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Hermans A, Winter HV, Gill AB, Murk AJ. Do electromagnetic fields from subsea power cables effect benthic elasmobranch behaviour? A risk-based approach for the Dutch Continental Shelf. Environ Pollut 2024; 346:123570. [PMID: 38360387 DOI: 10.1016/j.envpol.2024.123570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
Subsea power cables cause electromagnetic fields (EMFs) into the marine environment. Elasmobranchs (rays, skates, sharks) are particularly sensitive to EMFs as they use electromagnetic-receptive sensory systems for orientation, navigation, and locating conspecifics or buried prey. Cables may intersect with egg laying sites, mating, pupping, and nursery grounds, foraging habitat and migration routes of elasmobranchs and the effects of encountering EMFs on species of elasmobranchs are largely unknown. Demonstrated behavioural effects are attraction, disturbance and indifference, depending on EMF characteristics, exposed life stage, exposure level and duration. We estimated exposure levels of elasmobranchs to subsea power cable EMFs, based on modelled magnetic fields in the Dutch Continental Shelf and compared these to reported elasmobranch sensory sensitivity ranges and experimental effect levels. We conclude that the risk from subsea power cables has a large uncertainty and varies per life stage and species ecology. Based on estimated no-observed effect levels (from 10-3 to 10-1 μT) we discuss what will probably be the most affected species and life stage for six common benthic elasmobranchs in the Southern North Sea. We then identify critical knowledge gaps for reducing the uncertainty in the risk assessments for EMFs effects on benthic elasmobranchs.
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Affiliation(s)
- Annemiek Hermans
- Marine Animal Ecology Group, Wageningen University, P.O. Box 338, 6700 AH, Wageningen, the Netherlands.
| | - Hendrik V Winter
- Wageningen Marine Research, Wageningen University and Research, P.O. 68, 1970 AB, IJmuiden, the Netherlands
| | - Andrew B Gill
- Cefas, Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, Suffolk, NR33 0HT, UK
| | - Albertinka J Murk
- Marine Animal Ecology Group, Wageningen University, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
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2
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Baeza JA, Stephens NC, Baker A, Lyons A, Franks B, Pirro S, Feldheim KA. Insights into the nuclear and mitochondrial genome of the Lemon shark Negaprion brevirostris using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement. Gene 2024; 894:147939. [PMID: 38572145 PMCID: PMC10990291 DOI: 10.1016/j.gene.2023.147939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is slightly below the genome size estimated for other sharks belonging to the family Carcharhinidae. Using a k-mer analysis, approx. 64-71 % of the genome of N. brevirostris was composed of repetitive elements. A relatively large proportion of the 'repeatome' could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I - Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Negaprion brevirostris is closely related to the genera Carcharhinus, Glyphis and Lamiopsis in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this large coastal shark.
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Affiliation(s)
- J. Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA
- Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, Chile
| | | | - Alyssa Baker
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Andrew Lyons
- Marine Science Research Institute, Jacksonville University, Florida, USA
| | - Bryan Franks
- Marine Science Research Institute, Jacksonville University, Florida, USA
| | | | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, Chicago, IL, USA
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3
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Swenson JD, Brooks EN, Kacev D, Boyd C, Kinney MJ, Marcy‐Quay B, Sévêque A, Feldheim KA, Komoroske LM. Accounting for unobserved population dynamics and aging error in close-kin mark-recapture assessments. Ecol Evol 2024; 14:e10854. [PMID: 38327683 PMCID: PMC10847890 DOI: 10.1002/ece3.10854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 01/01/2024] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve the monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding the application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base-case CKMR model produces robust estimates of population abundance with stable populations that breed annually; however, if a population trend or non-annual breeding dynamics are present, or if year-specific estimates of abundance are desired, a more complex CKMR model must be constructed. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed (and aging error is minimal). Finally, we apply a CKMR model that has been adapted for population growth and intermittent breeding to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas, to demonstrate how application of CKMR to samples drawn solely from juveniles can contribute to monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, identifies key areas for future inquiry, and provides recommendations that can aid biologists in planning and implementing an effective CKMR study, particularly for long-lived data-limited species.
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Affiliation(s)
- John D. Swenson
- Department of Environmental ConservationThe University of Massachusetts AmherstAmherstMassachusettsUSA
| | - Elizabeth N. Brooks
- Population Dynamics Branch, Northeast Fisheries Science Center, National Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationWoods HoleMassachusettsUSA
| | - Dovi Kacev
- Marine Biology Research DivisionScripps Institution of OceanographySan DiegoCaliforniaUSA
| | - Charlotte Boyd
- International Union for Conservation of NatureNorth America OfficeWashington DCMarylandUSA
| | - Michael J. Kinney
- NOAA FisheriesPacific Island Fisheries Science CenterHonoluluHawaiiUSA
| | - Benjamin Marcy‐Quay
- Rubenstein Ecosystem Science LaboratoryUniversity of VermontBurlingtonVermontUSA
| | - Anthony Sévêque
- Department of Wildlife, Fisheries and Aquaculture, Forest and Wildlife Research CenterMississippi State UniversityMississippi StateMississippiUSA
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and EvolutionThe Field MuseumChicagoIllinoisUSA
| | - Lisa M. Komoroske
- Department of Environmental ConservationThe University of Massachusetts AmherstAmherstMassachusettsUSA
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4
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Eustache KB, Boissin É, Tardy C, Bouyoucos IA, Rummer JL, Planes S. Genetic evidence for plastic reproductive philopatry and matrotrophy in blacktip reef sharks (Carcharhinus melanopterus) of the Moorea Island (French Polynesia). Sci Rep 2023; 13:14913. [PMID: 37689802 PMCID: PMC10492826 DOI: 10.1038/s41598-023-40140-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/05/2023] [Indexed: 09/11/2023] Open
Abstract
The exploitation of sharks and the degradation of their habitats elevate the urgency to understand the factors that influence offspring survival and ultimately shark reproductive success. We monitored and sampled blacktip reef sharks (Carcharhinus melanopterus) in nursery habitats of Moorea Island (French Polynesia), to improve knowledge on shark reproductive behavior and biology. We sampled fin clips and morphometrics from 230 young-of-the-year sharks and used microsatellite DNA markers to process parentage analysis to study the reproductive philopatric behavior in female sharks and the matrotrophy within litters. These traits are driving the success of the local replenishment influencing selection through birth site and maternal reserves transmitted to pups. Parentage analysis revealed that some female sharks changed their parturition areas (inter-seasonally) while other female sharks came back to the same site for parturition, providing evidence for a plastic philopatric behavior. Morphometrics showed that there was no significant relationship between body condition indices and nursery locations. However, similarities and differences in body condition were observed between individuals sharing the same mother, indicating that resource allocation within some shark litters might be unbalanced. Our findings further our understanding of the reproductive biology and behavior that shape shark populations with the aim to introduce these parameters into future conservation strategies.
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Affiliation(s)
- Kim B Eustache
- PSL Research University, EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
| | - Émilie Boissin
- PSL Research University, EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- Laboratoire d'Excellence "CORAIL", Papetoai, Moorea, French Polynesia
| | - Céline Tardy
- PSL Research University, EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- WWF-France, 6 rue des Fabres, 13001, Marseille, France
| | - Ian A Bouyoucos
- PSL Research University, EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Australian Research Council Centre of Excellence for Coral Reef Studies and College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Jodie L Rummer
- Australian Research Council Centre of Excellence for Coral Reef Studies and College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Serge Planes
- PSL Research University, EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- Laboratoire d'Excellence "CORAIL", Papetoai, Moorea, French Polynesia
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5
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Swift DG, O'Leary SJ, Grubbs RD, Frazier BS, Fields AT, Gardiner JM, Drymon JM, Bethea DM, Wiley TR, Portnoy DS. Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales. Mol Ecol 2023; 32:4953-4970. [PMID: 37566208 DOI: 10.1111/mec.17096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023]
Abstract
Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and has direct implications for the spatial scales of management. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach employing mitochondrial control region sequences and 4339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units-the Atlantic, eastern Gulf, and western Gulf-that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighbouring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.
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Affiliation(s)
- Dominic G Swift
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
| | - Shannon J O'Leary
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
- Department of Biology, Saint Anselm College, Manchester, New Hampshire, USA
| | - R Dean Grubbs
- Florida State University Coastal and Marine Laboratory, St. Teresa, Florida, USA
| | - Bryan S Frazier
- South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, South Carolina, USA
| | - Andrew T Fields
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
| | - Jayne M Gardiner
- Division of Natural Sciences, New College of Florida, Sarasota, Florida, USA
| | - J Marcus Drymon
- Coastal Research and Extension Center, Mississippi State University, Biloxi, Mississippi, USA
- Mississippi-Alabama Sea Grant Consortium, Ocean Springs, Mississippi, USA
| | - Dana M Bethea
- NOAA Fisheries, U.S. Department of Commerce, Southeast Regional Office, Interagency Cooperation Branch, Protected Resources Division, St. Petersburg, Florida, USA
| | - Tonya R Wiley
- Havenworth Coastal Conservation, Palmetto, Florida, USA
| | - David S Portnoy
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
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6
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Sulikowski JA, Hammerschlag N. A novel intrauterine satellite transmitter to identify parturition in large sharks. Sci Adv 2023; 9:eadd6340. [PMID: 36857461 PMCID: PMC9977171 DOI: 10.1126/sciadv.add6340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Determining where and when animals give birth is critical for establishing effective conservation management that protects vulnerable life stages (e.g., pregnant females and newborns) and places (e.g., nursery grounds). To date, this information has been elusive in the case of highly migratory sharks in the wild. Here, we report on the deployment a of novel intrauterine satellite tag implanted in two highly mobile apex predators, the tiger shark (Galeocerdo cuvier) and the scalloped hammerhead (Sphyrna lewini), that remotely documented the location and timing of birth by a highly migratory oceanic animal in the wild. This novel technology will be especially valuable for the protection of threatened and endangered shark species, where protection of pupping and nursery grounds is a conservation priority.
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Affiliation(s)
- James A. Sulikowski
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, USA
| | - Neil Hammerschlag
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
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7
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Liu SYV, Chen YY, Cheng C. Genetic structure and relatedness of juvenile sicklefin lemon shark (Negaprion acutidens) at Dongsha Island. Sci Rep 2023; 13:988. [PMID: 36653472 PMCID: PMC9849347 DOI: 10.1038/s41598-023-28186-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Negaprion acutidens (sicklefin lemon shark) is distributed in the Indo-Pacific and in close association with coral reefs. Under the protection of the Dongsha Atoll National Park, a small but well-established juvenile population of N. acutidens inhabiting coastal areas of Dongsha Island was recently observed to display site fidelity by using acoustic telemetry. This study was designed to reveal the fine scale genetic structure and relatedness within and among 5 juvenile shark cohorts inhabiting 3 sampling sites at Dongsha Island. A total 188 juveniles were caught and sampled between 2016 and 2017, and genotyped with twelve loci. They were assigned to 5 year cohorts (2013-2017) based on the body length and date they were caught, also assigned to 3 sites based on where they were caught. Among five cohorts, the percentage of unrelated pairs within a cohort is more than 62% in average, suggesting a potential high mortality during their early life stage. The results of Fst and assignment testing showed that there was no significant genetic structure between sites and cohorts indicating that there was no fine scale genetic structure, even though the juveniles possessed strong site fidelity. A small effective population size (Ne) was detected (Ne = 86.7) which indicates the presence of a potentially isolated and vulnerable population at Dongsha. These results provide the genetic diversity as a baseline for future management and conservation of N. acutidens in the South China Sea.
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Affiliation(s)
- Shang Yin Vanson Liu
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan. .,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan. .,Graduate Institute of Natural Products College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Yu-Yun Chen
- Division of Natural Science, General Education Center, Aletheia University, New Taipei City, Taiwan
| | - Chi Cheng
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
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8
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Elizondo-Sancho M, Rodríguez-Arriatti Y, Albertazzi FJ, Bonilla-Salazar A, Arauz-Naranjo D, Arauz R, Areano E, Avalos-Castillo CG, Brenes Ó, Chávez EJ, Dominici-Arosemena A, Espinoza M, Heidemeyer M, Tavares R, Hernández S. Population structure and genetic connectivity of the scalloped hammerhead shark (Sphyrna lewini) across nursery grounds from the Eastern Tropical Pacific: Implications for management and conservation. PLoS One 2022; 17:e0264879. [PMID: 36525407 DOI: 10.1371/journal.pone.0264879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/18/2022] [Indexed: 12/23/2022] Open
Abstract
Defining demographically independent units and understanding patterns of gene flow between them is essential for managing and conserving exploited populations. The critically endangered scalloped hammerhead shark, Sphyrna lewini, is a coastal semi-oceanic species found worldwide in tropical and subtropical waters. Pregnant females give birth in shallow coastal estuarine habitats that serve as nursery grounds for neonates and small juveniles, whereas adults move offshore and become highly migratory. We evaluated the population structure and connectivity of S. lewini in coastal areas and one oceanic island (Cocos Island) across the Eastern Tropical Pacific (ETP) using both sequences of the mitochondrial DNA control region (mtCR) and 9 nuclear-encoded microsatellite loci. The mtCR defined two genetically discrete groups: one in the Mexican Pacific and another one in the central-southern Eastern Tropical Pacific (Guatemala, Costa Rica, Panama, and Colombia). Overall, the mtCR data showed low levels of haplotype diversity ranging from 0.000 to 0.608, while nucleotide diversity ranged from 0.000 to 0.0015. More fine-grade population structure was detected using microsatellite loci where Guatemala, Costa Rica, and Panama differed significantly. Relatedness analysis revealed that individuals within nursery areas were more closely related than expected by chance, suggesting that S. lewini may exhibit reproductive philopatric behaviour within the ETP. Findings of at least two different management units, and evidence of philopatric behaviour call for intensive conservation actions for this highly threatened species in the ETP.
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9
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Pratt HL, Pratt TC, Knotek RJ, Carrier JC, Whitney NM. Long-term use of a shark breeding ground: Three decades of mating site fidelity in the nurse shark, Ginglymostoma cirratum. PLoS One 2022; 17:e0275323. [PMID: 36251734 PMCID: PMC9576040 DOI: 10.1371/journal.pone.0275323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding shark mating dynamics and mating site use may be vital to species management. The Dry Tortugas courtship and mating ground (DTCMG) has been known as a mating site for nurse sharks, Ginglymostoma cirratum, since 1895. In a 30-yr (1992–2021) study we have documented long-term site fidelity to this area with data from 137 adult sharks (89 female, 48 male) tagged with PIT, fin, and acoustic tags. Of 118 sharks tagged from 1993 to 2014, at least 80 (68%) returned to the DTCMG in subsequent years during the June-July mating season. Known individuals returned in up to 16 different mating seasons and over periods of up 28 years, indicating that life span extends well into the forties for this species. Of all returning sharks, 59% (N = 47) have been monitored for over 10 years and 13% (N = 10) have been monitored for over 20 years. Males arrived annually in May and June and departed in July, whereas females arrived biennially or triennially in June, with a secondary peak in site use in September and August, likely associated with thermoregulation during gestation. During the mating season, males made more frequent visits of shorter duration (median = 34 visits for 1 h per visit) to the DTCMG, whereas females made fewer visits but remained on site for longer periods (median = 12.5 visits for 4.4 h per visit). Females typically mated biennially but showed a triennial cycle in 32% of cases, with many females switching cycles at least once. This pattern would reduce the potential reproductive lifetime output of a female by 11% compared to what would be projected from a strict biennial cycle. The long-term mating site fidelity of this shark population reveals the importance of identifying and protecting mating sites for this and other elasmobranch species.
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Affiliation(s)
- Harold L. Pratt
- Anderson Cabot Center for Ocean Life, New England Aquarium, Boston, Massachusetts, United States of America
| | - Theo C. Pratt
- Elasmobranch Field Research Association, South Thomaston, Maine, United States of America
| | - Ryan J. Knotek
- Anderson Cabot Center for Ocean Life, New England Aquarium, Boston, Massachusetts, United States of America
| | - Jeffrey C. Carrier
- Department of Biology, Albion College, Albion, Michigan, United States of America
| | - Nicholas M. Whitney
- Anderson Cabot Center for Ocean Life, New England Aquarium, Boston, Massachusetts, United States of America
- * E-mail:
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10
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Guttridge TL, Müller L, Keller BA, Bond ME, Grubbs RD, Winram W, Howey LA, Frazier BS, Gruber SH. Vertical space use and thermal range of the great hammerhead (Sphyrna mokarran), (Rüppell, 1837) in the western North Atlantic. J Fish Biol 2022; 101:797-810. [PMID: 36056454 DOI: 10.1111/jfb.15185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The great hammerhead (Sphyrna mokarran) is a highly mobile, large-bodied shark primarily found in coastal-pelagic and semi-oceanic waters across a circumtropical range. It is a target or by-catch species in multiple fisheries, and as a result, rapid population declines have occurred in many regions. These declines have contributed to the species being assessed as globally critically endangered on the IUCN Red List. Although conservation and management measures have yielded promising results in some regions, such as the United States, high levels of at-vessel and post-release mortality remain a major concern to the species population recovery. This examined the vertical space use and thermal range of pop-off archival satellite-tagged S. mokarran in the western North Atlantic Ocean, expanding the understanding of the ecological niche of this species and providing insight into by-catch mitigation strategies for fisheries managers. The results showed that S. mokarran predominantly used shallow depths (75% of records <30 m) and had a narrow temperature range (89% of records between 23 and 28°C). Individual differences in depth use were apparent, and a strong diel cycle was observed, with sharks occupying significantly deeper depths during the daytime. Furthermore, two individuals were confirmed pregnant with one migrating from the Bahamas to South Carolina, U.S.A., providing further evidence of regional connectivity and parturition off the U.S. East Coast. The findings suggest that S. mokarran may be vulnerable to incidental capture in the western North Atlantic commercial longline fisheries due to substantial vertical overlap between the species and the gear. The results can be incorporated into conservation and management efforts to develop and/or refine mitigation measures focused on reducing the by-catch and associated mortality of this species, which can ultimately aide S. mokarran population recovery in areas with poor conservation status.
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Affiliation(s)
- Tristan L Guttridge
- Saving the Blue, Cooper City, Florida, USA
- Bimini Biological Field Station Foundation, South Bimini, Bahamas
| | - Lukas Müller
- Marine Animal Ecology Group, Wageningen University, Wageningen, The Netherlands
- The Watermen Project, Geneva, Switzerland
| | - Bryan A Keller
- Saving the Blue, Cooper City, Florida, USA
- Coastal and Marine Laboratory, Florida State University, St. Teresa, Florida, USA
| | - Mark E Bond
- Department of Biological Sciences, Institute of Environment, Florida International University, North Miami, Florida, USA
| | - R Dean Grubbs
- South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, South Carolina, USA
| | | | - Lucy A Howey
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Bryan S Frazier
- South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, South Carolina, USA
| | - Samuel H Gruber
- Bimini Biological Field Station Foundation, South Bimini, Bahamas
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11
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Beal AP, Hackerott S, Feldheim K, Gruber SH, Eirin‐Lopez JM. Age group
DNA
methylation differences in lemon sharks (
Negaprion brevirostris
): Implications for future age estimation tools. Ecol Evol 2022; 12:e9226. [PMID: 36052296 PMCID: PMC9425014 DOI: 10.1002/ece3.9226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 11/11/2022] Open
Abstract
Age information is often non‐existent for most shark populations due to a lack of measurable physiological and morphological traits that can be used to estimate age. Recently, epigenetic clocks have been found to accurately estimate age for mammals, birds, and fish. However, since these clocks rely, among other things, on the availability of reference genomes, their application is hampered in non‐traditional model organisms lacking such molecular resources. The technique known as Methyl‐Sensitive Amplified Polymorphism (MSAP) has emerged as a valid alternative for studying DNA methylation biomarkers when reference genome information is missing, and large numbers of samples need to be processed. Accordingly, the MSAP technique was used in the present study to characterize global DNA methylation patterns in lemon sharks from three different age groups (juveniles, subadults, and adults). The obtained results reveal that, while MSAP analyses lack enough resolution as a standalone approach to infer age in these organisms, the global DNA methylation patterns observed using this technique displayed significant differences between age groups. Overall, these results confer that DNA methylation does change with age in sharks like what has been seen for other vertebrates and that MSAP could be useful as part of an epigenetics pipeline to infer the broad range of ages found in large samples sizes.
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Affiliation(s)
- Andria Paige Beal
- Environmental Epigenetics Laboratory, Institute of Environment Florida International University Miami Florida USA
| | - Serena Hackerott
- Environmental Epigenetics Laboratory, Institute of Environment Florida International University Miami Florida USA
| | - Kevin Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution Field Museum of Natural History Chicago Illinois USA
| | | | - Jose M. Eirin‐Lopez
- Environmental Epigenetics Laboratory, Institute of Environment Florida International University Miami Florida USA
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12
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Canfield SJ, Galván-Magaña F, Bowen BW. Little Sharks in a Big World: Mitochondrial DNA Reveals Small-scale Population Structure in the California Horn Shark (Heterodontus francisci). J Hered 2022; 113:298-310. [PMID: 35438775 DOI: 10.1093/jhered/esac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The California horn shark (Heterodontus francisci) is a small demersal species distributed from southern California and the Channel Islands to Baja California and the Gulf of California. These nocturnal reef predators maintain small home-ranges as adults, and lay auger-shaped egg cases that become wedged into the substrate. While population trends are not well documented, this species is subject to fishing pressure through portions of its range and has been identified as vulnerable to overexploitation. Here we present a survey of 318 specimens from across the range, using mtDNA control region sequences to provide the first genetic assessment of H. francisci. Overall population structure (ΦST = 0.266, P < 0.001) is consistent with limited dispersal as indicated by life history, with two distinct features. Population structure along the continuous coastline is low, with no discernable breaks from Santa Barbara, CA to Bahia Tortugas (Baja California Sur, Mexico); however, there is a notable partition at Punta Eugenia (BCS), a well-known biogeographic break between tropical and subtropical marine faunas. In contrast, population structure is much higher (max ΦST = 0.601, P < 0.05) between the coast and adjacent Channel Islands, a minimum distance of 19 km, indicating that horn sharks rarely disperse across deep habitat and open water. Population structure in most elasmobranchs is measured on a scale of hundreds to thousands of kilometers, but the California Horn Shark has population partitions on an unprecedented small scale, indicating a need for localized management strategies which ensure adequate protection of distinct stocks.
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Affiliation(s)
- Sean J Canfield
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, HI, USA
| | - Felipe Galván-Magaña
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, HI, USA
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13
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Liu X, Schjøtt SR, Granquist SM, Rosing-Asvid A, Dietz R, Teilmann J, Galatius A, Cammen K, O Corry-Crowe G, Harding K, Härkönen T, Hall A, Carroll EL, Kobayashi Y, Hammill M, Stenson G, Frie AK, Lydersen C, Kovacs KM, Andersen LW, Hoffman JI, Goodman SJ, Vieira FG, Heller R, Moltke I, Tange Olsen M. Origin and expansion of the world's most widespread pinniped: range-wide population genomics of the harbour seal (Phoca vitulina). Mol Ecol 2022; 31:1682-1699. [PMID: 35068013 PMCID: PMC9306526 DOI: 10.1111/mec.16365] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonised virtually the whole of the Northern Hemisphere. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic SNPs from 286 individuals sampled from 22 localities across the species' range. Our results point to a Northeast Pacific origin, colonisation of the North Atlantic via the Canadian Arctic, and subsequent stepping-stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer-scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal's remarkable ability to colonise and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations.
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Affiliation(s)
- Xiaodong Liu
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | | | - Sandra M Granquist
- Icelandic Seal Centre, Höfðabraut 6, 530, Hvammstangi, Iceland.,Marine and Freshwater Research Institute, Institute of Freshwater Fisheries Fornubúðir 5, 220, Hafnarfjörður, Iceland
| | | | - Rune Dietz
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Jonas Teilmann
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Anders Galatius
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | | | - Greg O Corry-Crowe
- Wildlife Evolution and Behavior Program, Florida Atlantic University, USA
| | - Karin Harding
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
| | | | - Ailsa Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St. Andrews, UK, KY16 8LB
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Yumi Kobayashi
- Laboratory of Animal Ecology, Research Faculty of Agriculture, Hokkaido University, Japan
| | - Mike Hammill
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, P.O. Box 1000, Mont-Joli, QC, Canada
| | - Garry Stenson
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, P.O. Box 5667, St. John's NL, Canada
| | | | | | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | | | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, 33501, Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Simon J Goodman
- School of Biology, Faculty of Biological Sciences, University of Leeds, UK
| | - Filipe G Vieira
- Center for Genomic Medicine, Copenhagen University Hospitalet, Denmark
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | - Morten Tange Olsen
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Denmark
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14
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Lohmann KJ, Goforth KM, Mackiewicz AG, Lim DS, Lohmann CMF. Magnetic maps in animal navigation. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2022. [PMID: 34999936 DOI: 10.1007/s00359-021-01529-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/21/2021] [Accepted: 11/25/2021] [Indexed: 12/03/2022]
Abstract
In addition to providing animals with a source of directional or ‘compass’ information, Earth’s magnetic field also provides a potential source of positional or ‘map’ information that animals might exploit to assess location. In less than a generation, the idea that animals use Earth’s magnetic field as a kind of map has gone from a contentious hypothesis to a well-established tenet of animal navigation. Diverse animals ranging from lobsters to birds are now known to use magnetic positional information for a variety of purposes, including staying on track along migratory pathways, adjusting food intake at appropriate points in a migration, remaining within a suitable oceanic region, and navigating toward specific goals. Recent findings also indicate that sea turtles, salmon, and at least some birds imprint on the magnetic field of their natal area when young and use this information to facilitate return as adults, a process that may underlie long-distance natal homing (a.k.a. natal philopatry) in many species. Despite recent progress, much remains to be learned about the organization of magnetic maps, how they develop, and how animals use them in navigation.
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15
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Gonzalez C, Postaire B, Domingues RR, Feldheim KA, Caballero S, Chapman D. Phylogeography and population genetics of the cryptic bonnethead shark Sphyrna aff. tiburo in Brazil and the Caribbean inferred from mtDNA markers. J Fish Biol 2021; 99:1899-1911. [PMID: 34476811 DOI: 10.1111/jfb.14896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Resolving the identity, phylogeny and distribution of cryptic species within species complexes is an essential precursor to management. The bonnethead shark, Sphyrna tiburo, is a small coastal shark distributed in the Western Atlantic from North Carolina (U.S.A.) to southern Brazil. Genetic analyses based on mitochondrial markers revealed that bonnethead sharks comprise a species complex with at least two lineages in the Northwestern Atlantic and the Caribbean (S. tiburo and Sphyrna aff. tiburo, respectively). The phylogeographic and phylogenetic analysis of two mitochondrial markers [control region (mtCR) and cytochrome oxidase I (COI)] showed that bonnethead sharks from southeastern Brazil correspond to S. aff. tiburo, extending the distribution of this cryptic species >5000 km. Bonnethead shark populations are only managed in the U.S.A. and in the 2000s were considered to be regionally extinct or collapsed in southeast Brazil. The results indicate that there is significant genetic differentiation between S. aff. tiburo from Brazil and other populations from the Caribbean (ΦST = 0.9053, P < 0.000), which means that collapsed populations in the former are unlikely to be replenished from Caribbean immigration. The species identity of bonnethead sharks in the Southwest Atlantic and their relationship to North Atlantic and Caribbean populations still remains unresolved. Taxonomic revision and further sampling are required to reevaluate the status of the bonnethead shark complex through its distribution range.
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Affiliation(s)
- Cindy Gonzalez
- Predator Ecology and Conservation Lab, Biological Sciences Department, Florida International University, Miami, Florida, 33181, USA
| | - Bautisse Postaire
- Predator Ecology and Conservation Lab, Biological Sciences Department, Florida International University, Miami, Florida, 33181, USA
| | - Rodrigo R Domingues
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Instituto do Mar, São Paulo, Brazil
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, Chicago, Illinois, USA
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Demian Chapman
- Predator Ecology and Conservation Lab, Biological Sciences Department, Florida International University, Miami, Florida, 33181, USA
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16
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Carle‐Pruneau E, Bélisle M, Pelletier F, Garant D. Determinants of nest box local recruitment and natal dispersal in a declining bird population. OIKOS 2021. [DOI: 10.1111/oik.08349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Marc Bélisle
- Dépt de Biologie, Univ. de Sherbrooke Sherbrooke QC Canada
| | | | - Dany Garant
- Dépt de Biologie, Univ. de Sherbrooke Sherbrooke QC Canada
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17
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Postaire BD, Feldheim KA, Clementi GM, Quinlan J, van Zinnicq Bergmann MPM, Brooks EJ, Grubbs RD, Guttridge TL, Henderson AC, Tavares R, Chapman DD. Small localized breeding populations in a widely distributed coastal shark species. CONSERV GENET. [DOI: 10.1007/s10592-021-01398-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Nosal AP, Cartamil DP, Ammann AJ, Bellquist LF, Ben‐Aderet NJ, Blincow KM, Burns ES, Chapman ED, Freedman RM, Klimley AP, Logan RK, Lowe CG, Semmens BX, White CF, Hastings PA. Triennial migration and philopatry in the critically endangered soupfin shark
Galeorhinus galeus. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13848] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew P. Nosal
- Department of Environmental and Ocean Sciences University of San Diego San Diego CA USA
- Marine Biology Research Division Scripps Institution of Oceanography University of California – San Diego La Jolla CA USA
| | - Daniel P. Cartamil
- Marine Biology Research Division Scripps Institution of Oceanography University of California – San Diego La Jolla CA USA
| | - Arnold J. Ammann
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries ServiceNOAA Santa Cruz CA USA
| | - Lyall F. Bellquist
- Marine Biology Research Division Scripps Institution of Oceanography University of California – San Diego La Jolla CA USA
- The Nature Conservancy San Francisco CA USA
| | - Noah J. Ben‐Aderet
- Fisheries Resources Division Southwest Fisheries Science Center NOAA Fisheries La Jolla CA USA
| | - Kayla M. Blincow
- Marine Biology Research Division Scripps Institution of Oceanography University of California – San Diego La Jolla CA USA
| | - Echelle S. Burns
- Bren School of Environmental Science and Management University of California – Santa Barbara Santa Barbara CA USA
| | - Eric D. Chapman
- Department of Wildlife, Fish and Conservation Biology University of California – Davis Davis CA USA
- ICF Sacramento CA USA
| | - Ryan M. Freedman
- NOAA Channel Islands National Marine Sanctuary University of California – Santa Barbara Santa Barbara CA USA
| | - A. Peter Klimley
- Department of Wildlife, Fish and Conservation Biology University of California – Davis Davis CA USA
- Biotelemetry Consultants Petaluma CA USA
| | - Ryan K. Logan
- Guy Harvey Research Institute Nova Southeastern University Dania Beach FL USA
| | | | - Brice X. Semmens
- Marine Biology Research Division Scripps Institution of Oceanography University of California – San Diego La Jolla CA USA
| | - Connor F. White
- Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Philip A. Hastings
- Marine Biology Research Division Scripps Institution of Oceanography University of California – San Diego La Jolla CA USA
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19
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Abstract
Abstract
Genetic relatedness in animal societies is often a factor that drives the structure of social groups. In the marine world, most studies which have investigated this question have focused on marine mammals such as whales and dolphins. For sharks, recent studies have demonstrated preferential associations among individuals from which social communities emerge. Assortment patterns have been found according to phenotypic or behavioral traits, but the role of genetic relatedness in shaping the social structure of adult shark populations has, to the best of our knowledge, never been investigated. Here, we used a social network analysis crossed with DNA microsatellite genotyping to investigate the role of the genetic relatedness in the social structure of a blacktip reef shark (Carcharhinus melanopterus) population. Based on the data from 156 groups of sharks, we used generalized affiliation indices to isolate social preferences from nonsocial associations, controlling for the contribution of sex, size, gregariousness, spatial, and temporal overlap on social associations, to test for the influence of genetic relatedness on social structure. A double-permutation procedure was employed to confirm our results and account for issues arising from potentially elevated type I and type II error rates. Kinship was not a predictor of associations and affiliations among sharks at the dyad or community levels as individuals tended to associate independently of the genetic relatedness among them. The lack of parental care in this species may contribute to the breakdown of family links in the population early in life, thereby preventing the formation of kin-based social networks.
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Affiliation(s)
- Johann Mourier
- PSL Research University, EPHE-UPVD-CNRS, USR 3278, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL”, EPHE, PSL Research University, UPVD, CNRS, USR CRIOBE, Papetoai, Moorea, French Polynesia
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Sète, France
| | - Serge Planes
- PSL Research University, EPHE-UPVD-CNRS, USR 3278, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL”, EPHE, PSL Research University, UPVD, CNRS, USR CRIOBE, Papetoai, Moorea, French Polynesia
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20
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Heinrich D, Dhellemmes F, Guttridge TL, Smukall M, Brown C, Rummer J, Gruber S, Huveneers C. Short-term impacts of daily feeding on the residency, distribution and energy expenditure of sharks. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2020.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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21
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Affiliation(s)
- K. E. Levasseur
- Department of Biological Sciences University of South Carolina Columbia SC USA
- Jumby Bay Hawksbill Project St John’s Antigua and Barbuda
| | - S. P. Stapleton
- Jumby Bay Hawksbill Project St John’s Antigua and Barbuda
- Department of Fisheries, Wildlife and Conservation Biology University of Minnesota St. Paul MN USA
| | - J. M. Quattro
- Department of Biological Sciences University of South Carolina Columbia SC USA
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22
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Grimmel HM, Bullock RW, Dedman SL, Guttridge TL, Bond ME. Assessment of faunal communities and habitat use within a shallow water system using non-invasive BRUVs methodology. Aquaculture and Fisheries 2020. [DOI: 10.1016/j.aaf.2019.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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23
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Feutry P, Devloo-Delva F, Tran Lu Y A, Mona S, Gunasekera RM, Johnson G, Pillans RD, Jaccoud D, Kilian A, Morgan DL, Saunders T, Bax NJ, Kyne PM. One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark. Mol Ecol Resour 2020; 20:1470-1485. [PMID: 32492756 DOI: 10.1111/1755-0998.13204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 01/25/2023]
Abstract
With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost-effectiveness.
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Affiliation(s)
| | - Floriaan Devloo-Delva
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.,School of Natural Sciences - Quantitative Marine Science, University of Tasmania, Hobart, TAS, Australia
| | - Adrien Tran Lu Y
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,EPHE, PSL University, Paris, France
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,EPHE, PSL University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | | | - Grant Johnson
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, Darwin, NT, Australia
| | | | - Damian Jaccoud
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - David L Morgan
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Thor Saunders
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, Darwin, NT, Australia
| | - Nicholas J Bax
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.,Institute for Marine and Antarctic Science, University of Tasmania, Hobart, TAS, Australia
| | - Peter M Kyne
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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24
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TinHan TC, O'Leary SJ, Portnoy DS, Rooker JR, Gelpi CG, Wells RJD. Natural tags identify nursery origin of a coastal elasmobranch
Carcharhinus leucas. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas C. TinHan
- Department of Marine Biology Texas A&M University at Galveston Galveston TX USA
| | - Shannon J. O'Leary
- Department of Life Sciences Texas A&M University‐Corpus Christi Corpus Christi TX USA
| | - David S. Portnoy
- Department of Life Sciences Texas A&M University‐Corpus Christi Corpus Christi TX USA
| | - Jay R. Rooker
- Department of Marine Biology Texas A&M University at Galveston Galveston TX USA
- Department of Wildlife and Fisheries Science Texas A&M University College Station TX USA
| | - Carey G. Gelpi
- Coastal Fisheries Division Texas Parks and Wildlife Department Port Arthur TX USA
| | - R. J. David Wells
- Department of Marine Biology Texas A&M University at Galveston Galveston TX USA
- Department of Wildlife and Fisheries Science Texas A&M University College Station TX USA
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25
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Krueck NC, Treml EA, Innes DJ, Ovenden JR. Ocean currents and the population genetic signature of fish migrations. Ecology 2020; 101:e02967. [PMID: 31925790 DOI: 10.1002/ecy.2967] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 10/04/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022]
Abstract
Animal migrations are a fascinating and global phenomenon, yet they are often difficult to study and sometimes poorly understood. Here, we build on classic ecological theory by hypothesizing that some enigmatic spawning migrations across coastal marine habitats can be inferred from the population genetic signature of larval dispersal by ocean currents. We test this assumption by integrating spatially realistic simulations of alternative spawning migration routes, associated patterns of larval dispersal, and associated variation in the population genetic structure of eastern Australian sea mullet (Mugil cephalus). We then use simulation results to assess the implications of alternative spawning destinations for larval replenishment, and we contrast simulated against measured population genetic variation. Both analyses suggest that the spawning migrations of M. cephalus in eastern Australia are likely to be localized (approximately 100 km along the shore), and that spawning is likely to occur in inshore waters. Our conclusions are supported by multiple lines of evidence available through independent studies, but they challenge the more traditional assumption of a single, long-distance migration event with subsequent offshore spawning in the East Australian Current. More generally, our study operationalizes classic theory on the relationship between fish migrations, ocean currents, and reproductive success. However, rather than confirming the traditionally assumed adaptation of migratory behavior to dominant ocean current flow, our findings support the concept of a genetically measurable link between fish migrations and local oceanographic conditions, specifically water temperature and coastal retention of larvae. We believe that future studies using similar approaches for high resolution and spatially realistic ecological-genetic scenario testing can help rapidly advance our understanding of key ecological processes in many other marine species.
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Affiliation(s)
- Nils C Krueck
- School of Biological Sciences, University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia.,Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Eric A Treml
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, 3216, Australia
| | - David J Innes
- Department of Agriculture and Fisheries, Queensland Government, P.O. Box 6097, Brisbane, Queensland, 4072, Australia
| | - Jennifer R Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia
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26
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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Axworthy JB, Smith JM, Wing MS, Quinn TP. Sex biased individual variation in movement patterns of a highly mobile, near-shore marine planktivore, the reef manta ray Mobula alfredi. J Fish Biol 2019; 95:1399-1406. [PMID: 31589768 DOI: 10.1111/jfb.14148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
We examined individual variation and the role of sex on the movements of the reef manta ray Mobula alfredi. Specifically, we analysed several movement metrics using 6 years of nightly observations (1 January 2009-31 December 2014) of 118 individually identifiable manta rays at two discrete but spatially proximate sites, locally known as Manta Heaven and Manta Village, 15 km apart on the west side of the island of Hawaii, USA. Males were slightly more often (33.5%, model fitted mean, P < 0.05) observed than females at Manta Heaven, but females were much more often (156.4%, model fitted mean, P < 0.05) observed at Manta Village. Movement patterns among individuals varied greatly, but the level of variation was similar between sexes. Some animals, mainly females, displayed more resident patterns, whereas other, more mobile, animals moved between sites more frequently and had longer gaps between sightings. We did not detect discrete behavioural groups; rather, individuals varied along a continuous spectrum from many observations and high affinity to few observations and low fidelity to survey locations. These complex and variable movement patterns observed at the individual level, between sexes and between two nearby sites, in Hawaii's manta rays highlight the need for finer scale considerations in conservation and management of highly mobile marine populations.
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Affiliation(s)
- Jeremy B Axworthy
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Joseph M Smith
- Fish Ecology Division, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Hammond, Oregon, USA
| | - Martina S Wing
- Ocean Wings Hawaii, Inc., dba Manta Ray Advocates, Kailua-Kona, Hawaii, USA
| | - Thomas P Quinn
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
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Lear KO, Whitney NM, Morgan DL, Brewster LR, Whitty JM, Poulakis GR, Scharer RM, Guttridge TL, Gleiss AC. Thermal performance responses in free-ranging elasmobranchs depend on habitat use and body size. Oecologia 2019; 191:829-42. [PMID: 31705273 DOI: 10.1007/s00442-019-04547-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 10/28/2019] [Indexed: 10/25/2022]
Abstract
Temperature is one of the most influential drivers of physiological performance and behaviour in ectotherms, determining how these animals relate to their ecosystems and their ability to succeed in particular habitats. Here, we analysed the largest set of acceleration data compiled to date for elasmobranchs to examine the relationship between volitional activity and temperature in 252 individuals from 8 species. We calculated activation energies for the thermal performance response in each species and estimated optimum temperatures using an Arrhenius breakpoint analysis, subsequently fitting thermal performance curves to the activity data. Juveniles living in confined nursery habitats not only spent substantially more time above their optimum temperature and at the upper limits of their performance breadths compared to larger, less site-restricted animals, but also showed lower activation energies and broader performance curves. Species or life stages occupying confined habitats featured more generalist behavioural responses to temperature change, whereas wider ranging elasmobranchs were characterised by more specialist behavioural responses. The relationships between the estimated performance regimes and environmental temperature limits suggest that animals in confined habitats, including many juvenile elasmobranchs within nursery habitats, are likely to experience a reduction of performance under a warming climate, although their flatter thermal response will likely dampen this impact. The effect of warming on less site-restricted species is difficult to forecast since three of four species studied here did not reach their optimum temperature in the wild, although their specialist performance characteristics may indicate a more rapid decline should optimum temperatures be exceeded.
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Sandoval-Castillo J. Conservation genetics of elasmobranchs of the Mexican Pacific Coast, trends and perspectives. Adv Mar Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gonzalez C, Gallagher AJ, Caballero S. Conservation genetics of the bonnethead shark Sphyrna tiburo in Bocas del Toro, Panama: Preliminary evidence of a unique stock. PLoS One 2019; 14:e0220737. [PMID: 31415593 PMCID: PMC6695166 DOI: 10.1371/journal.pone.0220737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/21/2019] [Indexed: 12/04/2022] Open
Abstract
The bonnethead shark, Sphyrna tiburo, is a small elasmobranch distributed in the Eastern Pacific from southern California to Ecuador, and along the Western Atlantic, with preferences for continental margins of North, Central and South America, the Gulf of Mexico, and the Caribbean. Recent studies have suggested that it could be under a process of cryptic speciation, with the possibility to find different species in similar geographic locations. Here we assessed the population structure and genetic diversity of this highly philopatric and non-dispersive species in the Bocas del Toro Archipelago, Panama. Fragments of the mitochondrial genes cytochrome oxidase I and control region, were used to test the genetic structure of adult and juvenile S. tiburo in this area, and were compared with other locations of the Western Atlantic and Belize. We found significant genetic differentiation between Caribbean bonnethead sharks from Bocas del Toro and Belize, when compared to bonnetheads from other locations of the Western Atlantic. These results also suggest that Bocas del Toro could constitute a different genetic population unit for this species, whereby bonnethead sharks in this area could belong to a unique stock. The information obtained in this study could improve our understanding of the population dynamics of the bonnethead shark throughout its distribution range, and may be used as a baseline for future conservation initiatives for coastal sharks in Central America, a poorly studied an often overlooked region for shark conservation and research.
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Affiliation(s)
- Cindy Gonzalez
- Departamento de Ciencias Biológicas, Universidad de los Andes, Laboratorio de Ecología Molecular de Vertebrados Acuáticos—LEMVA, Bogota, Colombia
- * E-mail:
| | - Austin J. Gallagher
- Beneath the Waves Inc, Herndon, Virginia, United States of America
- Smithsonian Tropical Research Institute, Balboa, Panama City, Republic of Panama
- Rosentiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida, United States of America
| | - Susana Caballero
- Departamento de Ciencias Biológicas, Universidad de los Andes, Laboratorio de Ecología Molecular de Vertebrados Acuáticos—LEMVA, Bogota, Colombia
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Weideli OC, Papastamatiou YP, Planes S. Size frequency, dispersal distances and variable growth rates of young sharks in a multi-species aggregation. J Fish Biol 2019; 94:789-797. [PMID: 30883741 DOI: 10.1111/jfb.13968] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
During a mark-recapture survey from November 2014 until April 2017, 333 neonatal and juvenile blacktip reef sharks Carcharhinus melanopterus and 302 neonatal and juvenile sicklefin lemon sharks Negaprion acutidens were tagged and measured at the uninhabited and isolated St. Joseph Atoll (Republic of Seychelles). Both species demonstrated seasonal reproductive synchronicity and relatively large sizes at birth. Despite the extended times at liberty > 2.5 years, the majority of recaptures were found in close proximity to the initial tagging location (< 500 m). Annual growth rates of C. melanopterus (n = 24) and N. acutidens (n = 62) ranged from 6.6 to 31.7 cm year-1 (mean ± SE; 16.2 ± 1.2 cm year-1 ) and 0.2 to 32.2 cm year-1 (11.8 ± 1 cm year-1 ), respectively and are to date the most variable ever recorded in wild juvenile sharks. High abundances of both species coupled with long-term and repeated recaptures are indicative of a habitat where juveniles can reside for their first years of life. However, large variability in annual growth rates in both species may suggest high intra and interspecific competition induced by a possibly resource limited, isolated habitat.
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Affiliation(s)
- Ornella C Weideli
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
- SOSF - D'Arros Research Centre (SOSF-DRC), Geneva, Switzerland
| | - Yannis P Papastamatiou
- Department of Biological Sciences, Marine Sciences Program, Florida International University, North Miami, Florida, USA
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
- Laboratoire d'excellence 'CORAIL', EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Papetoai, Moorea, French Polynesia
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Pirog A, Jaquemet S, Ravigné V, Cliff G, Clua E, Holmes BJ, Hussey NE, Nevill JEG, Temple AJ, Berggren P, Vigliola L, Magalon H. Genetic population structure and demography of an apex predator, the tiger shark Galeocerdo cuvier. Ecol Evol 2019; 9:5551-5571. [PMID: 31160982 PMCID: PMC6540675 DOI: 10.1002/ece3.5111] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 01/20/2019] [Accepted: 02/26/2019] [Indexed: 12/16/2022] Open
Abstract
Population genetics has been increasingly applied to study large sharks over the last decade. Whilst large shark species are often difficult to study with direct methods, improved knowledge is needed for both population management and conservation, especially for species vulnerable to anthropogenic and climatic impacts. The tiger shark, Galeocerdo cuvier, is an apex predator known to play important direct and indirect roles in tropical and subtropical marine ecosystems. While the global and Indo-West Pacific population genetic structure of this species has recently been investigated, questions remain over population structure and demographic history within the western Indian (WIO) and within the western Pacific Oceans (WPO). To address the knowledge gap in tiger shark regional population structures, the genetic diversity of 286 individuals sampled in seven localities was investigated using 27 microsatellite loci and three mitochondrial genes (CR,COI, and cytb). A weak genetic differentiation was observed between the WIO and the WPO, suggesting high genetic connectivity. This result agrees with previous studies and highlights the importance of the pelagic behavior of this species to ensure gene flow. Using approximate Bayesian computation to couple information from both nuclear and mitochondrial markers, evidence of a recent bottleneck in the Holocene (2,000-3,000 years ago) was found, which is the most probable cause for the low genetic diversity observed. A contemporary effective population size as low as 111 [43,369] was estimated during the bottleneck. Together, these results indicate low genetic diversity that may reflect a vulnerable population sensitive to regional pressures. Conservation measures are thus needed to protect a species that is classified as Near Threatened.
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Affiliation(s)
- Agathe Pirog
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint Denis, La RéunionFrance
| | - Sébastien Jaquemet
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint Denis, La RéunionFrance
| | | | - Geremy Cliff
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Eric Clua
- EPHE‐CNRS‐UPVDCNRS UPVDUSR 3278 CRIOBEPSL Research UniversityPerpignanFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
| | - Bonnie J. Holmes
- School of Biological SciencesUniversity of Queensland, St LuciaBrisbaneQueenslandAustralia
| | - Nigel E. Hussey
- Biological SciencesUniversity of WindsorWindsorOntarioCanada
| | | | - Andrew J. Temple
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Per Berggren
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Laurent Vigliola
- Laboratoire d'Excellence CORAILPerpignanFrance
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Institut de Recherche pour le DéveloppementNouméaNouvelle CalédonieFrance
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint Denis, La RéunionFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
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Abstract
Diverse marine animals migrate across vast expanses of seemingly featureless ocean before returning as adults to reproduce in the area where they originated. How animals accomplish such feats of natal homing is an enduring mystery. Growing evidence suggests, however, that sea turtles and salmon imprint on the magnetic field of their home area when young and then use this information to return as adults. Both turtles and salmon have the sensory abilities needed to detect the unique 'magnetic signature' of a coastal area. Analyses have revealed that, for both groups of animals, subtle changes in the geomagnetic field of the home region are correlated with changes in natal homing behavior. In turtles, a relationship between population genetic structure and the magnetic fields that exist at nesting beaches has also been detected, consistent with the hypothesis that turtles recognize their natal areas on the basis of magnetic cues. Salmon likely use a biphasic navigational strategy in which magnetic cues guide fish through the open sea and into the proximity of the home river where chemical cues allow completion of the spawning migration. Similarly, turtles may also exploit local cues to help pinpoint nesting areas once they have arrived in the vicinity. Throughout most of the natal homing migration, however, magnetic navigation appears to be the primary mode of long-distance guidance in both sea turtles and salmon.
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Affiliation(s)
- Kenneth J Lohmann
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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34
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Smukall MJ, Kessel ST, Franks BR, Feldheim KA, Guttridge TL, Gruber SH. No apparent negative tagging effects after 13 years at liberty for lemon shark, Negaprion brevirostris implanted with acoustic transmitter. J Fish Biol 2019; 94:173-177. [PMID: 30393865 DOI: 10.1111/jfb.13856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/25/2018] [Indexed: 06/08/2023]
Abstract
An intact and uncompromised internal acoustic transmitter was non-lethally recovered from a lemon shark Negaprion brevirostris, after 13 years at liberty. The shark, first tagged at an estimated age of 2 years old near South Bimini, Bahamas in 2004, was recaptured in 2017 with a total length of 264 cm. The tagged shark displayed typical growth rate, pregnancy, natal homing and pupping behaviour of other individuals in this population. This observation provides important evidence regarding the effects from long-term retention of implanted acoustic transmitters in a carcharhinid shark.
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Affiliation(s)
- Matthew J Smukall
- Department of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Bimini Biological Field Station Foundation, Bimini, Bahamas
| | - Steven T Kessel
- Bimini Biological Field Station Foundation, Bimini, Bahamas
- Daniel P. Haerther Center for Conservation and Research, Chicago, Illinois, USA
| | - Bryan R Franks
- Bimini Biological Field Station Foundation, Bimini, Bahamas
- Department of Biology and Marine Science, Marine Science Research Institute, Jacksonville University, Jacksonville, Florida, USA
| | - Kevin A Feldheim
- Bimini Biological Field Station Foundation, Bimini, Bahamas
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, Illinois, USA
| | | | - Samuel H Gruber
- Bimini Biological Field Station Foundation, Bimini, Bahamas
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida, USA
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35
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Abstract
Sharks and rays make up 96% of the class Chondrichthyes. They are among the most endangered of any taxa, threatened through habitat loss, overfishing and hunting for shark fin soup, traditional medicines or sport, and because many species are slow to mature and produce low numbers of offspring. Sharks and rays are ecologically and reproductively diverse, though basic knowledge of their reproductive physiology is lacking for many species. There has been a move towards non-lethal approaches of data collection in sharks and rays, especially with reproductive technologies such as ultrasound and hormone analysis. Additionally, technologies such as semen collection and artificial insemination are lending themselves to develop tools to manage small or closed populations, with cold-stored sperm being shipped between institutions to maximize genetic diversity in managed populations. The role of steroid hormones in elasmobranch reproduction appears broadly conserved, though heavily influenced by environmental cues, especially temperature. For this reason elasmobranchs are likely at risk of reproductive perturbations due to environmental changes such as ocean warming. Current reproductive technologies including computer assisted sperm assessments to study warming effects on sperm motility and intra-uterine satellite tags to determine birthing grounds will serve to generate data to mitigate anthropogenic changes that threaten the future of this vulnerable groups of fish.
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Affiliation(s)
- Linda M Penfold
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, FL, USA.
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36
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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37
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Corrigan S, Lowther AD, Beheregaray LB, Bruce BD, Cliff G, Duffy CA, Foulis A, Francis MP, Goldsworthy SD, Hyde JR, Jabado RW, Kacev D, Marshall L, Mucientes GR, Naylor GJP, Pepperell JG, Queiroz N, White WT, Wintner SP, Rogers PJ. Population Connectivity of the Highly Migratory Shortfin Mako (Isurus oxyrinchus Rafinesque 1810) and Implications for Management in the Southern Hemisphere. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00187] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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38
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Maduna SN, Rossouw C, Slabbert R, Wintner SP, da Silva C, Bester-van der Merwe AE. New polymorphic microsatellite loci revealed for the dusky shark Carcharhinus obscurus through Ion Proton double-digest RAD sequencing. Mol Biol Rep 2018; 45:2759-2763. [PMID: 30218351 DOI: 10.1007/s11033-018-4338-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 08/28/2018] [Indexed: 11/24/2022]
Abstract
The non-model shark species, dusky shark Carcharhinus obscurus, is a bio-economically and recreationally important shark in many areas of its range. Despite of the fishery importance of C. obscurus few genetic resources are currently available for the species. Here, we report on the isolation of eight novel microsatellite loci from C. obscurus using a double-digest restriction site associated DNA (RAD) sequencing approach on the Ion Proton semiconductor platform (ddRADseq-ion). We characterised the loci in 26 individuals and all loci were polymorphic, exhibiting 5-10 alleles (average 6.6), and observed and expected heterozygosities of 0.385-0.962 and 0.479-0.847, respectively. We found that all pairs of loci were in linkage equilibrium and conformed to Hardy-Weinberg expectations. The loci reported in this study are only the second set of microsatellite loci ever characterized for C. obscurus and will be valuable for molecular ecology studies for this vulnerable species.
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Affiliation(s)
- Simo N Maduna
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag XI, Stellenbosch, 7602, South Africa.
- Norwegian Institute of Bioeconomy Research, NIBIO - Svanhovd, Svanvik, Norway.
| | - Charné Rossouw
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag XI, Stellenbosch, 7602, South Africa
| | - Ruhan Slabbert
- Roche Sequencing Solutions Cape Town, 271 Victoria Road, Salt River, Cape Town, 7925, South Africa
| | - Sabine P Wintner
- KwaZulu-Natal Sharks Board, Private Bag 2, Umhlanga Rocks, 4320, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Charlene da Silva
- Fisheries Research, Department of Agriculture, Forestry and Fisheries, Private Bag X2, Rogge Bay, 8012, South Africa
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Aletta E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag XI, Stellenbosch, 7602, South Africa
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Bailleul D, Mackenzie A, Sacchi O, Poisson F, Bierne N, Arnaud‐Haond S. Large-scale genetic panmixia in the blue shark ( Prionace glauca): A single worldwide population, or a genetic lag-time effect of the "grey zone" of differentiation? Evol Appl 2018; 11:614-630. [PMID: 29875806 PMCID: PMC5978958 DOI: 10.1111/eva.12591] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/12/2017] [Indexed: 12/31/2022] Open
Abstract
The blue shark Prionace glauca, among the most common and widely studied pelagic sharks, is a top predator, exhibiting the widest distribution range. However, little is known about its population structure and spatial dynamics. With an estimated removal of 10-20 million individuals per year by fisheries, the species is classified as "Near Threatened" by International Union for Conservation of Nature. We lack the knowledge to forecast the long-term consequences of such a huge removal on this top predator itself and on its trophic network. The genetic analysis of more than 200 samples collected at broad scale (from Mediterranean Sea, North Atlantic and Pacific Oceans) using mtDNA and nine microsatellite markers allowed to detect signatures of genetic bottlenecks but a nearly complete genetic homogeneity across the entire studied range. This apparent panmixia could be explained by a genetic lag-time effect illustrated by simulations of demographic changes that were not detectable through standard genetic analysis before a long transitional phase here introduced as the "population grey zone." The results presented here can thus encompass distinct explanatory scenarios spanning from a single demographic population to several independent populations. This limitation prevents the genetic-based delineation of stocks and thus the ability to anticipate the consequences of severe depletions at all scales. More information is required for the conservation of population(s) and management of stocks, which may be provided by large-scale sampling not only of individuals worldwide, but also of loci genomewide.
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Affiliation(s)
- Diane Bailleul
- IFREMER, UMR MARBEC, Station de SèteSèteFrance
- OREME – Station MarineUniversité MontpellierSèteFrance
| | - Alicia Mackenzie
- IFREMER, UMR MARBEC, Station de SèteSèteFrance
- OREME – Station MarineUniversité MontpellierSèteFrance
| | - Olivier Sacchi
- IFREMER, UMR MARBEC, Station de SèteSèteFrance
- OREME – Station MarineUniversité MontpellierSèteFrance
| | | | - Nicolas Bierne
- OREME – Station MarineUniversité MontpellierSèteFrance
- CNRS, Institut des Sciences de l'EvolutionUniversité MontpellierMontpellierFrance
| | - Sophie Arnaud‐Haond
- IFREMER, UMR MARBEC, Station de SèteSèteFrance
- OREME – Station MarineUniversité MontpellierSèteFrance
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Brothers JR, Lohmann KJ. Evidence that Magnetic Navigation and Geomagnetic Imprinting Shape Spatial Genetic Variation in Sea Turtles. Curr Biol 2018; 28:1325-1329.e2. [DOI: 10.1016/j.cub.2018.03.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/12/2018] [Accepted: 03/12/2018] [Indexed: 10/17/2022]
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Domingues RR, Hilsdorf AWS, Gadig OBF. The importance of considering genetic diversity in shark and ray conservation policies. CONSERV GENET 2018; 19:501-25. [DOI: 10.1007/s10592-017-1038-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Marie AD, Miller C, Cawich C, Piovano S, Rico C. Fisheries-independent surveys identify critical habitats for young scalloped hammerhead sharks (Sphyrna lewini) in the Rewa Delta, Fiji. Sci Rep 2017; 7:17273. [PMID: 29222430 DOI: 10.1038/s41598-017-17152-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 11/21/2017] [Indexed: 11/09/2022] Open
Abstract
Sharp declines in numerous shark populations around the world have generated considerable interest in better understanding and characterising their biology, ecology and critical habitats. The scalloped hammerhead shark (SHS, Sphyrna lewini) is subject to a multitude of natural and anthropogenic threats that are often exacerbated within the coastal embayments and estuaries used during SHS early life stages. In this study, we describe the temporal and spatial distribution, age class composition, and reproductive biology of SHS in the Rewa Delta (RD), Fiji. A total of 1054 SHS (including 796 tagged individuals; 101 of which were recaptured) were captured from September 2014 to March 2016 in the RD. A majority of the captures in this area were neonates and young-of-the-year (YOY) (99.8%). Significant seasonality in patterns of occurrence of both neonates and YOY individuals suggests a defined parturition period during the austral summer. Between the seven sampling sites in the RD we also found significant differences in SHS neonate catch per unit of effort, and average total length of individuals. According to the data, the RD is likely to represent an important nursery area for SHS up to one year of age.
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Abstract
Whether marine fishes are capable of homing to their natal areas has long been something of an enigma. For some estuarine species or sharks (which have extended nondispersal juvenile stages or are born as relatively large, fully formed juveniles), the answer is clearly 'yes' (Thorrold et al. ; Feldheim et al. ), but for most marine fishes, the issue is much more mysterious. Many species have free-floating eggs, and most have pelagic, passively dispersing larvae. It is challenging to imagine how adult fish might navigate to a region of the ocean they experienced only as eggs or larvae, and easier to assume that such dispersal leads inexorably to high gene flow, and even panmixia. One way to resolve the conundrum would be to track fish from hatching to reproduction, but for marine fishes with tiny eggs and drifting larvae, this is notoriously difficult to do (Bradbury & Laurel ). In this issue of Molecular Ecology, Bonanomi et al. () use a creative approach to solve this challenge for Atlantic cod (Gadus morhua) populations that mingle in the vicinity of Greenland. They show that cod that disperse more than a 1000 km away from Iceland as eggs and larvae, then spend years growing on the far side of Greenland, while mixing with two local populations, return as adults to spawning areas near Iceland - and further, that this behaviour has remained stable over more than six decades. They manage this feat with a clever use of historical cod tracking data, modern genomic data and genetic analysis of decades-old DNA obtained from archived materials. Their results have important implications for our view of the biocomplexity of marine fish populations, and how we should manage them.
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Affiliation(s)
- Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, Canada, B3H 4R2
| | - Ian R Bradbury
- Salmonids Section, Science Branch, Department of Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, NF, Canada, A1C 5X1
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Aguilera O, Luz Z, Carrillo-Briceño JD, Kocsis L, Vennemann TW, de Toledo PM, Nogueira A, Amorim KB, Moraes-Santos H, Polck MR, Ruivo MDL, Linhares AP, Monteiro-Neto C. Neogene sharks and rays from the Brazilian 'Blue Amazon'. PLoS One 2017; 12:e0182740. [PMID: 28832664 PMCID: PMC5568136 DOI: 10.1371/journal.pone.0182740] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 07/24/2017] [Indexed: 11/18/2022] Open
Abstract
The lower Miocene Pirabas Formation in the North of Brazil was deposited under influence of the proto-Amazon River and is characterized by large changes in the ecological niches from the early Miocene onwards. To evaluate these ecological changes, the elasmobranch fauna of the fully marine, carbonate-rich beds was investigated. A diverse fauna with 24 taxa of sharks and rays was identified with the dominant groups being carcharhiniforms and myliobatiforms. This faunal composition is similar to other early Miocene assemblages from the proto-Carribbean bioprovince. However, the Pirabas Formation has unique features compared to the other localities; being the only Neogene fossil fish assemblage described from the Atlantic coast of Tropical Americas. Phosphate oxygen isotope composition of elasmobranch teeth served as proxies for paleotemperatures and paleoecology. The data are compatible with a predominantly tropical marine setting with recognized inshore and offshore habitats with some probable depth preferences (e.g., Aetomylaeus groups). Paleohabitat of taxa particularly found in the Neogene of the Americas (†Carcharhinus ackermannii, †Aetomylaeus cubensis) are estimated to have been principally coastal and shallow waters. Larger variation among the few analyzed modern selachians reflects a larger range for the isotopic composition of recent seawater compared to the early Miocene. This probably links to an increased influence of the Amazon River in the coastal regions during the Holocene.
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Affiliation(s)
- Orangel Aguilera
- Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brasil
- Instituto de Geociências, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Zoneibe Luz
- Instituto de Geociências, Universidade Federal do Pará, Belém, Pará, Brasil
- * E-mail:
| | | | - László Kocsis
- Faculty of Science, Geology Group, University of Brunei Darussalam, Jalan Tungku, Gadong, Brunei Darussalam
| | - Torsten W. Vennemann
- Institut des Dynamiques de la Surface Terrestre, Université de Lausanne, Lausanne, Vaud, Switzerland
| | - Peter Mann de Toledo
- Instituto Nacional de Pesquisas Espaciais, São José dos Campos, São Paulo, Brasil
| | - Afonso Nogueira
- Instituto de Geociências, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Kamilla Borges Amorim
- Instituto de Astronomia, Geofísica e Ciências Atmosféricas, Universidade de São Paulo, São Paulo, Brasil
| | - Heloísa Moraes-Santos
- Coordenação de Ciências da Terra e Ecologia, Museu Paraense Emilio Goeldi, Belém, Pará, Brasil
| | - Marcia Reis Polck
- Departamento Nacional de Produção Mineral, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Maria de Lourdes Ruivo
- Coordenação de Ciências da Terra e Ecologia, Museu Paraense Emilio Goeldi, Belém, Pará, Brasil
| | - Ana Paula Linhares
- Coordenação de Ciências da Terra e Ecologia, Museu Paraense Emilio Goeldi, Belém, Pará, Brasil
| | - Cassiano Monteiro-Neto
- Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brasil
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Abstract
Conservation genetics is an applied science that utilizes molecular tools to help solve problems in species conservation and management. It is an interdisciplinary specialty in which scientists apply the study of genetics in conjunction with traditional ecological fieldwork and other techniques to explore molecular variation, population boundaries, and evolutionary relationships with the goal of enabling resource managers to better protect biodiversity and identify unique populations. Several shark species in the northeast Pacific (NEP) have been studied using conservation genetics techniques, which are discussed here. The primary methods employed to study population genetics of sharks have historically been nuclear microsatellites and mitochondrial (mt) DNA. These markers have been used to assess genetic diversity, mating systems, parentage, relatedness, and genetically distinct populations to inform management decisions. Novel approaches in conservation genetics, including next-generation DNA and RNA sequencing, environmental DNA (eDNA), and epigenetics are just beginning to be applied to elasmobranch evolution, physiology, and ecology. Here, we review the methods and results of past studies, explore future directions for shark conservation genetics, and discuss the implications of molecular research and techniques for the long-term management of shark populations in the NEP.
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Affiliation(s)
| | | | - Nicole M Phillips
- The University of Southern Mississippi, Hattiesburg, MS, United States
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Poulakis GR, Urakawa H, Stevens PW, DeAngelo JA, Timmers AA, Grubbs RD, Fisk AT, Olin JA. Sympatric elasmobranchs and fecal samples provide insight into the trophic ecology of the smalltooth sawfish. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00824] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Hussey NE, DiBattista JD, Moore JW, Ward EJ, Fisk AT, Kessel S, Guttridge TL, Feldheim KA, Franks BR, Gruber SH, Weideli OC, Chapman DD. Risky business for a juvenile marine predator? Testing the influence of foraging strategies on size and growth rate under natural conditions. Proc Biol Sci 2017; 284:rspb.2017.0166. [PMID: 28381626 DOI: 10.1098/rspb.2017.0166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/09/2017] [Indexed: 11/12/2022] Open
Abstract
Mechanisms driving selection of body size and growth rate in wild marine vertebrates are poorly understood, thus limiting knowledge of their fitness costs at ecological, physiological and genetic scales. Here, we indirectly tested whether selection for size-related traits of juvenile sharks that inhabit a nursery hosting two dichotomous habitats, protected mangroves (low predation risk) and exposed seagrass beds (high predation risk), is influenced by their foraging behaviour. Juvenile sharks displayed a continuum of foraging strategies between mangrove and seagrass areas, with some individuals preferentially feeding in one habitat over another. Foraging habitat was correlated with growth rate, whereby slower growing, smaller individuals fed predominantly in sheltered mangroves, whereas larger, faster growing animals fed over exposed seagrass. Concomitantly, tracked juveniles undertook variable movement behaviours across both the low and high predation risk habitat. These data provide supporting evidence for the hypothesis that directional selection favouring smaller size and slower growth rate, both heritable traits in this shark population, may be driven by variability in foraging behaviour and predation risk. Such evolutionary pathways may be critical to adaptation within predator-driven marine ecosystems.
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Affiliation(s)
- Nigel E Hussey
- University of Windsor - Biological Sciences, Windsor, Ontario, N9B 3P4, Canada
| | - Joseph D DiBattista
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6845, PO Box U1987, Australia
| | - Jonathan W Moore
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Eric J Ward
- Northwest Fisheries Science Center, 2725 Montlake Blvd East, Seattle, WA 98112, USA
| | - Aaron T Fisk
- Great Lakes Institute for Environmental Science, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Steven Kessel
- University of Windsor - Biological Sciences, Windsor, Ontario, N9B 3P4, Canada
| | - Tristan L Guttridge
- Bimini Biological Field Station Foundation, 15 Elizabeth Drive, South Bimini, Bahamas
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Bryan R Franks
- Department of Biology, Florida Southern College, Lakeland, FL, USA
| | - Samuel H Gruber
- Bimini Biological Field Station Foundation, 15 Elizabeth Drive, South Bimini, Bahamas
| | - Ornella C Weideli
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Universite de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France
| | - Demian D Chapman
- Institute for Ocean Conservation Science/School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
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49
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Vargas-Caro C, Bustamante C, Bennett MB, Ovenden JR. Towards sustainable fishery management for skates in South America: The genetic population structure of Zearaja chilensis and Dipturus trachyderma (Chondrichthyes, Rajiformes) in the south-east Pacific Ocean. PLoS One 2017; 12:e0172255. [PMID: 28207832 DOI: 10.1371/journal.pone.0172255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/02/2017] [Indexed: 11/19/2022] Open
Abstract
The longnose skates (Zearaja chilensis and Dipturus trachyderma) are the main component of the elasmobranch fisheries in the south-east Pacific Ocean. Both species are considered to be a single stock by the fishery management in Chile however, little is known about the level of demographic connectivity within the fishery. In this study, we used a genetic variation (560 bp of the control region of the mitochondrial genome and ten microsatellite loci) to explore population connectivity at five locations along the Chilean coast. Analysis of Z. chilensis populations revealed significant genetic structure among off-shore locations (San Antonio, Valdivia), two locations in the Chiloé Interior Sea (Puerto Montt and Aysén) and Punta Arenas in southern Chile. For example, mtDNA haplotype diversity was similar across off-shore locations and Punta Arenas (h = 0.46-0.50), it was significantly different to those in the Chiloé Interior Sea (h = 0.08). These results raise concerns about the long-term survival of the species within the interior sea, as population resilience will rely almost exclusively on self-recruitment. In contrast, little evidence of genetic structure was found for D. trachyderma. Our results provide evidence for three management units for Z. chilensis, and we recommend that separate management arrangements are required for each of these units. However, there is no evidence to discriminate the extant population of Dipturus trachyderma as separate management units. The lack of genetic population subdivision for D. trachyderma appears to correspond with their higher dispersal ability and more offshore habitat preference.
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50
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Kershaw F, Carvalho I, Loo J, Pomilla C, Best PB, Findlay KP, Cerchio S, Collins T, Engel MH, Minton G, Ersts P, Barendse J, Kotze PGH, Razafindrakoto Y, Ngouessono S, Meÿer M, Thornton M, Rosenbaum HC. Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales. Mol Ecol 2017; 26:977-994. [DOI: 10.1111/mec.13943] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 10/01/2016] [Accepted: 11/16/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Francine Kershaw
- Columbia University; 116th Street and Broadway New York NY 10027 USA
| | - Inês Carvalho
- Population and Conservation Genetics Group; Instituto Gulbenkian de Ciência; Rua da Quinta Grande, 6 2780-156 Oeiras Portugal
- Centre for Environmental and Marine Studies (CESAM); Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Jacqueline Loo
- Department of Biology; New York University; 100 Washington Square New York NY 10012 USA
| | - Cristina Pomilla
- Wellcome Trust Sanger Institute; Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA UK
| | - Peter B. Best
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - Ken P. Findlay
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - Salvatore Cerchio
- Wildlife Conservation Society; Ocean Giants Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
| | - Tim Collins
- Wildlife Conservation Society; Ocean Giants Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
- Environment Society of Oman; P.O. Box 3955 PC 112 Ruwi Sultanate of Oman
| | - Marcia H. Engel
- Humpback Whale Project/Humpback Whale Institute; Rua Barão do Rio Branco, 125 Caravelas Bahia Brazil
| | - Gianna Minton
- Environment Society of Oman; P.O. Box 3955 PC 112 Ruwi Sultanate of Oman
| | - Peter Ersts
- Center for Biodiversity and Conservation; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
| | - Jaco Barendse
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - P. G. H. Kotze
- Department of Environmental Affairs; Branch Oceans and Coasts; Private Bag x2, Roggebaai 8012 Cape Town South Africa
| | - Yvette Razafindrakoto
- Wildlife Conservation Society-Madagascar Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
| | - Solange Ngouessono
- Agence Nationale des Parcs Nationaux; Batterie 4 BP 20379 Libreville Gabon
| | - Michael Meÿer
- Department of Environmental Affairs; Branch Oceans and Coasts; Private Bag x2, Roggebaai 8012 Cape Town South Africa
| | - Meredith Thornton
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - Howard C. Rosenbaum
- Wildlife Conservation Society; Ocean Giants Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
- Sackler Institute for Comparative Genomics; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
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