Smoothey AF, Temple AJ, Berggren P, Jaquemet S, Magalon H. Population structure, connectivity, and demographic history of an apex marine predator, the bull shark Carcharhinus leucas. Ecol Evol 2019; 9:12980-13000. [PMID: 31871624 PMCID: PMC6912899 DOI: 10.1002/ece3.5597] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 07/23/2019] [Accepted: 07/28/2019] [Indexed: 01/16/2023] Open
Abstract
Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analyzing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes (CR, nd4, and cytb). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DNA. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC-RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines, highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale.
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Affiliation(s)
- Agathe Pirog
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint DenisFrance
| | | | - Michaël C. Fontaine
- Laboratoire MIVEGEC (Université de Montpellier UMR CNRS 5290, IRD 229)Centre IRD de MontpellierMontpellierFrance
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | | | | | - Geremy Cliff
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Eric Clua
- EPHECNRS UPVDUSR 3278 CRIOBEPSL Research UniversityPerpignanFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
| | - Ryan Daly
- Oceanographic Research InstituteDurbanSouth Africa
- South African Institute for Aquatic BiodiversityGrahamstownSouth Africa
| | - Michael R. Heithaus
- Department of Biological SciencesFlorida International UniversityNorth MiamiFLUSA
| | - Jeremy J. Kiszka
- Department of Biological SciencesFlorida International UniversityNorth MiamiFLUSA
| | - Philip Matich
- Department of Biological SciencesFlorida International UniversityNorth MiamiFLUSA
| | | | - Amy F. Smoothey
- NSW Department of Primary IndustriesSydney Institute of Marine ScienceMosmanNSWAustralia
| | - Andrew J. Temple
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Per Berggren
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Sébastien Jaquemet
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint DenisFrance
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint DenisFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
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8
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Sandoval-Castillo J. Conservation genetics of elasmobranchs of the Mexican Pacific Coast, trends and perspectives. ADVANCES IN MARINE BIOLOGY 2019; 83:115-157. [PMID: 31606069 DOI: 10.1016/bs.amb.2019.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One of the most critical threats to biodiversity is the high extinction rate driven by human activities. Reducing extinction rates requires the implementation of conservation programmes based on robust scientific data. Elasmobranchs are important ecological components of the ocean, and several species sustain substantial economic activities. Unfortunately, elasmobranchs are one of the most threatened and understudied animal taxa. The Mexican Pacific Coast (MPC) is a region with high elasmobranch diversity and is the seat of major elasmobranch fisheries. But it is also a developing region with several conservation and management challenges which require national and international attention. Here, we review the conservation genetics literature of elasmobranchs from the MPC. We present a synthesis of the works using samples from the region and emphasize the main gaps and biases in these data. In addition, we discuss the benefits and challenges of generating genomic information to improve the management and conservation of an elasmobranch biodiversity hotspot in a developing country. We found 47 elasmobranch genetic articles that cover <30% of the elasmobranch diversity in the region. These studies mainly used mitochondrial DNA sequences to analyse the genetic structure of commercially important and abundant species of the order Carcharhiniformes. Some of these papers also assessed mating systems, demographic parameters, and taxonomic uncertainties, all of which are important topics for efficient management decisions. In terms of conservation genetics, elasmobranchs from the MPC remain understudied. However, high-throughput sequencing technologies have increased the power and accessibility of genomic tools, even in developing countries such as Mexico. The tools described here provide information relevant for biodiversity conservation. Therefore, we strongly suggest that investment in genomic research will assist implementation of efficient management strategies. In time, this will reduce the extinction risk of the unique elasmobranch biodiversity from the MPC.
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Affiliation(s)
- Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
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9
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Introgressive hybridisation between two widespread sharks in the east Pacific region. Mol Phylogenet Evol 2019; 136:119-127. [DOI: 10.1016/j.ympev.2019.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 03/27/2019] [Accepted: 04/10/2019] [Indexed: 11/21/2022]
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10
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O'Connell KA, Santo VD, Maldonado J, Molina E, Fujita MK. A Tale of Two Skates: Comparative Phylogeography of North American Skate Species with Implications for Conservation. COPEIA 2019. [DOI: 10.1643/cg-18-114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Kyle A. O'Connell
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Valentina Di Santo
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138
| | - Jose Maldonado
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Erika Molina
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Matthew K. Fujita
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
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11
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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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12
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Manuzzi A, Zane L, Muñoz-Merida A, Griffiths AM, Veríssimo A. Population genomics and phylogeography of a benthic coastal shark (Scyliorhinus canicula) using 2b-RAD single nucleotide polymorphisms. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Alice Manuzzi
- CIBIO – U.P. – Research Center for Biodiversity and Genetic Resources, Vairão, Portugal
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej, Silkeborg, Denmark
| | - Lorenzo Zane
- Department of Biology, University of Padova, Padova, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy
| | - Antonio Muñoz-Merida
- CIBIO – U.P. – Research Center for Biodiversity and Genetic Resources, Vairão, Portugal
| | | | - Ana Veríssimo
- CIBIO – U.P. – Research Center for Biodiversity and Genetic Resources, Vairão, Portugal
- Virginia Institute of Marine Science, College of William and Mary, VA, USA
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13
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Pazmiño DA, Maes GE, Green ME, Simpfendorfer CA, Hoyos-Padilla EM, Duffy CJA, Meyer CG, Kerwath SE, Salinas-de-León P, van Herwerden L. Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers. Heredity (Edinb) 2018; 120:407-421. [PMID: 29321624 PMCID: PMC5889387 DOI: 10.1038/s41437-017-0025-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/07/2017] [Accepted: 10/17/2017] [Indexed: 12/15/2022] Open
Abstract
The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise ΦST defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (FST = 0.023-0.035), mtDNA exhibited more divergence (ΦST = 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.
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Affiliation(s)
- Diana A Pazmiño
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- Universidad San Francisco de Quito - Galápagos Science Center, Quito, Ecuador.
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Leuven, Belgium
- Laboratory for Cytogenetics and Genome Research, Center for Human Genetics, Genomics Core, KU Leuven, Leuven, Belgium
| | - Madeline E Green
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS, Australia
- CSIRO Oceans & Atmosphere, Castray Esplanade, Battery Point, Hobart, TAS, Australia
| | - Colin A Simpfendorfer
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | | | - Clinton J A Duffy
- Auckland War Memorial Museum, The Domain, Auckland, New Zealand
- Department of Conservation, Private Bag 68908, Newton, Auckland, New Zealand
| | - Carl G Meyer
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Coconut Island, Kaneohe, HI, USA
| | - Sven E Kerwath
- Department of Biological Sciences, University of Cape Town, Private Bag × 3, Rondebosch, South Africa
- Department of Agriculture, Forestry and Fisheries: Fisheries Branch, Private Bag × 2, Vlaeberg, Cape Town, South Africa
| | - Pelayo Salinas-de-León
- Department of Marine Sciences, Charles Darwin Research Station. Av Charles Darwin s/n, Puerto Ayora, Galapagos Islands, Santa Cruz, Ecuador
- Pristine Seas, National Geographic Society, Washington, D. C., USA
| | - Lynne van Herwerden
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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14
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Case study of microsatellite polymorphism of European perch in selected commercially important lakes of Latvia. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0035-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Holmes BJ, Pope LC, Williams SM, Tibbetts IR, Bennett MB, Ovenden JR. Lack of multiple paternity in the oceanodromous tiger shark ( Galeocerdo cuvier). ROYAL SOCIETY OPEN SCIENCE 2018; 5:171385. [PMID: 29410842 PMCID: PMC5792919 DOI: 10.1098/rsos.171385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/01/2017] [Indexed: 06/08/2023]
Abstract
Multiple paternity has been documented as a reproductive strategy in both viviparous and ovoviviparous elasmobranchs, leading to the assumption that multiple mating may be ubiquitous in these fishes. However, with the majority of studies conducted on coastal and nearshore elasmobranchs that often form mating aggregations, parallel studies on pelagic, semi-solitary species are lacking. The tiger shark (Galeocerdo cuvier) is a large pelagic shark that has an aplacental viviparous reproductive mode which is unique among the carcharhinids. A total of 112 pups from four pregnant sharks were genotyped at nine microsatellite loci to assess the possibility of multiple paternity or polyandrous behaviour by female tiger sharks. Only a single pup provided evidence of possible multiple paternity, but with only seven of the nine loci amplifying for this individual, results were inconclusive. In summary, it appears that the tiger sharks sampled in this study were genetically monogamous. These findings may have implications for the genetic diversity and future sustainability of this population.
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Affiliation(s)
- Bonnie J. Holmes
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
- Department of Agriculture and Fisheries, Brisbane, Queensland 4001, Australia
| | - Lisa C. Pope
- Institute for Social Science Research, The University of Queensland, Long Pocket Precinct, Queensland 4072, Australia
| | - Samuel M. Williams
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
- Department of Agriculture and Fisheries, Brisbane, Queensland 4001, Australia
| | - Ian R. Tibbetts
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mike B. Bennett
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jennifer R. Ovenden
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
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16
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Feldheim KA, Fields AT, Chapman DD, Scharer RM, Poulakis GR. Insights into reproduction and behavior of the smalltooth sawfish Pristis pectinata. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00868] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Green ME, Appleyard SA, White W, Tracey S, Ovenden J. Variability in multiple paternity rates for grey reef sharks (Carcharhinus amblyrhynchos) and scalloped hammerheads (Sphyrna lewini). Sci Rep 2017; 7:1528. [PMID: 28484261 PMCID: PMC5431484 DOI: 10.1038/s41598-017-01416-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/28/2017] [Indexed: 11/29/2022] Open
Abstract
This study assessed the presence and prevalence of multiple paternity (MP) in litters of grey reef sharks (Carcharhinus amblyrhynchos) and scalloped hammerheads (Sphyrna lewini) opportunistically caught in Papua New Guinea (PNG). Litter size between species were significantly different with an average of 3.3 pups for grey reef sharks and 17.2 pups for scalloped hammerhead. Using 14 and 10 microsatellite loci respectively, we identified MP in 66% of grey reef sharks (4 out of 6 litters) and 100% MP in scalloped hammerheads (5 litters). We found high paternal skew (the uneven contribution of sires per litter) and a positive correlation between female adult size and litter size in scalloped hammerheads but not in grey reef sharks. Differences in the frequency of MP between species and the identification of paternal skew may be linked with mating strategies and post-copulatory mechanisms. Multiple paternity is thought to benefit populations by enhancing genetic diversity therefore increasing the population’s genetic resilience to extrinsic pressures. The identification of MP in two shark species reported here, further elucidates the complex breeding strategies elasmobranchs undertake.
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Affiliation(s)
- M E Green
- CSIRO Oceans & Atmosphere, Castray Esplanade, Battery Point, Hobart, TAS 7004, Australia. .,CSIRO Australian National Fish Collection, National Research Collections Australia, Castray Esplanade, Hobart, TAS 7004, Australia. .,Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS 7001, Australia.
| | - S A Appleyard
- CSIRO Oceans & Atmosphere, Castray Esplanade, Battery Point, Hobart, TAS 7004, Australia.,CSIRO Australian National Fish Collection, National Research Collections Australia, Castray Esplanade, Hobart, TAS 7004, Australia
| | - W White
- CSIRO Oceans & Atmosphere, Castray Esplanade, Battery Point, Hobart, TAS 7004, Australia.,CSIRO Australian National Fish Collection, National Research Collections Australia, Castray Esplanade, Hobart, TAS 7004, Australia
| | - S Tracey
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS 7001, Australia
| | - J Ovenden
- School of Biomedical Sciences, University of Queensland, Chancellors Pl, St. Lucia, Brisbane, OLD 4072, Australia
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18
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Switch from sexual to parthenogenetic reproduction in a zebra shark. Sci Rep 2017; 7:40537. [PMID: 28091617 PMCID: PMC5238396 DOI: 10.1038/srep40537] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/28/2016] [Indexed: 11/08/2022] Open
Abstract
Parthenogenesis is a natural form of asexual reproduction in which embryos develop in the absence of fertilisation. Most commonly found in plants and invertebrate organisms, an increasing number of vertebrate species have recently been reported employing this reproductive strategy. Here we use DNA genotyping to report the first demonstration of an intra-individual switch from sexual to parthenogenetic reproduction in a shark species, the zebra shark Stegostoma fasciatum. A co-housed, sexually produced daughter zebra shark also commenced parthenogenetic reproduction at the onset of maturity without any prior mating. The demonstration of parthenogenesis in these two conspecific individuals with different sexual histories provides further support that elasmobranch fishes may flexibly adapt their reproductive strategy to environmental circumstances.
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Bernard AM, Feldheim KA, Heithaus MR, Wintner SP, Wetherbee BM, Shivji MS. Global population genetic dynamics of a highly migratory, apex predator shark. Mol Ecol 2016; 25:5312-5329. [DOI: 10.1111/mec.13845] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Andrea M. Bernard
- Save Our Seas Shark Research Center Halmos College of Natural Sciences & Oceanography Nova Southeastern University 8000 N. Ocean Drive Dania Beach FL 33004 USA
| | - Kevin A. Feldheim
- The Field Museum of Natural History Pritzker Laboratory for Molecular Systematics and Evolution 1400 South Lake Shore Drive Chicago IL 60605 USA
| | - Michael R. Heithaus
- School of Environment and Society Florida International University Miami FL USA
| | - Sabine P. Wintner
- KwaZulu‐Natal Sharks Board Private Bag 2 Umhlanga Rocks 4320 South Africa
- Biomedical Resource Unit University of KwaZulu‐Natal Durban 4000 South Africa
| | - Bradley M. Wetherbee
- Department of Biological Sciences University of Rhode Island Kingston RI USA
- Guy Harvey Research Institute Dania Beach, FL 33004 USA
| | - Mahmood S. Shivji
- Save Our Seas Shark Research Center and Guy Harvey Research Institute Halmos College of Natural Sciences & Oceanography Nova Southeastern University 8000 N. Ocean Drive Dania Beach FL 33004 USA
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20
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Rossouw C, Wintner SP, Bester-Van Der Merwe AE. Assessing multiple paternity in three commercially exploited shark species: Mustelus mustelus, Carcharhinus obscurus and Sphyrna lewini. JOURNAL OF FISH BIOLOGY 2016; 89:1125-41. [PMID: 27237109 DOI: 10.1111/jfb.12996] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 04/06/2016] [Indexed: 05/15/2023]
Abstract
In this study, multiple paternity (MP) was investigated in three commercially important shark species, common smoothhound Mustelus mustelus, dusky shark Carcharhinus obscurus and scalloped hammerhead Sphyrna lewini occurring in southern Africa. Reduced marker panels of between five and six microsatellite loci were constructed for each species and used to genotype and assess the presence of MP in a total of 60 M. mustelus individuals from six litters, 90 C. obscurus individuals from 14 litters and 54 S. lewini individuals from 13 litters. Analysis in GERUD and COLONY revealed the presence of MP in all three species. Multiple paternities were observed in 67, 35 and 46% of the litters of M. mustelus, C. obscurus and S. lewini, with corresponding average sire size of 1·6, 1·4 and 2·0, respectively. The variation in the rate of MP among the three species is in accordance with previous studies whilst the comparatively high frequency of MP observed for M. mustelus, matches what has previously been reported for shark species demonstrating aggregation behaviour.
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Affiliation(s)
- C Rossouw
- Department of Genetics, Stellenbosch University, Private Bag 1X, Matieland, 7602, South Africa
| | - S P Wintner
- KwaZulu-Natal Sharks Board and Biomedical Resource Unit, University of KwaZulu-Natal, Durban, 4000, South Africa
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21
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Gledhill KS, Kessel ST, Guttridge TL, Hansell AC, Bester-van der Merwe AE, Feldheim KA, Gruber SH, Chapman DD. Genetic structure, population demography and seasonal occurrence of blacktip shark Carcharhinus limbatus in Bimini, the Bahamas. JOURNAL OF FISH BIOLOGY 2015; 87:1371-1388. [PMID: 26709212 DOI: 10.1111/jfb.12821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 09/18/2015] [Indexed: 06/05/2023]
Abstract
A longline survey was conducted from 2004 to 2014 to investigate the demographic population structure and seasonal abundance of the blacktip shark Carcharhinus limbatus in the Bimini Islands, the Bahamas. All individuals sampled (n = 242) were sub-adult or adults [70·1-145·1 cm pre-caudal length (LPC) range] with no neonates or YOY recorded in Bimini. Carcharhinus limbatus abundance peaked in September, coincident with the largest ratio of female to male sharks and a peak in fresh mating wounds on females. Mitochondrial control region (mtCR) DNA sequences were obtained from C. limbatus at Bimini to test whether Bimini C. limbatus are most closely related to geographically proximate populations sampled on the south-eastern coast of the U.S.A., the closest known nursery areas for this species. Nine mtCR haplotypes were observed in 32 individuals sampled at Bimini [haplotype diversity (h) = 0·821, nucleotide diversity (π) = 0·0015]. Four haplotypes observed from Bimini matched those previously found in the northern Yucatan (Mexico)-Belize and two matched a haplotype previously found in the U.S.A. Four haplotypes were novel but were closely related to the northern Yucatan-Belizean haplotypes. Pair-wise ΦST analysis showed that Bimini was significantly differentiated from all of the populations previously sampled (U.S.A. Atlantic, U.S.A. Gulf of Mexico, northern Yucatan, Belize and Brazil). This indicates that C. limbatus sampled from Bimini are unlikely from the described, proximate U.S.A. nurseries.
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Affiliation(s)
- K S Gledhill
- South African Shark Conservancy, Old Harbour Museum, Hermanus 7200, South Africa
| | - S T Kessel
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - T L Guttridge
- Bimini Biological Field Station Foundation, 15 Elizabeth Drive, South Bimini, Bahamas
| | - A C Hansell
- Department of Fisheries Oceanography, School for Marine Science and Technology, University of Massachusetts - Dartmouth, Fairhaven, MA 02719, U.S.A
| | - A E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - K A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, U.S.A
| | - S H Gruber
- Bimini Biological Field Station Foundation, 15 Elizabeth Drive, South Bimini, Bahamas
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL 33124, U.S.A
| | - D D Chapman
- Institute for Ocean Conservation Science/School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, U.S.A
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22
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Portnoy DS, Puritz JB, Hollenbeck CM, Gelsleichter J, Chapman D, Gold JR. Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation. Mol Ecol 2015; 24:5877-85. [DOI: 10.1111/mec.13441] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/27/2015] [Accepted: 10/27/2015] [Indexed: 01/18/2023]
Affiliation(s)
- D. S. Portnoy
- Department of Life Sciences; Marine Genomics Laboratory; Harte Research Institute; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
| | - J. B. Puritz
- Department of Life Sciences; Marine Genomics Laboratory; Harte Research Institute; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
| | - C. M. Hollenbeck
- Department of Life Sciences; Marine Genomics Laboratory; Harte Research Institute; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
| | - J. Gelsleichter
- University of North Florida; 1 UNF Drive Jacksonville FL 32224 USA
| | - D. Chapman
- Stony Brook University; Stony Brook NY 11776 USA
| | - J. R. Gold
- Department of Life Sciences; Marine Genomics Laboratory; Harte Research Institute; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
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23
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Corrigan S, Kacev D, Werry J. A case of genetic polyandry in the shortfin mako Isurus oxyrinchus. JOURNAL OF FISH BIOLOGY 2015. [PMID: 26219624 DOI: 10.1111/jfb.12743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This article documents a case of genetic polyandry in the oceanic and pelagic shortfin mako Isurus oxyrinchus and briefly comments on the implications of this finding.
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Affiliation(s)
- S Corrigan
- Hollings Marine Laboratory, College of Charleston, Charleston, SC 29412, U.S.A
| | - D Kacev
- Department of Biology, San Diego State University, San Diego, CA 92182, U.S.A
| | - J Werry
- Ocean and Coast Research, Main Beach, QLD 4217, Australia
- Griffith Centre for Coastal Management, Griffith University, Southport, QLD 4222, Australia
- Australian Rivers Institute, Griffith Centre for Environment, Griffith University, Southport, QLD 4222, Australia
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24
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Bester-van der Merwe AE, Gledhill KS. Molecular species identification and population genetics of chondrichthyans in South Africa: current challenges, priorities and progress. AFRICAN ZOOLOGY 2015. [DOI: 10.1080/15627020.2015.1063408] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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25
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Marino IAM, Riginella E, Gristina M, Rasotto MB, Zane L, Mazzoldi C. Multiple paternity and hybridization in two smooth-hound sharks. Sci Rep 2015; 5:12919. [PMID: 26257113 PMCID: PMC4530440 DOI: 10.1038/srep12919] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 07/02/2015] [Indexed: 11/09/2022] Open
Abstract
Multiple paternity appears to be a common trait of elasmobranch mating systems, with its occurrence likely driven by convenience, due to females seeking to minimize the stress of male harassment. Here we use molecular markers to analyse the frequency of multiple paternity in two related viviparous sharks, Mustelus mustelus and Mustelus punctulatus. We first applied molecular methods to assign pregnant females, embryos and additional reference adults (N = 792) to one of the two species. Paternity analysis was performed using a total of 9 polymorphic microsatellites on 19 females and 204 embryos of M. mustelus, and on 13 females and 303 embryos of M. punctulatus. Multiple paternity occurs in both species, with 47% of M. mustelus and 54% of M. punctulatus litters sired by at least two fathers. Female fecundity is not influenced by multiple mating and in 56% of polyandrous litters paternity is skewed, with one male siring most of the pups. Genetic analyses also revealed hybridization between the two species, with a M. punctulatus female bearing pups sired by a M. mustelus male. The frequency of polyandrous litters in these species is consistent with aspects of their reproductive biology, such as synchronous ovulation and possible occurrence of breeding aggregations.
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Affiliation(s)
- Ilaria A M Marino
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy
| | - Emilio Riginella
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy
| | - Michele Gristina
- IAMC-CNR, via Luigi Vaccara 61, 91026 Mazara del Vallo (TP), Italy
| | - Maria B Rasotto
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy
| | - Lorenzo Zane
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy
| | - Carlotta Mazzoldi
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy
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26
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Population Genetic Structure of the Bonnethead Shark,Sphyrna tiburo, from the Western North Atlantic Ocean Based on mtDNA Sequences. J Hered 2015; 106:355-65. [DOI: 10.1093/jhered/esv030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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27
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Insights into the antiviral immunity against grass carp (Ctenopharyngodon idella) reovirus (GCRV) in grass carp. J Immunol Res 2015; 2015:670437. [PMID: 25759845 PMCID: PMC4337036 DOI: 10.1155/2015/670437] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/12/2014] [Indexed: 12/13/2022] Open
Abstract
Global fish production from aquaculture has rapidly grown over the past decades, and grass carp shares the largest portion. However, hemorrhagic disease caused by grass carp reovirus (GCRV) results in tremendous loss of grass carp (Ctenopharyngodon idella) industry. During the past years, development of molecular biology and cellular biology technologies has promoted significant advances in the understanding of the pathogen and the immune system. Immunoprophylaxis based on stimulation of the immune system of fish has also got some achievements. In this review, authors summarize the recent progresses in basic researches on GCRV; viral nucleic acid sensors, high-mobility group box proteins (HMGBs); pattern recognition receptors (PRRs), Toll-like receptors (TLRs) and retinoic acid inducible gene I- (RIG-I-) like receptors (RLRs); antiviral immune responses induced by PRRs-mediated signaling cascades of type I interferon (IFN-I) and IFN-stimulated genes (ISGs) activation. The present review also notices the potential applications of molecule genetic markers. Additionally, authors discuss the current preventive and therapeutic strategies (vaccines, RNAi, and prevention medicine) and highlight the importance of innate immunity in long term control for grass carp hemorrhagic disease.
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28
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Portnoy DS, Hollenbeck CM, Belcher CN, Driggers WB, Frazier BS, Gelsleichter J, Grubbs RD, Gold JR. Contemporary population structure and post-glacial genetic demography in a migratory marine species, the blacknose shark, Carcharhinus acronotus. Mol Ecol 2014; 23:5480-95. [PMID: 25294029 DOI: 10.1111/mec.12954] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 11/30/2022]
Abstract
Patterns of population structure and historical genetic demography of blacknose sharks in the western North Atlantic Ocean were assessed using variation in nuclear-encoded microsatellites and sequences of mitochondrial (mt)DNA. Significant heterogeneity and/or inferred barriers to gene flow, based on microsatellites and/or mtDNA, revealed the occurrence of five genetic populations localized to five geographic regions: the southeastern U.S Atlantic coast, the eastern Gulf of Mexico, the western Gulf of Mexico, Bay of Campeche in the southern Gulf of Mexico and the Bahamas. Pairwise estimates of genetic divergence between sharks in the Bahamas and those in all other localities were more than an order of magnitude higher than between pairwise comparisons involving the other localities. Demographic modelling indicated that sharks in all five regions diverged after the last glacial maximum and, except for the Bahamas, experienced post-glacial, population expansion. The patterns of genetic variation also suggest that the southern Gulf of Mexico may have served as a glacial refuge and source for the expansion. Results of the study demonstrate that barriers to gene flow and historical genetic demography contributed to contemporary patterns of population structure in a coastal migratory species living in an otherwise continuous marine habitat. The results also indicate that for many marine species, failure to properly characterize barriers in terms of levels of contemporary gene flow could in part be due to inferences based solely on equilibrium assumptions. This could lead to erroneous conclusions regarding levels of connectivity in species of conservation concern.
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Affiliation(s)
- D S Portnoy
- Marine Genomics Laboratory, Department of Life Sciences, Harte Research Institute, Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX, 78412, USA
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29
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Geraghty PT, Williamson JE, Macbeth WG, Blower DC, Morgan JAT, Johnson G, Ovenden JR, Gillings MR. Genetic structure and diversity of two highly vulnerable carcharhinids in Australian waters. ENDANGER SPECIES RES 2014. [DOI: 10.3354/esr00580] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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30
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Farrell ED, O'Sullivan N, Sacchi C, Mariani S. Multiple paternity in the starry smooth-hound sharkMustelus asterias(Carcharhiniformes: Triakidae). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | - Niall O'Sullivan
- School of Biology and Environmental Science; University College Dublin; Belfield Dublin 4 Ireland
| | - Carlotta Sacchi
- School of Biology and Environmental Science; University College Dublin; Belfield Dublin 4 Ireland
| | - Stefano Mariani
- School of Environment and Life Sciences; University of Salford; Manchester UK
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31
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Castillo-Páez A, Sosa-Nishizaki O, Sandoval-Castillo J, Galván-Magaña F, Blanco-Parra MDP, Rocha-Olivares A. Strong Population Structure and Shallow Mitochondrial Phylogeny in the Banded Guitarfish, Zapteryx exasperata (Jordan y Gilbert, 1880), from the Northern Mexican Pacific. J Hered 2013; 105:91-100. [DOI: 10.1093/jhered/est067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Geraghty PT, Williamson JE, Macbeth WG, Wintner SP, Harry AV, Ovenden JR, Gillings MR. Population expansion and genetic structure in Carcharhinus brevipinna in the southern Indo-Pacific. PLoS One 2013; 8:e75169. [PMID: 24086462 PMCID: PMC3783459 DOI: 10.1371/journal.pone.0075169] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/12/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Quantifying genetic diversity and metapopulation structure provides insights into the evolutionary history of a species and helps develop appropriate management strategies. We provide the first assessment of genetic structure in spinner sharks (Carcharhinus brevipinna), a large cosmopolitan carcharhinid, sampled from eastern and northern Australia and South Africa. METHODS AND FINDINGS Sequencing of the mitochondrial DNA NADH dehydrogenase subunit 4 gene for 430 individuals revealed 37 haplotypes and moderately high haplotype diversity (h = 0.6770 ±0.025). While two metrics of genetic divergence (ΦST and F ST) revealed somewhat different results, subdivision was detected between South Africa and all Australian locations (pairwise ΦST, range 0.02717-0.03508, p values ≤ 0.0013; pairwise F ST South Africa vs New South Wales = 0.04056, p = 0.0008). Evidence for fine-scale genetic structuring was also detected along Australia's east coast (pairwise ΦST = 0.01328, p < 0.015), and between south-eastern and northern locations (pairwise ΦST = 0.00669, p < 0.04). CONCLUSIONS The Indian Ocean represents a robust barrier to contemporary gene flow in C. brevipinna between Australia and South Africa. Gene flow also appears restricted along a continuous continental margin in this species, with data tentatively suggesting the delineation of two management units within Australian waters. Further sampling, however, is required for a more robust evaluation of the latter finding. Evidence indicates that all sampled populations were shaped by a substantial demographic expansion event, with the resultant high genetic diversity being cause for optimism when considering conservation of this commercially-targeted species in the southern Indo-Pacific.
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Affiliation(s)
- Pascal T. Geraghty
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
- Cronulla Fisheries Research Centre of Excellence, New South Wales Department of Primary Industries, Sydney, New South Wales, Australia
| | - Jane E. Williamson
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - William G. Macbeth
- Cronulla Fisheries Research Centre of Excellence, New South Wales Department of Primary Industries, Sydney, New South Wales, Australia
| | - Sabine P. Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, KwaZulu-Natal, South Africa
| | - Alastair V. Harry
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - Jennifer R. Ovenden
- Molecular Fisheries Laboratory, the University of Queensland, St. Lucia, Queensland, Australia
| | - Michael R. Gillings
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
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33
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Boomer JJ, Harcourt RG, Francis MP, Walker TI, Braccini JM, Stow AJ. Frequency of multiple paternity in gummy shark, Mustelus antarcticus, and rig, Mustelus lenticulatus, and the implications of mate encounter rate, postcopulatory influences, and reproductive mode. J Hered 2013; 104:371-9. [PMID: 23505312 DOI: 10.1093/jhered/est010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Elasmobranchs (sharks and rays) show an amazing diversity of reproductive modes and behaviors. Multiple paternity (MP) has been identified in all species where more than 1 litter has been investigated; yet neither direct nor indirect benefits from MP have been determined in elasmobranchs. This has led to the suggestion that MP in this group may simply be a product of convenience polyandry with variation in the frequency of MP driven by differences in mate encounter rates. Here, we use molecular markers to investigate polyandry and MP in 2 closely related and commercially important species of shark, Mustelus antarcticus and Mustelus lenticulatus. In total, 328 M. antarcticus embryos originating from 29 different mothers and 75 M. lenticulatus embryos originating from 19 different mothers were genotyped using 8 microsatellite loci. We find that MP occurs in both species. However, in both species, the majority of litters were sired by a single father. Our results do not support increased fecundity per se as a driver of MP. Further, our results do not suggest that high population densities with resulting high mate encounter rates generated by breeding aggregations necessarily lead to high frequencies of MP. Importantly, we note evidence of reproductive skew within polyandrous litters, which is a predicted outcome of postcopulatory mechanisms.
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Affiliation(s)
- Jessica J Boomer
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia
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34
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Mourier J, Planes S. Direct genetic evidence for reproductive philopatry and associated fine-scale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia. Mol Ecol 2012; 22:201-14. [PMID: 23130666 DOI: 10.1111/mec.12103] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 11/29/2022]
Abstract
Conservation of top predators has been emphasized as essential in an ecosystem due to their role in trophic chain regulation. Optimizing conservation strategies for these endangered marine top predators requires direct estimates of breeding patterns and connectivity as these are essential to understanding the population dynamics. There have been some attempts to investigate breeding patterns of reef sharks from litter reconstruction using molecular analyses. However, direct fine-scale migrations of female sharks for parturition as well as connectivity at a medium scale like between islands remain mostly unknown. We used microsatellite DNA markers and a likelihood-based parentage analysis to determine breeding patterns of female blacktip reef sharks in Moorea (Society Islands, French Polynesia). Most females gave birth at their home island but some migrated to specific nursery areas outside the area they are attached to, sometimes going to another island 50 km away across deep ocean. Our analysis also revealed that females migrated to the same nursery for every birthing event. Many offspring showed a high level of inbreeding indicating an overall reduced population size, restricted movements and dispersal, or specific mating behaviour. Females represent the vectors that transport the genes at nursery grounds, and their fidelity should thus define reproductive units. As females seem to be philopatric, males could be the ones dispersing genes between populations. These results highlight the need to conserve coastal zones where female reef sharks seem to exhibit philopatry during the breeding season.
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Affiliation(s)
- Johann Mourier
- Laboratoire d'Excellence CORAIL, USR 3278 CNRS-EPHE, CRIOBE, BP 1013, 98729, Moorea, French Polynesia.
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White WT, Blaber SJM, Craig JF. The current status of elasmobranchs: biology, fisheries and conservation. JOURNAL OF FISH BIOLOGY 2012; 80:897-900. [PMID: 22497366 DOI: 10.1111/j.1095-8649.2012.03268.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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