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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] [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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2
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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] [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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3
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Small localized breeding populations in a widely distributed coastal shark species. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01398-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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Lyons K, Kacev D, Mull CG. An inconvenient tooth: Evaluating female choice in multiple paternity using an evolutionarily and ecologically important vertebrate clade. Mol Ecol 2021; 30:1574-1593. [PMID: 33586211 PMCID: PMC8251896 DOI: 10.1111/mec.15844] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 12/29/2022]
Abstract
Understanding mating systems is a pillar of behavioural ecology, placing the complex interactions between females and males into a reproductive context. The field of multiple paternity, the phenomenon whereby many sires contribute to an individual litter, has traditionally viewed females as passive players in a male–male competitive framework. With the emergence of feminist perspectives in ecological fields, novel alternative mechanisms and evolutionary theories across invertebrate and vertebrate taxa recognize females are active stakeholders in the reproductive process. Despite their evolutionary significance, ecological diversity and myriad reproductive modes, elasmobranch (sharks, skates and rays) research lags behind other fields regarding complex biological processes, such as multiple paternity which is often ascribed to convenience polyandry. Here, we layout hypotheses and resynthesize multiple paternity literature from a female and life history perspective to highlight how alternative mechanisms influence the predominance of multiple paternity across elasmobranchs. We draw upon parallels in other invertebrate and vertebrate taxa to demonstrate how female elasmobranchs can influence multiple paternity outcomes that benefit their reproductive success. Our article challenges dogma that has resulted from years of dismissing the female perspective as important and provides a framework for future advancement using more holistic approaches to studying mating systems.
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Affiliation(s)
| | - Dovi Kacev
- Scripps Institution of Oceanography, San Diego, CA, USA
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5
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Schlaff AM, Heupel MR, Udyawer V, Simpfendorfer CA. Sex-based differences in movement and space use of the blacktip reef shark, Carcharhinus melanopterus. PLoS One 2020; 15:e0231142. [PMID: 32271802 PMCID: PMC7145100 DOI: 10.1371/journal.pone.0231142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 03/17/2020] [Indexed: 11/18/2022] Open
Abstract
Information on the spatial ecology of reef sharks is critical to understanding life-history patterns, yet gaps remain in our knowledge of how these species move and occupy space. Previous studies have focused on offshore reefs and atolls with little information available on the movement and space use of sharks utilising reef habitats closer to shore. Cross-shelf differences in physical and biological properties of reefs can alter regional ecosystem processes resulting in different movement patterns for resident sharks. Passive acoustic telemetry was used to examine residency, space use and depth use of 40 blacktip reef sharks, Carcharhinus melanopterus, on an inshore reef in Queensland, Australia, and assess temporal or biological influences. All sharks showed strong site-attachment to inshore reefs with residency highest among adult females. Sharks exhibited a sex-based, seasonal pattern in space use where males moved more, occupied more space and explored new areas during the reproductive season, while females utilised the same amount of space throughout the year, but shifted the location of the space used. A positive relationship was also observed between space use and size. There was evidence of seasonal site fidelity and long-distance movement with the coordinated, annual migration of two adult males to the study site during the mating season. Depth use was segregated with some small sharks occupying shallower depths than adults throughout the day and year, most likely as refuge from predation. Results highlight the importance of inshore reef habitats to blacktip reef sharks and provide evidence of connectivity with offshore reefs, at least for adult males.
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Affiliation(s)
- Audrey M. Schlaff
- Centre for Sustainable Tropical Fisheries and Aquaculture & College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- * E-mail:
| | - Michelle R. Heupel
- Centre for Sustainable Tropical Fisheries and Aquaculture & College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Integrated Marine Observing System, University of Tasmania, Hobart, Tasmania, Australia
| | - Vinay Udyawer
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Colin A. Simpfendorfer
- Centre for Sustainable Tropical Fisheries and Aquaculture & College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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Lieber L, Hall G, Hall J, Berrow S, Johnston E, Gubili C, Sarginson J, Francis M, Duffy C, Wintner SP, Doherty PD, Godley BJ, Hawkes LA, Witt MJ, Henderson SM, de Sabata E, Shivji MS, Dawson DA, Sims DW, Jones CS, Noble LR. Spatio-temporal genetic tagging of a cosmopolitan planktivorous shark provides insight to gene flow, temporal variation and site-specific re-encounters. Sci Rep 2020; 10:1661. [PMID: 32015388 PMCID: PMC6997447 DOI: 10.1038/s41598-020-58086-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 12/29/2019] [Indexed: 12/30/2022] Open
Abstract
Migratory movements in response to seasonal resources often influence population structure and dynamics. Yet in mobile marine predators, population genetic consequences of such repetitious behaviour remain inaccessible without comprehensive sampling strategies. Temporal genetic sampling of seasonally recurring aggregations of planktivorous basking sharks, Cetorhinus maximus, in the Northeast Atlantic (NEA) affords an opportunity to resolve individual re-encounters at key sites with population connectivity and patterns of relatedness. Genetic tagging (19 microsatellites) revealed 18% of re-sampled individuals in the NEA demonstrated inter/multi-annual site-specific re-encounters. High genetic connectivity and migration between aggregation sites indicate the Irish Sea as an important movement corridor, with a contemporary effective population estimate (Ne) of 382 (CI = 241-830). We contrast the prevailing view of high gene flow across oceanic regions with evidence of population structure within the NEA, with early-season sharks off southwest Ireland possibly representing genetically distinct migrants. Finally, we found basking sharks surfacing together in the NEA are on average more related than expected by chance, suggesting a genetic consequence of, or a potential mechanism maintaining, site-specific re-encounters. Long-term temporal genetic monitoring is paramount in determining future viability of cosmopolitan marine species, identifying genetic units for conservation management, and for understanding aggregation structure and dynamics.
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Affiliation(s)
- Lilian Lieber
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK
- School of Chemistry and Chemical Engineering, Queen´s University Belfast, Marine Laboratory, Portaferry, BT22 1PF, Northern Ireland, UK
| | - Graham Hall
- Manx Basking Shark Watch and Manx Wildlife Trust, Peel, Isle of Man, IM9 5PJ, UK
| | - Jackie Hall
- Manx Basking Shark Watch and Manx Wildlife Trust, Peel, Isle of Man, IM9 5PJ, UK
| | - Simon Berrow
- Irish Basking Shark Study Group, Merchants Quay, Kilrush, County Clare, UK
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Ireland
| | - Emmett Johnston
- Irish Basking Shark Study Group, Merchants Quay, Kilrush, County Clare, UK
- School of Biological Sciences, Queen´s University Belfast, Belfast, Northern Ireland, UK
| | - Chrysoula Gubili
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK
- Hellenic Agricultural Organisation, Fisheries Research Institute, Nea Peramos, Kavala, Macedonia, 64007, Greece
| | - Jane Sarginson
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK
- Faculty of Science and Engineering, John Dalton Building, Manchester Metropolitan University, Chester Street, Manchester, M1 5GD, UK
| | - Malcolm Francis
- National Institute of Water and Atmospheric Research, Private Bag 14901, Kilbirnie, Wellington, 6241, New Zealand
| | - Clinton Duffy
- Department of Conservation, Private Bag 68908, Wellesley Street, Auckland, 1141, New Zealand
| | - 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
| | - Philip D Doherty
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
- Environment and Sustainability Institute, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
| | - Brendan J Godley
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
- Environment and Sustainability Institute, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
| | - Lucy A Hawkes
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
| | - Matthew J Witt
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
- Environment and Sustainability Institute, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
| | - Suzanne M Henderson
- Scottish Natural Heritage Great Glen House, Inverness, IV3 8NW, Scotland, UK
| | | | - Mahmood S Shivji
- Save Our Seas Shark Research Center and Guy Harvey Research Institute, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA
| | - Deborah A Dawson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, South Yorkshire, UK
| | - David W Sims
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Waterfront Campus, Southampton, SO14 3ZH, UK
| | - Catherine S Jones
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK
| | - Leslie R Noble
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland, UK.
- Faculty of Biosciences and Aquaculture, Nord University, Postboks 1490, 8049, Bodø, Norway.
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7
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Thorburn J, Neat F, Burrett I, Henry LA, Bailey DM, Jones CS, Noble LR. Ontogenetic Variation in Movements and Depth Use, and Evidence of Partial Migration in a Benthopelagic Elasmobranch. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00353] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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8
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Poulakis GR, Grubbs RD. Biology and ecology of sawfishes: global status of research and future outlook. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Lyons K, Bigman JS, Kacev D, Mull CG, Carlisle AB, Imhoff JL, Anderson JM, Weng KC, Galloway AS, Cave E, Gunn TR, Lowe CG, Brill RW, Bedore CN. Bridging disciplines to advance elasmobranch conservation: applications of physiological ecology. CONSERVATION PHYSIOLOGY 2019; 7:coz011. [PMID: 31110763 PMCID: PMC6519003 DOI: 10.1093/conphys/coz011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/02/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
A strength of physiological ecology is its incorporation of aspects of both species' ecology and physiology; this holistic approach is needed to address current and future anthropogenic stressors affecting elasmobranch fishes that range from overexploitation to the effects of climate change. For example, physiology is one of several key determinants of an organism's ecological niche (along with evolutionary constraints and ecological interactions). The fundamental role of physiology in niche determination led to the development of the field of physiological ecology. This approach considers physiological mechanisms in the context of the environment to understand mechanistic variations that beget ecological trends. Physiological ecology, as an integrative discipline, has recently experienced a resurgence with respect to conservation applications, largely in conjunction with technological advances that extended physiological work from the lab into the natural world. This is of critical importance for species such as elasmobranchs (sharks, skates and rays), which are an especially understudied and threatened group of vertebrates. In 2017, at the American Elasmobranch Society meeting in Austin, Texas, the symposium entitled `Applications of Physiological Ecology in Elasmobranch Research' provided a platform for researchers to showcase work in which ecological questions were examined through a physiological lens. Here, we highlight the research presented at this symposium, which emphasized the strength of linking physiological tools with ecological questions. We also demonstrate the applicability of using physiological ecology research as a method to approach conservation issues, and advocate for a more available framework whereby results are more easily accessible for their implementation into management practices.
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Affiliation(s)
- K Lyons
- Georgia Aquarium, Atlanta, GA, USA
| | - J S Bigman
- Simon Fraser University, Burnaby, Canada
| | - D Kacev
- Southwest Fisheries Science Center, La Jolla, CA, USA
| | - C G Mull
- Simon Fraser University, Burnaby, Canada
| | | | - J L Imhoff
- Florida State University Coastal and Marine Laboratory, St. Teresa, FL, USA
| | - J M Anderson
- University of Hawai`i at Mānoa, Honolulu, HI, USA
| | - K C Weng
- Virginia Institute of Marine Science, Gloucester Point, VA, USA
| | - A S Galloway
- South Carolina Department of Natural Resources, SC, USA
| | - E Cave
- Florida Atlantic University, Boca Raton, FL, USA
| | - T R Gunn
- Georgia Southern University, Statesboro, GA USA
| | - C G Lowe
- California State University Long Beach, Long Beach, CA, USA
| | - R W Brill
- Virginia Institute of Marine Science, Gloucester Point, VA, USA
| | - C N Bedore
- Georgia Southern University, Statesboro, GA USA
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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. JOURNAL OF FISH BIOLOGY 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] [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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Rossouw C, Wintner SP, Bester-Van Der Merwe AE. Assessing multiple paternity in three commercially exploited shark species: Mustelus mustelus, Carcharhinus obscurus and Sphyrna lewini. JOURNAL OF FISH BIOLOGY 2016; 89:1125-41. [PMID: 27237109 DOI: 10.1111/jfb.12996] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 04/06/2016] [Indexed: 05/15/2023]
Abstract
In this study, multiple paternity (MP) was investigated in three commercially important shark species, common smoothhound Mustelus mustelus, dusky shark Carcharhinus obscurus and scalloped hammerhead Sphyrna lewini occurring in southern Africa. Reduced marker panels of between five and six microsatellite loci were constructed for each species and used to genotype and assess the presence of MP in a total of 60 M. mustelus individuals from six litters, 90 C. obscurus individuals from 14 litters and 54 S. lewini individuals from 13 litters. Analysis in GERUD and COLONY revealed the presence of MP in all three species. Multiple paternities were observed in 67, 35 and 46% of the litters of M. mustelus, C. obscurus and S. lewini, with corresponding average sire size of 1·6, 1·4 and 2·0, respectively. The variation in the rate of MP among the three species is in accordance with previous studies whilst the comparatively high frequency of MP observed for M. mustelus, matches what has previously been reported for shark species demonstrating aggregation behaviour.
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Affiliation(s)
- C Rossouw
- Department of Genetics, Stellenbosch University, Private Bag 1X, Matieland, 7602, South Africa
| | - S P Wintner
- KwaZulu-Natal Sharks Board and Biomedical Resource Unit, University of KwaZulu-Natal, Durban, 4000, South Africa
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12
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Brooks JL, Guttridge TL, Franks BR, Grubbs RD, Chapman DD, Gruber SH, Dibattista JD, Feldheim KA. Using genetic inference to re-evaluate the minimum longevity of the lemon shark Negaprion brevirostris. JOURNAL OF FISH BIOLOGY 2016; 88:2067-2074. [PMID: 27060882 DOI: 10.1111/jfb.12943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
Abstract
A combination of mark-recapture and genetic sampling was used to extend the minimum longevity of an elasmobranch species and the life span estimate of the lemon shark Negaprion brevirostris was increased conservatively from 20·2 to 37 years. This increase in longevity means higher vulnerability and a longer recovery time from exploitation.
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Affiliation(s)
- J L Brooks
- Bimini Biological Field Station Foundation, South Bimini, Bahamas
- Fish Ecology and Conservation Physiology Lab., Carleton Technology and Training Centre, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - T L Guttridge
- Bimini Biological Field Station Foundation, South Bimini, Bahamas
| | - B R Franks
- Department of Biology, Florida Southern College, Lakeland, FL, 33801, U.S.A
| | - R D Grubbs
- FSU Coastal and Marine Laboratory, 3618 Coastal Highway 98, St Teresa, FL, 32358-2702, U.S.A
| | - D D Chapman
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, U.S.A
| | - S H Gruber
- Bimini Biological Field Station Foundation, South Bimini, Bahamas
- Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, U.S.A
| | - J D Dibattista
- Department of Environment and Agriculture, Curtin University, P. O. Box U1987, Perth, WA 6845, Australia
| | - K A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, U.S.A
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13
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Marino IAM, Riginella E, Gristina M, Rasotto MB, Zane L, Mazzoldi C. Multiple paternity and hybridization in two smooth-hound sharks. Sci Rep 2015; 5:12919. [PMID: 26257113 PMCID: PMC4530440 DOI: 10.1038/srep12919] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 07/02/2015] [Indexed: 11/09/2022] Open
Abstract
Multiple paternity appears to be a common trait of elasmobranch mating systems, with its occurrence likely driven by convenience, due to females seeking to minimize the stress of male harassment. Here we use molecular markers to analyse the frequency of multiple paternity in two related viviparous sharks, Mustelus mustelus and Mustelus punctulatus. We first applied molecular methods to assign pregnant females, embryos and additional reference adults (N = 792) to one of the two species. Paternity analysis was performed using a total of 9 polymorphic microsatellites on 19 females and 204 embryos of M. mustelus, and on 13 females and 303 embryos of M. punctulatus. Multiple paternity occurs in both species, with 47% of M. mustelus and 54% of M. punctulatus litters sired by at least two fathers. Female fecundity is not influenced by multiple mating and in 56% of polyandrous litters paternity is skewed, with one male siring most of the pups. Genetic analyses also revealed hybridization between the two species, with a M. punctulatus female bearing pups sired by a M. mustelus male. The frequency of polyandrous litters in these species is consistent with aspects of their reproductive biology, such as synchronous ovulation and possible occurrence of breeding aggregations.
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Affiliation(s)
- Ilaria A M Marino
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy
| | - Emilio Riginella
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy
| | - Michele Gristina
- IAMC-CNR, via Luigi Vaccara 61, 91026 Mazara del Vallo (TP), Italy
| | - Maria B Rasotto
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy
| | - Lorenzo Zane
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy
| | - Carlotta Mazzoldi
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy
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15
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Chapman DD, Feldheim KA, Papastamatiou YP, Hueter RE. There and back again: a review of residency and return migrations in sharks, with implications for population structure and management. ANNUAL REVIEW OF MARINE SCIENCE 2015; 7:547-70. [PMID: 25251267 DOI: 10.1146/annurev-marine-010814-015730] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The overexploitation of sharks has become a global environmental issue in need of a comprehensive and multifaceted management response. Tracking studies are beginning to elucidate how shark movements shape the internal dynamics and structure of populations, which determine the most appropriate scale of these management efforts. Tracked sharks frequently either remain in a restricted geographic area for an extended period of time (residency) or return to a previously resided-in area after making long-distance movements (site fidelity). Genetic studies have shown that some individuals of certain species preferentially return to their exact birthplaces (natal philopatry) or birth regions (regional philopatry) for either parturition or mating, even though they make long-distance movements that would allow them to breed elsewhere. More than 80 peer-reviewed articles, constituting the majority of published shark tracking and population genetic studies, provide evidence of at least one of these behaviors in a combined 31 shark species from six of the eight extant orders. Residency, site fidelity, and philopatry can alone or in combination structure many coastal shark populations on finer geographic scales than expected based on their potential for dispersal. This information should therefore be used to scale and inform assessment, management, and conservation activities intended to restore depleted shark populations.
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Affiliation(s)
- Demian D Chapman
- Institute for Ocean Conservation Science and School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000;
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16
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Gubili C, Sims DW, Veríssimo A, Domenici P, Ellis J, Grigoriou P, Johnson AF, McHugh M, Neat F, Satta A, Scarcella G, Serra-Pereira B, Soldo A, Genner MJ, Griffiths AM. A tale of two seas: contrasting patterns of population structure in the small-spotted catshark across Europe. ROYAL SOCIETY OPEN SCIENCE 2014; 1:140175. [PMID: 26064555 PMCID: PMC4448844 DOI: 10.1098/rsos.140175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Elasmobranchs represent important components of marine ecosystems, but they can be vulnerable to overexploitation. This has driven investigations into the population genetic structure of large-bodied pelagic sharks, but relatively little is known of population structure in smaller demersal taxa, which are perhaps more representative of the biodiversity of the group. This study explores spatial population genetic structure of the small-spotted catshark (Scyliorhinus canicula), across European seas. The results show significant genetic differences among most of the Mediterranean sample collections, but no significant structure among Atlantic shelf areas. The data suggest the Mediterranean populations are likely to have persisted in a stable and structured environment during Pleistocene sea-level changes. Conversely, the Northeast Atlantic populations would have experienced major changes in habitat availability during glacial cycles, driving patterns of population reduction and expansion. The data also provide evidence of male-biased dispersal and female philopatry over large spatial scales, implying complex sex-determined differences in the behaviour of elasmobranchs. On the basis of this evidence, we suggest that patterns of connectivity are determined by trends of past habitat stability that provides opportunity for local adaptation in species exhibiting philopatric behaviour, implying that resilience of populations to fisheries and other stressors may differ across the range of species.
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Affiliation(s)
- Chrysoula Gubili
- School of Environment and Life Sciences, University of Salford, Salford, Greater Manchester M5 4WU, UK
| | - David W. Sims
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
| | - Ana Veríssimo
- CIBIO-U.P., Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão 4485-661, Portugal
| | | | - Jim Ellis
- Centre for Environment, Fisheries and Aquaclture Science (CEFAS), Pakefield Road, Lowestoft, Suffolk NR33 0HT, UK
| | - Panagiotis Grigoriou
- Cretaquarium, Thalassocosmos, Hellenic Centre for Marine Research (HCMR), PO Box 2214, Heraklion Crete 71003, Greece
| | - Andrew F. Johnson
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography 0202, University of California, 9500 Gilman Drive, San Diego, CA 92083-0202, USA
| | - Matthew McHugh
- Marine and Estuarine Ecology Unit, School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Francis Neat
- Marine Scotland—Science, Marine Laboratory, PO Box 101, Aberdeen AB11 9DB, UK
| | - Andrea Satta
- CNR-IAMC Località Sa Mardini, Torregrande 09170, Italy
| | - Giuseppe Scarcella
- ISMAR-CNR—Istituto di Scienze Marine, Consiglio Nazionale delle Ricerche, Largo Fiera della Pesca 2, Ancona 60125, Italy
| | - Bárbara Serra-Pereira
- Departamento do Mar e Recursos Marinhos, IPMA, Instituto Português do Mar e da Atmosfera, Av. Brasilia, Lisboa 1449-006, Portugal
| | - Alen Soldo
- Department of Marine Studies, University of Split, Livanjska 5, Split 21000, Croatia
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Andrew M. Griffiths
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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17
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Aykanat T, Johnston SE, Cotter D, Cross TF, Poole R, Prodőhl PA, Reed T, Rogan G, McGinnity P, Primmer CR. Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis. BMC Evol Biol 2014; 14:68. [PMID: 24684698 PMCID: PMC4021076 DOI: 10.1186/1471-2148-14-68] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/24/2014] [Indexed: 12/04/2022] Open
Abstract
Background Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system. Results We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h2 ~ 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers. Conclusion The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.
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Affiliation(s)
- Tutku Aykanat
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
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Feldheim KA, Gruber SH, DiBattista JD, Babcock EA, Kessel ST, Hendry AP, Pikitch EK, Ashley MV, Chapman DD. Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks. Mol Ecol 2013; 23:110-7. [DOI: 10.1111/mec.12583] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 10/25/2013] [Accepted: 10/25/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution; Field Museum of Natural History; 1400 South Lake Shore Drive Chicago IL 60605 USA
| | - Samuel H. Gruber
- Division of Marine Biology and Fisheries; Rosenstiel School of Marine and Atmospheric Science; 4600 Rickenbacker Causeway Miami FL 33149 USA
- Bimini Biological Field Station Foundation; Miami FL 33176 USA
| | - Joseph D. DiBattista
- Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Saudi Arabia
| | - Elizabeth A. Babcock
- Division of Marine Biology and Fisheries; Rosenstiel School of Marine and Atmospheric Science; 4600 Rickenbacker Causeway Miami FL 33149 USA
| | - Steven T. Kessel
- Great Lakes Institute for Environmental Research; 401 Sunset Avenue Windsor ON N9B 3P4 Canada
| | - Andrew P. Hendry
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke Street West Montréal QC H3A 2K6 Canada
| | - Ellen K. Pikitch
- Institute for Ocean Conservation Science/School of Marine and Atmospheric Sciences; Stony Brook University; Stony Brook NY 11794-5000 USA
| | - Mary V. Ashley
- Department of Biological Sciences; University of Illinois at Chicago; 845 West Taylor Street Chicago IL 60608 USA
| | - 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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Mourier J, Buray N, Schultz JK, Clua E, Planes S. Genetic network and breeding patterns of a sicklefin lemon shark (Negaprion acutidens) population in the Society Islands, French Polynesia. PLoS One 2013; 8:e73899. [PMID: 23967354 PMCID: PMC3742621 DOI: 10.1371/journal.pone.0073899] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/23/2013] [Indexed: 11/19/2022] Open
Abstract
Human pressures have put many top predator populations at risk of extinction. Recent years have seen alarming declines in sharks worldwide, while their resilience remains poorly understood. Studying the ecology of small populations of marine predators is a priority to better understand their ability to withstand anthropogenic and environmental stressors. In the present study, we monitored a naturally small island population of 40 adult sicklefin lemon sharks in Moorea, French Polynesia over 5 years. We reconstructed the genetic relationships among individuals and determined the population's mating system. The genetic network illustrates that all individuals, except one, are interconnected at least through one first order genetic relationship. While this species developed a clear inbreeding avoidance strategy involving dispersal and migration, the small population size, low number of breeders, and the fragmented environment characterizing these tropical islands, limits its complete effectiveness.
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Affiliation(s)
- Johann Mourier
- LabEx CORAIL - USR 3278 CNRS-EPHE, Centre de Recherche Insulaire et Observatoire de l'Environnement (CRIOBE), Papetoai, Moorea, French Polynesia.
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Boomer JJ, Harcourt RG, Francis MP, Walker TI, Braccini JM, Stow AJ. Frequency of multiple paternity in gummy shark, Mustelus antarcticus, and rig, Mustelus lenticulatus, and the implications of mate encounter rate, postcopulatory influences, and reproductive mode. J Hered 2013; 104:371-9. [PMID: 23505312 DOI: 10.1093/jhered/est010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Elasmobranchs (sharks and rays) show an amazing diversity of reproductive modes and behaviors. Multiple paternity (MP) has been identified in all species where more than 1 litter has been investigated; yet neither direct nor indirect benefits from MP have been determined in elasmobranchs. This has led to the suggestion that MP in this group may simply be a product of convenience polyandry with variation in the frequency of MP driven by differences in mate encounter rates. Here, we use molecular markers to investigate polyandry and MP in 2 closely related and commercially important species of shark, Mustelus antarcticus and Mustelus lenticulatus. In total, 328 M. antarcticus embryos originating from 29 different mothers and 75 M. lenticulatus embryos originating from 19 different mothers were genotyped using 8 microsatellite loci. We find that MP occurs in both species. However, in both species, the majority of litters were sired by a single father. Our results do not support increased fecundity per se as a driver of MP. Further, our results do not suggest that high population densities with resulting high mate encounter rates generated by breeding aggregations necessarily lead to high frequencies of MP. Importantly, we note evidence of reproductive skew within polyandrous litters, which is a predicted outcome of postcopulatory mechanisms.
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Affiliation(s)
- Jessica J Boomer
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia
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21
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Puckridge M, Last PR, White WT, Andreakis N. Phylogeography of the Indo-West Pacific maskrays (Dasyatidae, Neotrygon): a complex example of chondrichthyan radiation in the Cenozoic. Ecol Evol 2012; 3:217-32. [PMID: 23467194 PMCID: PMC3586632 DOI: 10.1002/ece3.448] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 11/14/2012] [Accepted: 11/15/2012] [Indexed: 12/03/2022] Open
Abstract
Maskrays of the genus Neotrygon (Dasyatidae) have dispersed widely in the Indo-West Pacific being represented largely by an assemblage of narrow-ranging coastal endemics. Phylogenetic reconstruction methods reproduced nearly identical and statistically robust topologies supporting the monophyly of the genus Neotrygon within the family Dasyatidae, the genus Taeniura being consistently basal to Neotrygon, and Dasyatis being polyphyletic to the genera Taeniurops and Pteroplatytrygon. The Neotrygon kuhlii complex, once considered to be an assemblage of color variants of the same biological species, is the most derived and widely dispersed subgroup of the genus. Mitochondrial (COI, 16S) and nuclear (RAG1) phylogenies used in synergy with molecular dating identified paleoclimatic fluctuations responsible for periods of vicariance and dispersal promoting population fragmentation and speciation in Neotrygon. Signatures of population differentiation exist in N. ningalooensis and N. annotata, yet a large-scale geological event, such as the collision between the Australian and Eurasian Plates, coupled with subsequent sea-level falls, appears to have separated a once homogeneous population of the ancestral form of N. kuhlii into southern Indian Ocean and northern Pacific taxa some 4–16 million years ago. Repeated climatic oscillations, and the subsequent establishment of land and shallow sea connections within and between Australia and parts of the Indo-Malay Archipelago, have both promoted speciation and established zones of secondary contact within the Indian and Pacific Ocean basins.
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Affiliation(s)
- Melody Puckridge
- Institute for Marine and Antarctic Studies, University of Tasmania Private Bag 129, Hobart, TAS, 7001, Australia ; Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research Castray Esplanade, Hobart, TAS, 7000, Australia
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22
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Faria VV, McDavitt MT, Charvet P, Wiley TR, Simpfendorfer CA, Naylor GJP. Species delineation and global population structure of Critically Endangered sawfishes (Pristidae). Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00872.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
| | - Matthew T. McDavitt
- National Legal Research Group Inc.; 2421 Ivy Road; Charlottesville; VA; 22903-4971; USA
| | - Patricia Charvet
- SENAI/PR; Av. Cândido de Abreu 200; Curitiba; PR; 80530-902; Brazil
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23
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Mourier J, Planes S. Direct genetic evidence for reproductive philopatry and associated fine-scale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia. Mol Ecol 2012; 22:201-14. [PMID: 23130666 DOI: 10.1111/mec.12103] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 11/29/2022]
Abstract
Conservation of top predators has been emphasized as essential in an ecosystem due to their role in trophic chain regulation. Optimizing conservation strategies for these endangered marine top predators requires direct estimates of breeding patterns and connectivity as these are essential to understanding the population dynamics. There have been some attempts to investigate breeding patterns of reef sharks from litter reconstruction using molecular analyses. However, direct fine-scale migrations of female sharks for parturition as well as connectivity at a medium scale like between islands remain mostly unknown. We used microsatellite DNA markers and a likelihood-based parentage analysis to determine breeding patterns of female blacktip reef sharks in Moorea (Society Islands, French Polynesia). Most females gave birth at their home island but some migrated to specific nursery areas outside the area they are attached to, sometimes going to another island 50 km away across deep ocean. Our analysis also revealed that females migrated to the same nursery for every birthing event. Many offspring showed a high level of inbreeding indicating an overall reduced population size, restricted movements and dispersal, or specific mating behaviour. Females represent the vectors that transport the genes at nursery grounds, and their fidelity should thus define reproductive units. As females seem to be philopatric, males could be the ones dispersing genes between populations. These results highlight the need to conserve coastal zones where female reef sharks seem to exhibit philopatry during the breeding season.
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Affiliation(s)
- Johann Mourier
- Laboratoire d'Excellence CORAIL, USR 3278 CNRS-EPHE, CRIOBE, BP 1013, 98729, Moorea, French Polynesia.
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24
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Wright LI, Fuller WJ, Godley BJ, McGowan A, Tregenza T, Broderick AC. Reconstruction of paternal genotypes over multiple breeding seasons reveals male green turtles do not breed annually. Mol Ecol 2012; 21:3625-35. [PMID: 22591073 DOI: 10.1111/j.1365-294x.2012.05616.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
For species of conservation concern, knowledge of key life-history and demographic components, such as the number and sex ratio of breeding adults, is essential for accurate assessments of population viability. Species with temperature-dependent sex determination can produce heavily biased primary sex ratios, and there is concern that adult sex ratios may be similarly skewed or will become so as a result of climate warming. Prediction and mitigation of such impacts are difficult when life-history information is lacking. In marine turtles, owing to the difficultly in observing males at sea, the breeding interval of males is unknown. It has been suggested that male breeding periodicity may be shorter than that of females, which could help to compensate for generally female-biased sex ratios. Here we outline how the use of molecular-based paternity analysis has allowed us, for the first time, to assess the breeding interval of male marine turtles across multiple breeding seasons. In our study rookery of green turtles (Chelonia mydas), 97% of males were assigned offspring in only one breeding season within the 3-year study period, strongly suggesting that male breeding intervals are frequently longer than 1year at this site. Our results also reveal a sex ratio of breeding adults of at least 1.3 males to each female. This study illustrates the utility of molecular-based parentage inference using reconstruction of parental genotypes as a method for monitoring the number and sex ratio of breeders in species where direct observations or capture are difficult.
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Affiliation(s)
- Lucy I Wright
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
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25
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Portnoy DS, Heist EJ. Molecular markers: progress and prospects for understanding reproductive ecology in elasmobranchs. JOURNAL OF FISH BIOLOGY 2012; 80:1120-40. [PMID: 22497375 DOI: 10.1111/j.1095-8649.2011.03206.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Application of modern molecular tools is expanding the understanding of elasmobranch reproductive ecology. High-resolution molecular markers provide information at scales ranging from the identification of reproductively isolated populations in sympatry (i.e. cryptic species) to the relationships among parents, offspring and siblings. This avenue of study has not only augmented the current understanding of the reproductive biology of elasmobranchs but has also provided novel insights that could not be obtained through experimental or observational techniques. Sharing of genetic polymorphisms across ocean basins indicates that for some species there may be gene flow on global scales. The presence, however, of morphologically similar but genetically distinct entities in sympatry suggests that reproductive isolation can occur with minimal morphological differentiation. This review discusses the recent findings in elasmobranch reproductive biology like philopatry, hybridization and polyandry while highlighting important molecular and analytical techniques. Furthermore, the review examines gaps in current knowledge and discusses how new technologies may be applied to further the understanding of elasmobranch reproductive ecology.
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Affiliation(s)
- D S Portnoy
- Department of Wildlife and Fisheries Sciences, Center for Biosystematics and Biodiversity, Texas A&M University, College Station, TX 77843-2258, USA.
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26
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Dudgeon CL, Blower DC, Broderick D, Giles JL, Holmes BJ, Kashiwagi T, Krück NC, Morgan JAT, Tillett BJ, Ovenden JR. A review of the application of molecular genetics for fisheries management and conservation of sharks and rays. JOURNAL OF FISH BIOLOGY 2012; 80:1789-1843. [PMID: 22497408 DOI: 10.1111/j.1095-8649.2012.03265.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.
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Affiliation(s)
- C L Dudgeon
- The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
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27
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Fitzpatrick JL, Kempster RM, Daly-Engel TS, Collin SP, Evans JP. Assessing the potential for post-copulatory sexual selection in elasmobranchs. JOURNAL OF FISH BIOLOGY 2012; 80:1141-58. [PMID: 22497376 PMCID: PMC3842027 DOI: 10.1111/j.1095-8649.2012.03256.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This review highlights the potential role that post-copulatory sexual selection plays in elasmobranch reproductive systems and the utility of this group to further understanding of evolutionary responses to the post-copulatory processes of sperm competition and cryptic female choice. The growing genetic evidence for female multiple mating (polyandry) in elasmobranchs is summarized. While polyandry appears to be common in this group, rates of multiple paternity are highly variable between species suggesting that there is large variance in the strength of post-copulatory sexual selection among elasmobranchs. Possible adaptations of traits important for post-copulatory sexual selection are then considered. Particular emphasis is devoted to explore the potential for sperm competition and cryptic female choice to influence the evolution of testes size, sperm morphology, genital morphology and sperm storage organs. Finally, it is argued that future work should take advantage of the wealth of information on these reproductive traits already available in elasmobranchs to gain a better understanding of how post-copulatory sexual selection operates in this group.
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Affiliation(s)
- J L Fitzpatrick
- Centre for Evolutionary Biology, School of Animal Biology, University of Western Australia, WA 6009, Australia.
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28
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Knip DM, Heupel MR, Simpfendorfer CA. Habitat use and spatial segregation of adult spottail sharks Carcharhinus sorrah in tropical nearshore waters. JOURNAL OF FISH BIOLOGY 2012; 80:767-784. [PMID: 22471798 DOI: 10.1111/j.1095-8649.2012.03223.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
An array of acoustic receivers deployed in Cleveland Bay, north Queensland, Australia, passively tracked 20 adult spottail sharks Carcharhinus sorrah over 2 years (2009-2010) to define patterns in movement and habitat use. Individuals were present in the study site for long periods, ranging from 8 to 408 days (mean = 185). Size and location of home ranges did not vary over time. A high level of segregation occurred among C. sorrah, with individuals using different types of habitat and showing strong attachment to specific regions. The depth of habitat individuals used varied between sexes. Males tended to use a narrow range of habitat depths within the study site (2·8-6·0 m), whereas females used shallower habitats (1·4-6·2 m) and displayed a seasonal shift in the depth of habitat used. Mean monthly habitat depth used varied by as much as 2 m for females, with individuals using shallower habitats during the winter months. Long-term presence and consistent home ranges suggest that Cleveland Bay provides important habitat for C. sorrah. By defining patterns in the use of nearshore habitats for C. sorrah, this study improves the understanding of the movement and habitat use of smaller-bodied coastal sharks and may help provide guidance for the management of their populations.
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Affiliation(s)
- D M Knip
- Fishing and Fisheries Research Centre, School of Earth and Environmental Sciences, James Cook University, Townsville, Qld 4811, Australia.
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29
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Daly-Engel TS, Seraphin KD, Holland KN, Coffey JP, Nance HA, Toonen RJ, Bowen BW. Global phylogeography with mixed-marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini). PLoS One 2012; 7:e29986. [PMID: 22253848 PMCID: PMC3254628 DOI: 10.1371/journal.pone.0029986] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 12/09/2011] [Indexed: 11/18/2022] Open
Abstract
Background The scalloped hammerhead shark, Sphyrna lewini, is a large endangered predator with a circumglobal distribution, observed in the open ocean but linked ontogenetically to coastal embayments for parturition and juvenile development. A previous survey of maternal (mtDNA) markers demonstrated strong genetic partitioning overall (global ΦST = 0.749) and significant population separations across oceans and between discontinuous continental coastlines. Methodology/Principal Findings We surveyed the same global range with increased sample coverage (N = 403) and 13 microsatellite loci to assess the male contribution to dispersal and population structure. Biparentally inherited microsatellites reveal low or absent genetic structure across ocean basins and global genetic differentiation (FST = 0.035) over an order of magnitude lower than the corresponding measures for maternal mtDNA lineages (ΦST = 0.749). Nuclear allelic richness and heterozygosity are high throughout the Indo-Pacific, while genetic structure is low. In contrast, allelic diversity is low while population structure is higher for populations at the ends of the range in the West Atlantic and East Pacific. Conclusions/Significance These data are consistent with the proposed Indo-Pacific center of origin for S. lewini, and indicate that females are philopatric or adhere to coastal habitats while males facilitate gene flow across oceanic expanses. This study includes the largest sampling effort and the most molecular loci ever used to survey the complete range of a large oceanic predator, and findings emphasize the importance of incorporating mixed-marker analysis into stock assessments of threatened and endangered shark species.
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Affiliation(s)
- Toby S Daly-Engel
- Department of Zoology, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America.
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Griffiths AM, Jacoby DMP, Casane D, McHugh M, Croft DP, Genner MJ, Sims DW. First analysis of multiple paternity in an oviparous shark, the small-spotted catshark (Scyliorhinus canicula L.). ACTA ACUST UNITED AC 2011; 103:166-73. [PMID: 22058410 DOI: 10.1093/jhered/esr112] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Multiple paternity (MP) has been demonstrated in a variety of sharks, although its prevalence and the number of sires per litter vary considerably among species. To date, such analyses have focused on viviparous species that possess only part of the wide spectrum of reproductive strategies developed in elasmobranchs. We analyzed MP in an oviparous species, the small-spotted catshark (Scyliorhinus canicula). In total, 150 neonates originating from 13 different mothers were genotyped using 12 microsatellite loci. MP was commonplace, with progeny from 92% of females sired by multiple males. This result is consistent with the reproductive biology of the species, particularly its protracted breeding season and potential for long-term sperm storage. The significance of these findings is discussed in light of small-spotted catshark behavior, which suggests that the cost of avoiding mating attempts initiated by males may be high and is therefore supportive of convenience polyandry as an explanation for MP. Eggs were followed from the time they were laid to when they hatched, offering a rare opportunity to investigate juvenile development in more detail.
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Affiliation(s)
- Andrew M Griffiths
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK.
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Sandoval-Castillo J, Rocha-Olivares A. Deep mitochondrial divergence in Baja California populations of an aquilopelagic elasmobranch: the golden cownose ray. J Hered 2011; 102:269-74. [PMID: 21414964 DOI: 10.1093/jhered/esr004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Assessing the realized effect of dispersal in the genetic makeup of a species has significant evolutionary, ecological, and economical consequences. Here, we investigate the genetic diversity and population differentiation in the aquilopelagic golden cownose ray Rhinoptera steindachneri from the Gulf of California (GC) and the Pacific coast of Baja California (PCBC) using the mitochondrial NADH2 gene. Low levels of genetic diversity were found with only 4 polymerase chain reaction-restriction fragment length polymorphism haplotypes among 76 specimens. Pacific coast organisms were fixed for a unique haplotype not shared with rays from the gulf; 92% of GC rays possessed a single NADH2 haplotype not found in the Pacific. This produced significant differentiation between the GC and the PCBC (Φ(CT) = 0.972, P < 0.001). A pronounced phylogeographic pattern was found in which GC haplotypes were reciprocally monophyletic relative to a very divergent Pacific lineage (d = 10%). Our results indicate that despite high dispersal potential, GC and PCBC golden cownose ray populations are characterized by highly divergent mitochondrial lineages. Although more evidence is needed to corroborate the genetic isolation and systematic status of PCBC and GC golden cownose rays, our results suggest a possible cryptic species in the region.
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Affiliation(s)
- Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, Department of Biological Oceanography, CICESE, Ensenada, Baja California, México
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Phylogeography and conservation of the bull shark (Carcharhinus leucas) inferred from mitochondrial and microsatellite DNA. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0145-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Serbezov D, Bernatchez L, Olsen EM, Vøllestad LA. Mating patterns and determinants of individual reproductive success in brown trout (Salmo trutta) revealed by parentage analysis of an entire stream living population. Mol Ecol 2010; 19:3193-205. [PMID: 20629953 DOI: 10.1111/j.1365-294x.2010.04744.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Reproductive success and its determinants are difficult to infer for wild populations of species with no parental care where behavioural observations are difficult or impossible. In this study, we characterized the breeding system and provide estimates of individual reproductive success under natural conditions for an exhaustively sampled stream-resident brown trout (Salmo trutta) population. We inferred parentage using a full probability Bayesian model that combines genetic (microsatellite) with phenotypic data. By augmenting the potential parents file with inferred parental genotypes from sib-ship analysis in cases where large families had unsampled parents, we could make more precise inference on variance of family size. We observed both polygamous and monogamous matings and large reproductive skew for both sexes, particularly in males. Correspondingly, we found evidence for sexual selection on body size for both sexes. We show that the mating system of brown trout has the potential to be very flexible and we conjecture that environmental uncertainty could be driving the evolution and perhaps select for the maintenance of plasticity of the mating system in this species.
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Affiliation(s)
- Dimitar Serbezov
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway.
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Veríssimo A, Grubbs D, McDowell J, Musick J, Portnoy D. Frequency of multiple paternity in the spiny dogfish Squalus acanthias in the western north Atlantic. J Hered 2010; 102:88-93. [PMID: 20650933 DOI: 10.1093/jhered/esq084] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multiple paternity (MP) has been shown to be widespread in elasmobranch fishes although its prevalence and the number of sires per litter vary considerably among species. In the squaloid shark Squalus acanthias, MP has been reported, but whether it is a common feature of the species' reproductive strategy is unknown. In this study, we determined the frequency of MP in 29 litters of S. acanthias sampled from the lower Chesapeake Bay and coastal Virginia waters, using 7 highly polymorphic nuclear DNA microsatellite loci. Only 5 litters (17% of the total) were genetically polyandrous, with at least 2 sires per litter. Litter size increased with female size but was similar between polyandrous and monandrous females.
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Affiliation(s)
- Ana Veríssimo
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062, USA.
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DiBattista JD, Feldheim KA, Garant D, Gruber SH, Hendry AP. Anthropogenic disturbance and evolutionary parameters: a lemon shark population experiencing habitat loss. Evol Appl 2010; 4:1-17. [PMID: 25567949 PMCID: PMC3352521 DOI: 10.1111/j.1752-4571.2010.00125.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 02/19/2010] [Indexed: 11/26/2022] Open
Abstract
The level of genetic variation in natural populations influences evolutionary potential, and may therefore influence responses to selection in the face of future environmental changes. By combining long-term monitoring of marked individuals with genetic pedigree reconstruction, we assessed whether habitat loss influenced genetic variation in a lemon shark (Negaprion brevirostris) population at an isolated nursery lagoon (Bimini, Bahamas). We also tracked changes in the strength and direction of natural selection. Contrary to initial expectations, we found that after the habitat loss neutral genetic variation increased, as did additive genetic variance for juvenile morphological traits (body length and mass). We hypothesize that these effects might result from philopatric behavior in females coupled with a possible influx of male genotypes from other nursery sites. We also found changes in the strength of selection on morphological traits, which weakened considerably after the disturbance; habitat loss therefore changed the phenotypes favored by natural selection. Because such human-induced shifts in the adaptive landscape may be common, we suggest that conservation biologists should not simply focus on neutral genetic variation per se, but also on assessing and preserving evolutionary parameters, such as additive genetic variation and selection.
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Affiliation(s)
- Joseph D DiBattista
- Redpath Museum and Department of Biology, McGill University Montréal, QC, Canada
| | - Kevin A Feldheim
- Field Museum, Pritzker Laboratory for Molecular Systematics and Evolution Chicago, IL, USA
| | - Dany Garant
- Département de Biologie, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Samuel H Gruber
- Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science Miami, FL, USA
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University Montréal, QC, Canada
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Chapman DD, Babcock EA, Gruber SH, Dibattista JD, Franks BR, Kessel SA, Guttridge T, Pikitch EK, Feldheim KA. Long-term natal site-fidelity by immature lemon sharks (Negaprion brevirostris) at a subtropical island. Mol Ecol 2009; 18:3500-7. [PMID: 19659480 DOI: 10.1111/j.1365-294x.2009.04289.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Although many sharks begin their life confined in nursery habitats, it is unknown how rapidly they disperse away from their natal area once they leave the nursery. We examine this issue in immature lemon sharks (Negaprion brevirostris) from the time they leave the nursery (approximately age 3) at a subtropical island (Bimini, Bahamas), through to the onset of sexual maturity (approximately age 12). From 1995 to 2007 we tagged and genotyped a large fraction of the nursery-bound sharks at this location (0-3 years of age, N = 1776 individuals). From 2003 to 2007 we sampled immature sharks aged from 3 to 11 years (N = 150) living around the island and used physical/genetic tag recaptures coupled with kinship analysis to determine whether or not each of these 'large immature sharks' was locally born. We show that many island-born lemon sharks remain close to their natal area for long periods (years) after leaving the nursery; more than half of the sampled sharks up to 135 cm total length ( approximately 6 years old) were locally born. The fraction of locally born sharks gradually declined with increasing shark size, indicating that dispersal is relatively slow and does not primarily occur after sharks reach a threshold size. Local conservation measures (e.g. localized fishery closures, marine protected areas) can therefore help protect island-born lemon sharks even after they leave the nursery habitat.
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Affiliation(s)
- Demian D Chapman
- Institute for Ocean Conservation Science & School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11794, USA.
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DiBattista JD, Feldheim KA, Garant D, Gruber SH, Hendry AP. EVOLUTIONARY POTENTIAL OF A LARGE MARINE VERTEBRATE: QUANTITATIVE GENETIC PARAMETERS IN A WILD POPULATION. Evolution 2009; 63:1051-67. [DOI: 10.1111/j.1558-5646.2008.00605.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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SCHULTZ JK, FELDHEIM KA, GRUBER SH, ASHLEY MV, MCGOVERN TM, BOWEN BW. Global phylogeography and seascape genetics of the lemon sharks (genusNegaprion). Mol Ecol 2008; 17:5336-48. [DOI: 10.1111/j.1365-294x.2008.04000.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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