1
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Reynolds SD, Franklin CE, Norman BM, Richardson AJ, Everett JD, Schoeman DS, White CR, Lawson CL, Pierce SJ, Rohner CA, Bach SS, Comezzi FG, Diamant S, Jaidah MY, Robinson DP, Dwyer RG. Effects of climate warming on energetics and habitat of the world's largest marine ectotherm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175832. [PMID: 39197762 DOI: 10.1016/j.scitotenv.2024.175832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 08/23/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
Responses of organisms to climate warming are variable and complex. Effects on species distributions are already evident and mean global surface ocean temperatures are likely to warm by up to 4.1 °C by 2100, substantially impacting the physiology and distributions of ectotherms. The largest marine ectotherm, the whale shark Rhincodon typus, broadly prefers sea surface temperatures (SST) ranging from 23 to 30 °C. Whole-species distribution models have projected a poleward range shift under future scenarios of climate change, but these models do not consider intraspecific variation or phenotypic plasticity in thermal limits when modelling species responses, and the impact of climate warming on the energetic requirements of whale sharks is unknown. Using a dataset of 111 whale shark movement tracks from aggregation sites in five countries across the Indian Ocean and the latest Earth-system modelling produced from Coupled Model Intercomparison Project Phase 6 for the Intergovernmental Panel on Climate Change, we examined how SST and total zooplankton biomass, their main food source, may change in the future, and what this means for the energetic balance and extent of suitable habitat for whale sharks. Earth System Models, under three Shared Socioeconomic Pathways (SSPs; SSP1-2.6, SSP3-7.0 and SSP5-8.5), project that by 2100 mean SST in four regions where whale shark aggregations are found will increase by up to 4.9 °C relative to the present, while zooplankton biomass will decrease. This reduction in zooplankton is projected to be accompanied by an increase in the energetic requirements of whale sharks because warmer water temperatures will increase their metabolic rate. We found marked differences in projected changes in the extent of suitable habitat when comparing a whole-species distribution model to one including regional variation. This suggests that the conventional approach of combining data from different regions within a species' distribution could underestimate the amount of local adaptation in populations, although parameterising local models could also suffer from having insufficient data and lead to model mis-specification or highly uncertain estimates. Our study highlights the need for further research into whale shark thermal tolerances and energetics, the complexities involved in projecting species responses to climate change, and the potential importance of considering intraspecific variation when building species distribution models.
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Affiliation(s)
- Samantha D Reynolds
- School of the Environment, The University of Queensland, Brisbane, QLD, Australia; ECOCEAN Inc., 162/3 Powell Rd, Coogee, WA, Australia; Harry Butler Institute, Murdoch University, Murdoch, WA, Australia.
| | - Craig E Franklin
- School of the Environment, The University of Queensland, Brisbane, QLD, Australia
| | - Bradley M Norman
- ECOCEAN Inc., 162/3 Powell Rd, Coogee, WA, Australia; Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Anthony J Richardson
- School of the Environment, The University of Queensland, Brisbane, QLD, Australia; Centre for Biodiversity and Conservation Science (CBCS), The University of Queensland, Brisbane, QLD, Australia; CSIRO Environment, Queensland Biosciences Precinct, St Lucia, QLD, AUSTRALIA
| | - Jason D Everett
- School of the Environment, The University of Queensland, Brisbane, QLD, Australia; CSIRO Environment, Queensland Biosciences Precinct, St Lucia, QLD, AUSTRALIA; Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW, Australia
| | - David S Schoeman
- Ocean Futures Research Cluster, School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia; Centre for African Conservation Ecology, Department of Zoology, Nelson Mandela University, Gqeberha, South Africa
| | - Craig R White
- School of Biological Sciences and Centre for Geometric Biology, Monash University, Clayton, VIC, Australia
| | - Christopher L Lawson
- School of the Environment, The University of Queensland, Brisbane, QLD, Australia
| | - Simon J Pierce
- Marine Megafauna Foundation, West Palm Beach, FL, USA; School of Science, Technology and Engineering, The University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | | | - Steffen S Bach
- Ramboll, Copenhagen, Denmark; Qatar Whale Shark Research Project, Doha, Qatar
| | - Francesco G Comezzi
- Department of Natural Resources and Environment Tasmania, Marine Resources, Hobart, Tasmania, Australia
| | - Stella Diamant
- Marine Megafauna Foundation, West Palm Beach, FL, USA; Madagascar Whale Shark Project, Nosy Be, Madagascar
| | | | - David P Robinson
- Qatar Whale Shark Research Project, Doha, Qatar; Sundive Research, Byron Bay, New South Wales, Australia
| | - Ross G Dwyer
- School of Science, Technology and Engineering, The University of the Sunshine Coast, Sippy Downs, QLD, Australia
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2
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Winn JC, Maduna SN, Bester-van der Merwe AE. A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae. Genomics 2024; 116:110771. [PMID: 38147941 DOI: 10.1016/j.ygeno.2023.110771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2023]
Abstract
The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.
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Affiliation(s)
- Jessica C Winn
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa
| | - Simo N Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway
| | - Aletta E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa.
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3
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Jose A, Sukumaran S, Roul SK, Azeez PA, Kizhakudan SJ, Raj N, Nisha K, Gopalakrishnan A. Genetic analyses reveal panmixia in Indian waters and population subdivision across Indian Ocean and Indo-Malay Archipelago for Decapterus russelli. Sci Rep 2023; 13:22860. [PMID: 38129501 PMCID: PMC10739887 DOI: 10.1038/s41598-023-49805-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The Indian Scad, Decapterus russelli is an important pelagic carangid widely distributed throughout the Indian Ocean and the Indo-West Pacific. Despite being widely distributed in the Indian Ocean, the information regarding genetic structuring and diversity has been lacking compared to its Indo Malay Archipelago counterparts. The present study was conducted to investigate the genetic stock structure of D. russelli based on mitochondrial (Cyt b) and nuclear (DrAldoB1) markers along Indian waters. The results indicated the presence of a single panmictic stock across the Indian Ocean region. High haplotype diversity associated with low nucleotide diversity suggested a population bottleneck followed by rapid population growth. Phylogenetic analysis revealed the absence of geographical clustering of lineages with the most common haplotype distributed globally. The pelagic life style, migratory capabilities, and larval dispersal may be the contributing factors to the observed spatial homogeneity of D. russelli. However, significant genetic differentiation was observed between the populations from Indian Ocean and Indo-Malay Archipelago. Hierarchical molecular variance analysis (AMOVA), pairwise FST comparisons and SAMOVA showed existence of two distinct genetic stocks of D. russelli in the Indian Ocean and IMA. The observed interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the Indo-Malay Archipelago and the Indian Ocean regions suggest the influence of historic isolation, ocean surface currents and biotic and abiotic features of the ocean. Also, there was a significant relationship between genetic distance and geographical distance between population pairs in a manner consistent with isolation-by-distance. These resulted in the evolution of a phylogeographic break for this species between these regions. The findings of these results suggest that D. russelli from the Indian Ocean shall be managed in its entire area of distribution as a single stock. Further, the Indian Ocean and Indo-Malayan stocks can be managed separately.
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Affiliation(s)
- Anjaly Jose
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India.
- Mangalore University, Mangalagangotri, Mangalore, Karnataka, 574199, India.
| | - Sandhya Sukumaran
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - Subal Kumar Roul
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - P Abdul Azeez
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - Shoba Joe Kizhakudan
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - Neenu Raj
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - K Nisha
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
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4
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Gore M, Camplisson E, Ormond R. The biology and ecology of the basking shark: A review. ADVANCES IN MARINE BIOLOGY 2023; 95:113-257. [PMID: 37923538 DOI: 10.1016/bs.amb.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Here we review the literature on the basking shark (Cetorhinus maximus, Gunnerus, 1765), well known as the second largest extant shark (and fish) species globally. Previous reviews were published by Kunzlik in 1988 and Sims in 2008, but in the last 15 years modern electronic and DNA sequencing technologies have resulted in considerable advances in our knowledge of the species' behaviour and ecology. Basking sharks are planktivores and under appropriate conditions spend prolonged periods at the ocean surface feeding on copepod prey that primarily make up their diet, the behaviour that gave rise to their common name. In general, they are migratory and move into higher latitude waters during the summer months, when loose surface-feeding aggregations may form at favoured sites, the best known of which at present occur at hotspots on the west coasts of Britain and Ireland. The species is found circumglobally in temperate waters, but they are also now known on occasion to migrate at depth between northern and southern hemispheres, as well as across oceans within the northern hemisphere. In the past basking shark were more abundant across much of their range, but, consequent on targeted fisheries and in some places intentional eradication, became everywhere scarce, with recent population recovery in the north-east Atlantic being the result of protective measures initiated in the 1990s. Despite their charismatic nature, some of their most fundamental biological processes including copulation, gestation and birth remain largely unknown, due to their migratory and often deep-water lifestyle. In contrast, the deployment of small-scale archival and satellite tags has revealed the details of both broadscale migratory movements and horizontal and vertical foraging behaviours. Recent genetic studies support evidence suggesting a degree of site fidelity in relation to seasonal feeding grounds, which likely explains why in the past local populations have collapsed following periods of intensive fishing. Other recent research using aerial drones and towed cameras has revealed within loose feeding aggregations elements of social behaviour that may have a courtship function as well as enhance feeding efficiency.
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Affiliation(s)
- Mauvis Gore
- Marine Conservation International, South Queensferry, Edinburgh, Scotland, United Kingdom; Centre for Marine Biodiversity & Biotechnology, Heriot-Watt University, Edinburgh, Scotland, United Kingdom
| | - Ewan Camplisson
- Centre for Marine Biodiversity & Biotechnology, Heriot-Watt University, Edinburgh, Scotland, United Kingdom; School of Science, University of Manchester, Manchester, England, United Kingdom
| | - Rupert Ormond
- Marine Conservation International, South Queensferry, Edinburgh, Scotland, United Kingdom; Centre for Marine Biodiversity & Biotechnology, Heriot-Watt University, Edinburgh, Scotland, United Kingdom.
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5
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Kottillil S, Rao C, Bowen BW, Shanker K. Phylogeography of sharks and rays: a global review based on life history traits and biogeographic partitions. PeerJ 2023; 11:e15396. [PMID: 37283899 PMCID: PMC10239618 DOI: 10.7717/peerj.15396] [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: 06/13/2022] [Accepted: 04/20/2023] [Indexed: 06/08/2023] Open
Abstract
Considerable research exists on the life history traits, evolutionary history, and environmental factors that shape the population genetic structure of marine organisms, including sharks and rays. Conservation concerns are particularly strong for this group as they are highly susceptible to anthropogenic stressors due to a combination of life history traits including late maturity and low fecundity. Here, we provide a review and synthesis of the global phylogeography of sharks and rays. We examined existing data for 40 species of sharks belonging to 17 genera and 19 species of rays belonging to 11 genera. Median joining haplotype networks were constructed for each species for the mtDNA cytochrome C oxidase subunit I (COI), and an Analysis of Molecular Variance (AMOVA) was conducted to understand patterns of genetic diversity and structure across the three major ocean basins-the Indian, Atlantic and Pacific Oceans. Haplotype networks showed very shallow coalescence in most species, a finding previously reported for marine teleosts. Star topologies were predominant among sharks while complex mutational topologies predominated among rays, a finding we attribute to extremely limited dispersal in the early life history of rays. Population structuring varied amongst species groups, apparently due to differences in life history traits including reproductive philopatry, site fidelity, pelagic habitat, migratory habits, and dispersal ability. In comparison to reef-associated and demersal species, pelagic and semi pelagic species showed lower levels of structure between and within ocean basins. As expected, there is variation between taxa and groups, but there are also some broad patterns that can guide management and conservation strategies.
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Affiliation(s)
- Sudha Kottillil
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
- Department of Energy and Environment, TERI School of Advanced Studies, New Delhi, India
| | - Chetan Rao
- Dakshin Foundation, Bengaluru, Karnataka, India
| | - Brian W. Bowen
- Hawai‘i Institute of Marine Biology, University of Hawaii, Kaneohe, Hawai‘i, United States of America
| | - Kartik Shanker
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
- Dakshin Foundation, Bengaluru, Karnataka, India
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6
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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] [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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7
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Hardenstine RS, He S, Cochran JEM, Braun CD, Cagua EF, Pierce SJ, Prebble CEM, Rohner CA, Saenz‐Angudelo P, Sinclair‐Taylor TH, Skomal GB, Thorrold SR, Watts AM, Zakroff CJ, Berumen ML. Pieces in a global puzzle: Population genetics at two whale shark aggregations in the western Indian Ocean. Ecol Evol 2022; 12:e8492. [PMID: 35127024 PMCID: PMC8796955 DOI: 10.1002/ece3.8492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/30/2021] [Accepted: 11/10/2021] [Indexed: 02/01/2023] Open
Abstract
The whale shark Rhincodon typus is found throughout the world's tropical and warm-temperate ocean basins. Despite their broad physical distribution, research on the species has been concentrated at a few aggregation sites. Comparing DNA sequences from sharks at different sites can provide a demographically neutral understanding of the whale shark's global ecology. Here, we created genetic profiles for 84 whale sharks from the Saudi Arabian Red Sea and 72 individuals from the coast of Tanzania using a combination of microsatellite and mitochondrial sequences. These two sites, separated by approximately 4500 km (shortest over-water distance), exhibit markedly different population demographics and behavioral ecologies. Eleven microsatellite DNA markers revealed that the two aggregation sites have similar levels of allelic richness and appear to be derived from the same source population. We sequenced the mitochondrial control region to produce multiple global haplotype networks (based on different alignment methodologies) that were broadly similar to each other in terms of population structure but suggested different demographic histories. Data from both microsatellite and mitochondrial markers demonstrated the stability of genetic diversity within the Saudi Arabian aggregation site throughout the sampling period. These results contrast previously measured declines in diversity at Ningaloo Reef, Western Australia. Mapping the geographic distribution of whale shark lineages provides insight into the species' connectivity and can be used to direct management efforts at both local and global scales. Similarly, understanding historical fluctuations in whale shark abundance provides a baseline by which to assess current trends. Continued development of new sequencing methods and the incorporation of genomic data could lead to considerable advances in the scientific understanding of whale shark population ecology and corresponding improvements to conservation policy.
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Affiliation(s)
- Royale S. Hardenstine
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Song He
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Jesse E. M. Cochran
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Camrin D. Braun
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Edgar Fernando Cagua
- School of Biological SciencesCentre for Integrative EcologyUniversity of CanterburyChristchurchNew Zealand
- WorldFishBayan LepasMalaysia
| | | | - Clare E. M. Prebble
- Marine Megafauna FoundationTruckeeCaliforniaUSA
- National Oceanography CentreUniversity of South HamptonSouth HamtonUK
| | | | - Pablo Saenz‐Angudelo
- Facultad de CienciasInstituo de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | | | - Gregory B. Skomal
- Massachusetts Division of Marine FisheriesNew BedfordMassachusettsUSA
| | - Simon R. Thorrold
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Alexandra M. Watts
- Marine Megafauna FoundationTruckeeCaliforniaUSA
- Ecological Genetics and Conservation LaboratoryManchester Metropolitan UniversityManchesterUK
| | - Casey J. Zakroff
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Michael L. Berumen
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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8
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9
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Dugal L, Thomas L, Jensen MR, Sigsgaard EE, Simpson T, Jarman S, Thomsen PF, Meekan M. Individual haplotyping of whale sharks from seawater environmental DNA. Mol Ecol Resour 2021; 22:56-65. [PMID: 34146448 DOI: 10.1111/1755-0998.13451] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/07/2021] [Accepted: 06/03/2021] [Indexed: 01/04/2023]
Abstract
Population genetic data can provide valuable information on the demography of a species. For rare and elusive marine megafauna, samples for generating the data are traditionally obtained from tissue biopsies, which can be logistically difficult and expensive to collect and require invasive sampling techniques. Analysis of environmental DNA (eDNA) offers an alternative, minimally invasive approach to provide important genetic information. Although eDNA approaches have been studied extensively for species detection and biodiversity monitoring in metabarcoding studies, the potential for the technique to address population-level questions remains largely unexplored. Here, we applied "eDNA haplotyping" to obtain estimates of the intraspecific genetic diversity of a whale shark (Rhincodon typus) aggregation at Ningaloo reef, Australia. Over 2 weeks, we collected seawater samples directly behind individual sharks prior to taking a tissue biopsy sample from the same animal. Our data showed a 100% match between mtDNA sequences recovered in the eDNA and tissue sample for all 28 individuals sampled. In the seawater samples, >97% of all reads were assigned to six dominant haplotypes, and a clear dominant signal (~99% of sample reads) was recovered in each sample. Our study demonstrates accurate individual-level haplotyping from seawater eDNA. When DNA from one individual clearly dominates each eDNA sample, it provides many of the same opportunities for population genetic analyses as a tissue sample, potentially removing the need for tissue sampling. Our results show that eDNA approaches for population-level analyses have the potential to supply critical demographic data for the conservation and management of marine megafauna.
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Affiliation(s)
- Laurence Dugal
- Australian Institute of Marine Science, Crawley, WA, Australia.,The UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia
| | - Luke Thomas
- Australian Institute of Marine Science, Crawley, WA, Australia.,The UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia
| | | | | | - Tiffany Simpson
- Trace and Environmental DNA (TrEnD) Laboratory and eDNA Frontiers Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Simon Jarman
- The UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia.,School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | | | - Mark Meekan
- Australian Institute of Marine Science, Crawley, WA, Australia.,The UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia
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10
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Nam BH, Kim H, Seol D, Kim H, Noh ES, Kim EM, Noh JK, Kim YO, Park JY, Kwak W. Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow. PLoS One 2021; 16:e0247815. [PMID: 33826655 PMCID: PMC8026068 DOI: 10.1371/journal.pone.0247815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. Using PstI enzyme for genome reduction, we demonstrated the resultant library represented the whole genome region with even spacing, and as a result 16,603 single nucleotide variants (SNVs) were produced. Genetic diversity and population structure were investigated using several methods, and a strong genetic heterogeneity was observed in the Korean abalone populations. Additionally, by comparison of the variant sets among population groups, we were able to discover 26 Korean abalone population-specific SNVs, potentially associated with phenotype differences. This is the first study demonstrating the feasibility of GBS for population genetic study on H. discus. Our results will provide valuable data for the genetic conservation and management of wild abalone populations in Korea and help future GBS studies on the marine mollusks.
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Affiliation(s)
- Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Eun Mi Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jae Koo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Woori Kwak
- Genome, Inc, Seoul, Republic of Korea
- * E-mail:
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11
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Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs. Genes (Basel) 2021; 12:genes12030324. [PMID: 33668210 PMCID: PMC7995966 DOI: 10.3390/genes12030324] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 11/16/2022] Open
Abstract
Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes.
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12
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Womersley F, Hancock J, Perry CT, Rowat D. Wound-healing capabilities of whale sharks ( Rhincodon typus) and implications for conservation management. CONSERVATION PHYSIOLOGY 2021; 9:coaa120. [PMID: 33569175 PMCID: PMC7859907 DOI: 10.1093/conphys/coaa120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 10/08/2020] [Accepted: 12/03/2020] [Indexed: 05/03/2023]
Abstract
Wound healing is important for marine taxa such as elasmobranchs, which can incur a range of natural and anthropogenic wounds throughout their life history. There is evidence that this group shows a high capacity for external wound healing. However, anthropogenic wounds may become more frequent due to increasing commercial and recreational marine activities. Whale sharks are particularly at risk of attaining injuries given their use of surface waters and wildlife tourism interest. There is limited understanding as to how whale sharks recover from injuries, and often insights are confined to singular opportunistic observations. The present study makes use of a unique and valuable photographic data source from two whale shark aggregation sites in the Indian Ocean. Successional injury-healing progression cases were reviewed to investigate the characteristics of injuries and quantify a coarse healing timeframe. Wounds were measured over time using an image standardization method. This work shows that by Day 25 major injury surface area decreased by an average of 56% and the most rapid healing case showed a surface area reduction of 50% in 4 days. All wounds reached a point of 90% surface area closure by Day 35. There were differences in healing rate based on wound type, with lacerations and abrasions taking 50 and 22 days to reach 90% healing, respectively. This study provides baseline information for wound healing in whale sharks and the methods proposed could act as a foundation for future research. Use of a detailed classification system, as presented here, may also assist in ocean scale injury comparisons between research groups and aid reliable descriptive data. Such findings can contribute to discussions regarding appropriate management in aggregation areas with an aim to reduce the likelihood of injuries, such as those resulting from vessel collisions, in these regions or during movements between coastal waters.
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Affiliation(s)
- Freya Womersley
- 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, Southampton, SO17 1BJ, UK
- Marine Conservation Society Seychelles, Mahé, PO Box 384, Seychelles
- Corresponding author: Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK.
| | - James Hancock
- Maldives Whale Shark Research Programme, Popeshead Court Offices, Peter Lane, York, Yorkshire, Y01 8SU, UK
| | - Cameron T Perry
- Maldives Whale Shark Research Programme, Popeshead Court Offices, Peter Lane, York, Yorkshire, Y01 8SU, UK
| | - David Rowat
- Marine Conservation Society Seychelles, Mahé, PO Box 384, Seychelles
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13
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Kraft DW, Conklin EE, Barba EW, Hutchinson M, Toonen RJ, Forsman ZH, Bowen BW. Genomics versus mtDNA for resolving stock structure in the silky shark ( Carcharhinus falciformis). PeerJ 2020; 8:e10186. [PMID: 33150082 PMCID: PMC7585369 DOI: 10.7717/peerj.10186] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
Conservation genetic approaches for elasmobranchs have focused on regions of the mitochondrial genome or a handful of nuclear microsatellites. High-throughput sequencing offers a powerful alternative for examining population structure using many loci distributed across the nuclear and mitochondrial genomes. These single nucleotide polymorphisms are expected to provide finer scale and more accurate population level data; however, there have been few genomic studies applied to elasmobranch species. The desire to apply next-generation sequencing approaches is often tempered by the costs, which can be offset by pooling specimens prior to sequencing (pool-seq). In this study, we assess the utility of pool-seq by applying this method to the same individual silky sharks, Carcharhinus falciformis, previously surveyed with the mtDNA control region in the Atlantic and Indian Oceans. Pool-seq methods were able to recover the entire mitochondrial genome as well as thousands of nuclear markers. This volume of sequence data enabled the detection of population structure between regions of the Atlantic Ocean populations, undetected in the previous study (inter-Atlantic mitochondrial SNPs FST values comparison ranging from 0.029 to 0.135 and nuclear SNPs from 0.015 to 0.025). Our results reinforce the conclusion that sampling the mitochondrial control region alone may fail to detect fine-scale population structure, and additional sampling across the genome may increase resolution for some species. Additionally, this study shows that the costs of analyzing 4,988 loci using pool-seq methods are equivalent to the standard Sanger-sequenced markers and become less expensive when large numbers of individuals (>300) are analyzed.
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Affiliation(s)
- Derek W. Kraft
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Emily E. Conklin
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Evan W. Barba
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Melanie Hutchinson
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
- Joint Institute of Marine and Atmospheric Research, Pacific Islands Fisheries Science Center, NOAA, University of Hawai’i, Honolulu, HI, USA
| | - Robert J. Toonen
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Zac H. Forsman
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Brian W. Bowen
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
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14
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Sigsgaard EE, Jensen MR, Winkelmann IE, Møller PR, Hansen MM, Thomsen PF. Population-level inferences from environmental DNA-Current status and future perspectives. Evol Appl 2020; 13:245-262. [PMID: 31993074 PMCID: PMC6976968 DOI: 10.1111/eva.12882] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms. This approach offers several potential advantages compared with conventional tissue-based methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, eDNA approaches have been limited to single-marker studies of mitochondrial DNA (mtDNA), and the relationship between eDNA haplotype composition and true haplotype composition still needs to be thoroughly verified. This will require testing of bioinformatic and statistical software to correct for erroneous sequences, as well as biases and random variation in relative sequence abundances. However, eDNA-based population genetic methods have far-reaching potential for both basic and applied research. In this paper, we present a brief overview of the achievements of eDNA-based population genetics to date, and outline the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information. We discuss the challenges associated with eDNA samples as opposed to those of individual tissue samples and assess whether eDNA might offer additional types of information unobtainable with tissue samples. Lastly, we provide recommendations for determining whether an eDNA approach would be a useful and suitable choice in different research settings. We limit our discussion largely to contemporary aquatic systems, but the advantages, challenges, and perspectives can to a large degree be generalized to eDNA studies with a different spatial and temporal focus.
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Affiliation(s)
| | | | | | - Peter Rask Møller
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen ØDenmark
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15
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Sandoval-Castillo J. Conservation genetics of elasmobranchs of the Mexican Pacific Coast, trends and perspectives. ADVANCES IN MARINE BIOLOGY 2019; 83:115-157. [PMID: 31606069 DOI: 10.1016/bs.amb.2019.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One of the most critical threats to biodiversity is the high extinction rate driven by human activities. Reducing extinction rates requires the implementation of conservation programmes based on robust scientific data. Elasmobranchs are important ecological components of the ocean, and several species sustain substantial economic activities. Unfortunately, elasmobranchs are one of the most threatened and understudied animal taxa. The Mexican Pacific Coast (MPC) is a region with high elasmobranch diversity and is the seat of major elasmobranch fisheries. But it is also a developing region with several conservation and management challenges which require national and international attention. Here, we review the conservation genetics literature of elasmobranchs from the MPC. We present a synthesis of the works using samples from the region and emphasize the main gaps and biases in these data. In addition, we discuss the benefits and challenges of generating genomic information to improve the management and conservation of an elasmobranch biodiversity hotspot in a developing country. We found 47 elasmobranch genetic articles that cover <30% of the elasmobranch diversity in the region. These studies mainly used mitochondrial DNA sequences to analyse the genetic structure of commercially important and abundant species of the order Carcharhiniformes. Some of these papers also assessed mating systems, demographic parameters, and taxonomic uncertainties, all of which are important topics for efficient management decisions. In terms of conservation genetics, elasmobranchs from the MPC remain understudied. However, high-throughput sequencing technologies have increased the power and accessibility of genomic tools, even in developing countries such as Mexico. The tools described here provide information relevant for biodiversity conservation. Therefore, we strongly suggest that investment in genomic research will assist implementation of efficient management strategies. In time, this will reduce the extinction risk of the unique elasmobranch biodiversity from the MPC.
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Affiliation(s)
- Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
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16
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Van Cise AM, Baird RW, Baker CS, Cerchio S, Claridge D, Fielding R, Hancock-Hanser B, Marrero J, Martien KK, Mignucci-Giannoni AA, Oleson EM, Oremus M, Poole MM, Rosel PE, Taylor BL, Morin PA. Oceanographic barriers, divergence, and admixture: Phylogeography and taxonomy of two putative subspecies of short-finned pilot whale. Mol Ecol 2019; 28:2886-2902. [PMID: 31002212 DOI: 10.1111/mec.15107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/10/2019] [Indexed: 12/11/2022]
Abstract
Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short-finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the "Naisa" and "Shiho" forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short-finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short-finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally-distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.
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Affiliation(s)
- Amy M Van Cise
- Scripps Institution of Oceanography, La Jolla, California.,Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California.,Woods Hole Oceanographic Institution, Woods Hole, Massachusetts
| | | | - Charles Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, Oregon
| | | | - Diane Claridge
- Bahamas Marine Mammal Research Organisation, Abaco, Bahamas
| | - Russell Fielding
- Department of Earth & Environmental Systems, University of the South, Sewanee, Tennessee
| | - Brittany Hancock-Hanser
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
| | - Jacobo Marrero
- Asociación Tonina, Investigación y Divulgación del medio natural Marino, San Cristóbal de La Laguna, Spain.,BIOECOMAC, Department of Animal Biology, La Laguna University, La Laguna, Tenerife, Canary Islands, Spain
| | - Karen K Martien
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
| | | | - Erin M Oleson
- Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, Honolulu, Hawaii
| | - Marc Oremus
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, Oregon
| | | | - Patricia E Rosel
- Southeast Fisheries Science Center, National Marine Fisheries Service, NOAA, Lafayette, Louisiana
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
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17
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Almojil D, Cliff G, Spaet JLY. Weak population structure of the Spot-tail shark Carcharhinus sorrah and the Blacktip shark C. limbatus along the coasts of the Arabian Peninsula, Pakistan, and South Africa. Ecol Evol 2018; 8:9536-9549. [PMID: 30377521 PMCID: PMC6194305 DOI: 10.1002/ece3.4468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 07/22/2018] [Accepted: 07/23/2018] [Indexed: 11/24/2022] Open
Abstract
The increase in demand for shark meat and fins has placed shark populations worldwide under high fishing pressure. In the Arabian region, the spot-tail shark Carcharhinus sorrah and the Blacktip shark Carcharhinus limbatus are among the most exploited species. In this study, we investigated the population genetic structure of C. sorrah (n = 327) along the coasts of the Arabian Peninsula and of C. limbatus (n = 525) along the Arabian coasts, Pakistan, and KwaZulu-Natal, South Africa, using microsatellite markers (15 and 11 loci, respectively). Our findings support weak population structure in both species. Carcharhinus sorrah exhibited a fine structure, subdividing the area into three groups. The first group comprises all samples from Bahrain, the second from the UAE and Yemen, and the third from Oman. Similarly, C. limbatus exhibited population subdivision into three groups. The first group, comprising samples from Bahrain and Kuwait, was highly differentiated from the second and third groups, comprising samples from Oman, Pakistan, the UAE, and Yemen; and South Africa and the Saudi Arabian Red Sea, respectively. Population divisions were supported by pairwise F ST values and discriminant analysis of principal components (DAPC), but not by STRUCTURE. We suggest that the mostly low but significant pairwise F ST values in our study are suggestive of fine population structure, which is possibly attributable to behavioral traits such as residency in C. sorrah and site fidelity and philopatry in C. limbatus. However, for all samples obtained from the northern parts of the Gulf (Bahrain and/or Kuwait) in both species, the higher but significant pairwise F ST values could possibly be a result of founder effects during the Tethys Sea closure. Based on DAPC and F ST results, we suggest each population to be treated as independent management unit, as conservation concerns emerge.
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Affiliation(s)
| | - Geremy Cliff
- KwaZulu‐Natal Shark BoardUmhlanga, South Africa and School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Julia L. Y. Spaet
- Department of ZoologyUniversity of CambridgeCambridgeUK
- Red Sea Research CenterDivision of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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18
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Lait LA, Marshall HD, Carr SM. Phylogeographic mitogenomics of Atlantic cod Gadus morhua: Variation in and among trans-Atlantic, trans-Laurentian, Northern cod, and landlocked fjord populations. Ecol Evol 2018; 8:6420-6437. [PMID: 30038745 PMCID: PMC6053584 DOI: 10.1002/ece3.3873] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 12/21/2017] [Accepted: 01/01/2018] [Indexed: 01/16/2023] Open
Abstract
The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High-resolution, whole-genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans-Atlantic comparisons (ΦST = .029-.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000-.060) or defined management stocks (ΦST = .000-.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans-Atlantic phylogeography versus absence of such structure within various partitions of trans-Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near-identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153-.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200-250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.
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Affiliation(s)
- Linda A. Lait
- Genetics, Evolution, and Molecular Systematics LaboratoryDepartment of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
- Centre for Biodiversity Genomics, Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - H. Dawn Marshall
- Genetics, Evolution, and Molecular Systematics LaboratoryDepartment of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
| | - Steven M. Carr
- Genetics, Evolution, and Molecular Systematics LaboratoryDepartment of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
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19
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Diamant S, Rohner CA, Kiszka JJ, Guillemain d’Echon A, Guillemain d’Echon T, Sourisseau E, Pierce SJ. Movements and habitat use of satellite-tagged whale sharks off western Madagascar. ENDANGER SPECIES RES 2018. [DOI: 10.3354/esr00889] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Dudoit 'A, Iacchei M, Coleman RR, Gaither MR, Browne WE, Bowen BW, Toonen RJ. The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages. PeerJ 2018. [PMID: 29527409 PMCID: PMC5844259 DOI: 10.7717/peerj.4409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120-253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000-400,000 yr) than the Western Atlantic population (95% HPD = 300,000-760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000-1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species.
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Affiliation(s)
- 'Ale'alani Dudoit
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Zoology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Matthew Iacchei
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America.,Department of Natural Science, Hawai'i Pacific University, Kāne'ohe, HI, United States of America
| | - Richard R Coleman
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Zoology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Michelle R Gaither
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Current affiliation: Department of Biology, University of Central Florida, Orlando, FL, United States of America
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, United States of America
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
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21
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Selwyn JD, Johnson JE, Downey-Wall AM, Bynum AM, Hamner RM, Hogan JD, Bird CE. Simulations indicate that scores of lionfish ( Pterois volitans) colonized the Atlantic Ocean. PeerJ 2018; 5:e3996. [PMID: 29302383 PMCID: PMC5740958 DOI: 10.7717/peerj.3996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/13/2017] [Indexed: 11/20/2022] Open
Abstract
The invasion of the western Atlantic Ocean by the Indo-Pacific red lionfish (Pterois volitans) has had devastating consequences for marine ecosystems. Estimating the number of colonizing lionfish can be useful in identifying the introduction pathway and can inform policy decisions aimed at preventing similar invasions. It is well-established that at least ten lionfish were initially introduced. However, that estimate has not faced probabilistic scrutiny and is based solely on the number of haplotypes in the maternally-inherited mitochondrial control region. To rigorously estimate the number of lionfish that were introduced, we used a forward-time, Wright-Fisher, population genetic model in concert with a demographic, life-history model to simulate the invasion across a range of source population sizes and colonizing population fecundities. Assuming a balanced sex ratio and no Allee effects, the simulations indicate that the Atlantic population was founded by 118 (54–514, 95% HPD) lionfish from the Indo-Pacific, the Caribbean by 84 (22–328, 95% HPD) lionfish from the Atlantic, and the Gulf of Mexico by at least 114 (no upper bound on 95% HPD) lionfish from the Caribbean. Increasing the size, and therefore diversity, of the Indo-Pacific source population and fecundity of the founding population caused the number of colonists to decrease, but with rapidly diminishing returns. When the simulation was parameterized to minimize the number of colonists (high θ and relative fecundity), 96 (48–216, 95% HPD) colonists were most likely. In a more realistic scenario with Allee effects (e.g., 50% reduction in fecundity) plaguing the colonists, the most likely number of lionfish increased to 272 (106–950, 95% HPD). These results, in combination with other published data, support the hypothesis that lionfish were introduced to the Atlantic via the aquarium trade, rather than shipping. When building the model employed here, we made assumptions that minimize the number of colonists, such as the lionfish being introduced in a single event. While we conservatively modelled the introduction pathway as a single release of lionfish in one location, it is more likely that a combination of smaller and larger releases from a variety of aquarium trade stakeholders occurred near Miami, Florida, which could have led to even larger numbers of colonists than simulated here. Efforts to prevent future invasions via the aquarium trade should focus on the education of stakeholders and the prohibition of release, with adequate rewards for compliance and penalties for violations.
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Affiliation(s)
- Jason D Selwyn
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - John E Johnson
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Alan M Downey-Wall
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America.,Marine Science Center, Northeastern University, Nahant, MA, United States of America
| | - Adam M Bynum
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Rebecca M Hamner
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - J Derek Hogan
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America
| | - Christopher E Bird
- HoBi Lab, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States of America.,Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States of America
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22
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23
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Abstract
Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.
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McKinney JA, Hoffmayer ER, Holmberg J, Graham RT, Driggers WB, de la Parra-Venegas R, Galván-Pastoriza BE, Fox S, Pierce SJ, Dove ADM. Long-term assessment of whale shark population demography and connectivity using photo-identification in the Western Atlantic Ocean. PLoS One 2017; 12:e0180495. [PMID: 28817569 PMCID: PMC5560665 DOI: 10.1371/journal.pone.0180495] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 06/15/2017] [Indexed: 11/18/2022] Open
Abstract
The predictable occurrence of whale sharks, Rhincodon typus, has been well documented in several areas. However, information relating to their migratory patterns, residency times and connectivity across broad spatial scales is limited. In the present study photo-identification data is used to describe whale shark population structure and connectivity among known aggregation sites within the Western Central Atlantic Ocean (WCA). From 1999 to 2015, 1,361 individuals were identified from four distinct areas: the Yucatan Peninsula, Mexico (n = 1,115); Honduras (n = 146); northern Gulf of Mexico, United States (n = 112), and Belize (n = 49). Seasonal patterns in whale shark occurrence were evident with encounters occurring in the western Caribbean Sea earlier in the year than in the GOM. There was also a significant sex bias with 2.6 times more males present than females. Seventy sharks were observed in more than one area and the highest degree of connectivity occurred among three aggregation sites along the Mesoamerican Reef. Despite this, the majority of resightings occurred in the area where the respective sharks were first identified. This was true for the WCA as a whole, with the exception of Belize. Site fidelity was highest in Mexico. Maximum likelihood modelling resulted in a population estimate of 2,167 (95% c.i. 1585.21-2909.86) sharks throughout the entire region. This study is the first attempt to provide a broad, regional population estimate using photo-identification data from multiple whale shark aggregations. Our aim is to provide population metrics, along with the description of region-scale connectivity, that will help guide conservation action in the WCA. At a global level, rapidly growing photographic databases are allowing for researchers to look beyond the description of single aggregation sites and into the ocean-scale ecology of this pelagic species.
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Affiliation(s)
- Jennifer A. McKinney
- Louisiana Department of Wildlife and Fisheries, New Orleans, LA, United States of America
- * E-mail:
| | - Eric R. Hoffmayer
- National Marine Fisheries Service, Southeast Fisheries Science Center, Mississippi Laboratories, Pascagoula, MS, United States of America
| | | | | | - William B. Driggers
- National Marine Fisheries Service, Southeast Fisheries Science Center, Mississippi Laboratories, Pascagoula, MS, United States of America
| | | | | | - Steve Fox
- Utila Whale Shark Research, Utila, Bay Islands, Honduras
| | - Simon J. Pierce
- Wild Me, Portland, OR, United States of America
- Marine Megafauna Foundation, Truckee, CA, United States of America
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25
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Larson SE, Daly-Engel TS, Phillips NM. Review of Current Conservation Genetic Analyses of Northeast Pacific Sharks. ADVANCES IN MARINE BIOLOGY 2017; 77:79-110. [PMID: 28882215 DOI: 10.1016/bs.amb.2017.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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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26
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Read TD, Petit RA, Joseph SJ, Alam MT, Weil MR, Ahmad M, Bhimani R, Vuong JS, Haase CP, Webb DH, Tan M, Dove ADM. Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828. BMC Genomics 2017; 18:532. [PMID: 28709399 PMCID: PMC5513125 DOI: 10.1186/s12864-017-3926-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/06/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to as fishes. As both a phenotypic extreme and a member of the group Chondrichthyes - the sister group to the remaining gnathostomes, which includes all tetrapods and therefore also humans - its genome is of substantial comparative interest. Whale sharks are also listed as an endangered species on the International Union for Conservation of Nature's Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. RESULTS We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which yielded a draft assembly of 1,213,200 contigs and 997,976 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the holocephalan elephant shark. The whale shark contained a novel Toll-like-receptor (TLR) protein with sequence similarity to both the TLR4 and TLR13 proteins of mammals and TLR21 of teleosts. The data are publicly available on GenBank, FigShare, and from the NCBI Short Read Archive under accession number SRP044374. CONCLUSIONS This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.
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Affiliation(s)
- Timothy D Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Robert A Petit
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Sandeep J Joseph
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Md Tauqeer Alam
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - M Ryan Weil
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Maida Ahmad
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Ravila Bhimani
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Jocelyn S Vuong
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Chad P Haase
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - D Harry Webb
- , Georgia Aquarium, 225 Baker Street, Atlanta, GA, 30313, USA
| | - Milton Tan
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA. .,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.
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27
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Veríssimo A, Sampaio Í, McDowell JR, Alexandrino P, Mucientes G, Queiroz N, da Silva C, Jones CS, Noble LR. World without borders-genetic population structure of a highly migratory marine predator, the blue shark ( Prionace glauca). Ecol Evol 2017; 7:4768-4781. [PMID: 28690806 PMCID: PMC5496551 DOI: 10.1002/ece3.2987] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 01/21/2023] Open
Abstract
Highly migratory, cosmopolitan oceanic sharks often exhibit complex movement patterns influenced by ontogeny, reproduction, and feeding. These elusive species are particularly challenging to population genetic studies, as representative samples suitable for inferring genetic structure are difficult to obtain. Our study provides insights into the genetic population structure one of the most abundant and wide-ranging oceanic shark species, the blue shark Prionace glauca, by sampling the least mobile component of the populations, i.e., young-of-year and small juveniles (<2 year; N = 348 individuals), at three reported nursery areas, namely, western Iberia, Azores, and South Africa. Samples were collected in two different time periods (2002-2008 and 2012-2015) and were screened at 12 nuclear microsatellites and at a 899-bp fragment of the mitochondrial control region. Our results show temporally stable genetic homogeneity among the three Atlantic nurseries at both nuclear and mitochondrial markers, suggesting basin-wide panmixia. In addition, comparison of mtDNA CR sequences from Atlantic and Indo-Pacific locations also indicated genetic homogeneity and unrestricted female-mediated gene flow between ocean basins. These results are discussed in light of the species' life history and ecology, but suggest that blue shark populations may be connected by gene flow at the global scale. The implications of the present findings to the management of this important fisheries resource are also discussed.
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Affiliation(s)
- Ana Veríssimo
- CIBIO – U.P. – Research Center for Biodiversity and Genetic ResourcesVairãoPortugal
- Virginia Institute of Marine ScienceCollege of William and MaryGloucester PointVAUSA
| | - Íris Sampaio
- CIBIO – U.P. – Research Center for Biodiversity and Genetic ResourcesVairãoPortugal
| | - Jan R. McDowell
- Virginia Institute of Marine ScienceCollege of William and MaryGloucester PointVAUSA
| | - Paulo Alexandrino
- CIBIO – U.P. – Research Center for Biodiversity and Genetic ResourcesVairãoPortugal
| | - Gonzalo Mucientes
- CIBIO – U.P. – Research Center for Biodiversity and Genetic ResourcesVairãoPortugal
- Centro Tecnológico del MarFundación CETMARVigoSpain
| | - Nuno Queiroz
- CIBIO – U.P. – Research Center for Biodiversity and Genetic ResourcesVairãoPortugal
| | - Charlene da Silva
- Department of Agriculture, Forestry and FisheriesBranch FisheriesRogge BaySouth Africa
| | - Catherine S. Jones
- Institute of Biological and Environmental SciencesSchool of Biological SciencesUniversity of AberdeenAberdeenUK
| | - Leslie R. Noble
- Institute of Biological and Environmental SciencesSchool of Biological SciencesUniversity of AberdeenAberdeenUK
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28
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Abstract
Background Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments. Results A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P < 0.01). However, embryos derived from oocytes with Bos indicus mtDNA had the same ability to develop to the blastocyst stage and the levels of mtDNA copy number in their blastocysts were similar to blastocysts derived from oocytes harbouring Bos taurus mtDNA. Nevertheless, oocytes originating from the Bos indicus phenotype exhibited lower developmental potential due to low mtDNA copy number when compared with oocytes from cattle with a Bos taurus phenotype. Conclusions The phenotype of cattle is not always related to their mtDNA profiles. MtDNA profiles should be considered for breeding programmes as they also influence phenotypic traits and reproductive capacity in terms of oocyte quality. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0523-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kanokwan Srirattana
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Kieren McCosker
- Department of Primary Industry and Resources, Darwin, NT, 0800, Australia
| | - Tim Schatz
- Department of Primary Industry and Resources, Darwin, NT, 0800, Australia
| | - Justin C St John
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia. .,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia.
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29
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Vella N, Vella A. Population genetics of the deep-sea bluntnose sixgill shark, Hexanchus griseus, revealing spatial genetic heterogeneity. Mar Genomics 2017; 36:25-32. [PMID: 28602510 DOI: 10.1016/j.margen.2017.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/23/2017] [Accepted: 05/29/2017] [Indexed: 01/30/2023]
Abstract
Hexanchus griseus is a globally distributed deep-water shark species. It inhabits tropical and temperate waters throughout the world, including the Mediterranean Sea where it is by-caught by small-scale fisheries in the region. In this study, we analysed the genetic variation of H. griseus specimens collected from different areas within and outside the Mediterranean region, to assess its genetic connectivity. The mitochondrial DNA (mtDNA) sequence analysed in this study ranged from cytochrome b to 16S rRNA genes including the control region, the 12S rRNA gene and the interspersed tRNA genes in the region, covering a total of 3731 to 3914 nucleotides. Results have shown that this species exhibits geographically distinct maternal lineages, indicating population structure along geographical ranges. These findings reveal population subdivisions not only between the Pacific Ocean and the Atlantic Ocean, but also within the oceans and on a smaller scale within the Mediterranean Sea. This highlights the need to consider each population subdivision separately when designing management plans for the conservation of this species.
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Affiliation(s)
- Noel Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida MSD2080, Malta.
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida MSD2080, Malta.
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30
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Momigliano P, Harcourt R, Robbins WD, Jaiteh V, Mahardika GN, Sembiring A, Stow A. Genetic structure and signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Heredity (Edinb) 2017; 119:142-153. [PMID: 28422134 DOI: 10.1038/hdy.2017.21] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 02/17/2017] [Accepted: 03/02/2017] [Indexed: 01/01/2023] Open
Abstract
With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Using samples from Australia, Indonesia and oceanic reefs in the Indian Ocean, we established that large oceanic distances represent barriers to gene flow, whereas genetic differentiation on continental shelves follows an isolation by distance model. In Australia and Indonesia differentiation at nuclear SNPs was weak, with coral reefs acting as stepping stones maintaining connectivity across large distances. Differentiation of mtDNA was stronger, and more pronounced in females, suggesting sex-biased dispersal. Four independent tests identified a set of loci putatively under selection, indicating that grey reef sharks in eastern Australia are likely under different selective pressures to those in western Australia and Indonesia. Genetic distances averaged across all loci were uncorrelated with genetic distances calculated from outlier loci, supporting the conclusion that different processes underpin genetic divergence in these two data sets. This pattern of heterogeneous genomic differentiation, suggestive of local adaptation, has implications for the conservation of grey reef sharks; furthermore, it highlights that marine species showing little genetic differentiation at neutral loci may exhibit patterns of cryptic genetic structure driven by local selection.
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Affiliation(s)
- P Momigliano
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.,Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - R Harcourt
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - W D Robbins
- College of Marine and Environmental Science, James Cook University, Townsville, Queensland, Australia.,Wildlife Marine, Perth, Western Australia, Australia
| | - V Jaiteh
- Centre for Fish and Fisheries Research, Murdoch University, Murdoch, Western Australia, Australia
| | - G N Mahardika
- The Indonesian Biodiversity Research Centre, Udayana University, Denpasar, Bali, Indonesia
| | - A Sembiring
- The Indonesian Biodiversity Research Centre, Udayana University, Denpasar, Bali, Indonesia
| | - A Stow
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
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31
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32
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Sigsgaard EE, Nielsen IB, Bach SS, Lorenzen ED, Robinson DP, Knudsen SW, Pedersen MW, Jaidah MA, Orlando L, Willerslev E, Møller PR, Thomsen PF. Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA. Nat Ecol Evol 2016; 1:4. [DOI: 10.1038/s41559-016-0004] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/11/2016] [Indexed: 11/09/2022]
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Andrzejaczek S, Meeuwig J, Rowat D, Pierce S, Davies T, Fisher R, Meekan M. The ecological connectivity of whale shark aggregations in the Indian Ocean: a photo-identification approach. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160455. [PMID: 28018629 PMCID: PMC5180127 DOI: 10.1098/rsos.160455] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/18/2016] [Indexed: 05/19/2023]
Abstract
Genetic and modelling studies suggest that seasonal aggregations of whale sharks (Rhincodon typus) at coastal sites in the tropics may be linked by migration. Here, we used photo-identification (photo-ID) data collected by both citizen scientists and researchers to assess the connectedness of five whale shark aggregation sites across the entire Indian Ocean at timescales of up to a decade. We used the semi-automated program I3S (Individual Interactive Identification System) to compare photographs of the unique natural marking patterns of individual whale sharks collected from aggregations at Mozambique, the Seychelles, the Maldives, Christmas Island (Australia) and Ningaloo Reef (Australia). From a total of 6519 photos, we found no evidence of connectivity of whale shark aggregations at ocean-basin scales within the time frame of the study and evidence for only limited connectivity at regional (hundreds to thousands of kilometres) scales. A male whale shark photographed in January 2010 at Mozambique was resighted eight months later in the Seychelles and was the only one of 1724 individuals in the database to be photographed at more than one site. On average, 35% of individuals were resighted at the same site in more than one year. A Monte Carlo simulation study showed that the power of this photo-ID approach to document patterns of emigration and immigration was strongly dependent on both the number of individuals identified in aggregations and the size of resident populations.
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Affiliation(s)
- Samantha Andrzejaczek
- The UWA Oceans Institute, School of Environmental Systems Engineering, University of Western Australia, Crawley, Western Australia, Australia
- Australian Institute of Marine Science, Crawley, Western Australia, Australia
- Author for correspondence: Samantha Andrzejaczek e-mail:
| | - Jessica Meeuwig
- Centre for Marine Futures, Oceans Institute, University of Western Australia, Crawley, Western Australia, Australia
| | - David Rowat
- Marine Conservation Society Seychelles, Victoria, Mahe, Seychelles
| | - Simon Pierce
- Marine Megafauna Foundation, Truckee, CA 96161, USA
| | - Tim Davies
- MRAG Ltd, 18 Queen Street, London W1 J 5PN, UK
| | - Rebecca Fisher
- Australian Institute of Marine Science, Crawley, Western Australia, Australia
| | - Mark Meekan
- Australian Institute of Marine Science, Crawley, Western Australia, Australia
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34
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Bernard AM, Feldheim KA, Heithaus MR, Wintner SP, Wetherbee BM, Shivji MS. Global population genetic dynamics of a highly migratory, apex predator shark. Mol Ecol 2016; 25:5312-5329. [DOI: 10.1111/mec.13845] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Andrea M. Bernard
- Save Our Seas Shark Research Center Halmos College of Natural Sciences & Oceanography Nova Southeastern University 8000 N. Ocean Drive Dania Beach FL 33004 USA
| | - Kevin A. Feldheim
- The Field Museum of Natural History Pritzker Laboratory for Molecular Systematics and Evolution 1400 South Lake Shore Drive Chicago IL 60605 USA
| | - Michael R. Heithaus
- School of Environment and Society Florida International University Miami FL USA
| | - Sabine P. Wintner
- KwaZulu‐Natal Sharks Board Private Bag 2 Umhlanga Rocks 4320 South Africa
- Biomedical Resource Unit University of KwaZulu‐Natal Durban 4000 South Africa
| | - Bradley M. Wetherbee
- Department of Biological Sciences University of Rhode Island Kingston RI USA
- Guy Harvey Research Institute Dania Beach, FL 33004 USA
| | - Mahmood S. Shivji
- Save Our Seas Shark Research Center and Guy Harvey Research Institute Halmos College of Natural Sciences & Oceanography Nova Southeastern University 8000 N. Ocean Drive Dania Beach FL 33004 USA
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35
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Liu J, Ding X, Zeng Y, Yue Y, Guo X, Guo T, Chu M, Wang F, Han J, Feng R, Sun X, Niu C, Yang B, Guo J, Yuan C. Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences. PLoS One 2016; 11:e0159308. [PMID: 27463976 PMCID: PMC4963133 DOI: 10.1371/journal.pone.0159308] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 06/30/2016] [Indexed: 11/18/2022] Open
Abstract
The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries) is not well understood, and little is known about this species' genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D) were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- * E-mail:
| | - Xuezhi Ding
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Yufeng Zeng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Xian Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Min Chu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Fan Wang
- China Agricultural Veterinarian Biology Science and Technology Co. Ltd, Xujiaping, Lanzhou, China
| | - Jilong Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Ruilin Feng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Xiaoping Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Jian Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
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Camargo SM, Coelho R, Chapman D, Howey-Jordan L, Brooks EJ, Fernando D, Mendes NJ, Hazin FHV, Oliveira C, Santos MN, Foresti F, Mendonça FF. Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA. PLoS One 2016; 11:e0155623. [PMID: 27187497 PMCID: PMC4871334 DOI: 10.1371/journal.pone.0155623] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 05/02/2016] [Indexed: 11/18/2022] Open
Abstract
Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (ɸST = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers.
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Affiliation(s)
- Sâmia M. Camargo
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, (UNESP), Botucatu, São Paulo, Brasil
- Laboratório de Genética Pesqueira e Conservação, Instituto do Mar, Universidade Federal de São Paulo (UNIFESP), Santos, São Paulo, Brasil
| | - Rui Coelho
- Instituto Português do Mar e da Atmosfera (IPMA), Olhão, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade Algarve, Faro, Portugal
| | - Demian Chapman
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, New York, United States of America
| | - Lucy Howey-Jordan
- Microwave Telemetry, Inc., Columbia, Maryland, United States of America
| | - Edward J. Brooks
- Shark Research and Conservation Program, Cape Eleuthera Institute, Eleuthera, The Bahamas
| | - Daniel Fernando
- The Manta Trust, Catemwood House, Corscombe, Dorchester, United Kingdom
- Department of Biology and Environmental Science, Linnaeus University, Lund, Sweden
- Blue Resources, Colombo, Sri Lanka
| | - Natalia J. Mendes
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, (UNESP), Botucatu, São Paulo, Brasil
| | - Fabio H. V. Hazin
- Departamento de Pesca e Aquicultura, Universidade Federal Rural de Pernambuco, UFRPE, Recife, Pernambuco, Brasil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, (UNESP), Botucatu, São Paulo, Brasil
| | - Miguel N. Santos
- Instituto Português do Mar e da Atmosfera (IPMA), Olhão, Portugal
| | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, (UNESP), Botucatu, São Paulo, Brasil
| | - Fernando F. Mendonça
- Laboratório de Genética Pesqueira e Conservação, Instituto do Mar, Universidade Federal de São Paulo (UNIFESP), Santos, São Paulo, Brasil
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Faulks L, Östman Ö. Genetic Diversity and Hybridisation between Native and Introduced Salmonidae Fishes in a Swedish Alpine Lake. PLoS One 2016; 11:e0152732. [PMID: 27032100 PMCID: PMC4816307 DOI: 10.1371/journal.pone.0152732] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 03/18/2016] [Indexed: 01/11/2023] Open
Abstract
Understanding the processes underlying diversification can aid in formulating appropriate conservation management plans that help maintain the evolutionary potential of taxa, particularly under human-induced activities and climate change. Here we assessed the microsatellite genetic diversity and structure of three salmonid species, two native (Arctic charr, Salvelinus alpinus and brown trout, Salmo trutta) and one introduced (brook charr, Salvelinus fontinalis), from an alpine lake in sub-arctic Sweden, Lake Ånn. The genetic diversity of the three species was similar and sufficiently high from a conservation genetics perspective: corrected total heterozygosity, H’T = 0.54, 0.66, 0.60 and allelic richness, AR = 4.93, 5.53 and 5.26 for Arctic charr, brown trout and brook charr, respectively. There were indications of elevated inbreeding coefficients in brown trout (GIS = 0.144) and brook charr (GIS = 0.129) although sibling relationships were likely a confounding factor, as a high proportion of siblings were observed in all species within and among sampling locations. Overall genetic structure differed between species, Fst = 0.01, 0.02 and 0.04 in Arctic charr, brown trout and brook charr respectively, and there was differentiation at only a few specific locations. There was clear evidence of hybridisation between the native Arctic charr and the introduced brook charr, with 6% of individuals being hybrids, all of which were sampled in tributary streams. The ecological and evolutionary consequences of the observed hybridisation are priorities for further research and the conservation of the evolutionary potential of native salmonid species.
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Affiliation(s)
- Leanne Faulks
- Department of Ecology and Genetics – Animal Ecology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Sugadaira Montane Research Centre, University of Tsukuba, Sugadaira-kogen 1278–294, Ueda, Nagano, 386–2204, Japan
- * E-mail:
| | - Örjan Östman
- Department of Ecology and Genetics – Animal Ecology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Department of Aquatic Resources, Institute of Coastal Research, Skolvägen 6, 742 42 Öregrund, Sweden
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Abstract
Among terrestrial arthropods, the dragonfly species Pantala flavescens is remarkable due to their nearly global distribution and extensive migratory ranges; the largest of any known insect. Capable of migrating across oceans, the potential for high rates of gene flow among geographically distant populations is significant. It has been hypothesized that P. flavescens may be a global panmictic population but no sufficient genetic evidence has been collected thus far. Through a population genetic analysis of P. flavescens samples from North America, South America, and Asia, the current study aimed to examine the extent at which gene flow is occurring on a global scale and discusses the implications of the genetic patterns we uncovered on population structure and genetic diversity of the species. This was accomplished using PCR-amplified cytochrome oxidase one (CO1) mitochondrial DNA data to reconstruct phylogenetic trees, a haplotype network, and perform molecular variance analyses. Our results suggested high rates of gene flow are occurring among all included geographic regions; providing the first significant evidence that Pantala flavescens should be considered a global panmictic population.
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Sequeira AMM, Thums M, Brooks K, Meekan MG. Error and bias in size estimates of whale sharks: implications for understanding demography. ROYAL SOCIETY OPEN SCIENCE 2016; 3:150668. [PMID: 27069656 PMCID: PMC4821267 DOI: 10.1098/rsos.150668] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 02/18/2016] [Indexed: 05/30/2023]
Abstract
Body size and age at maturity are indicative of the vulnerability of a species to extinction. However, they are both difficult to estimate for large animals that cannot be restrained for measurement. For very large species such as whale sharks, body size is commonly estimated visually, potentially resulting in the addition of errors and bias. Here, we investigate the errors and bias associated with total lengths of whale sharks estimated visually by comparing them with measurements collected using a stereo-video camera system at Ningaloo Reef, Western Australia. Using linear mixed-effects models, we found that visual lengths were biased towards underestimation with increasing size of the shark. When using the stereo-video camera, the number of larger individuals that were possibly mature (or close to maturity) that were detected increased by approximately 10%. Mean lengths calculated by each method were, however, comparable (5.002 ± 1.194 and 6.128 ± 1.609 m, s.d.), confirming that the population at Ningaloo is mostly composed of immature sharks based on published lengths at maturity. We then collated data sets of total lengths sampled from aggregations of whale sharks worldwide between 1995 and 2013. Except for locations in the East Pacific where large females have been reported, these aggregations also largely consisted of juveniles (mean lengths less than 7 m). Sightings of the largest individuals were limited and occurred mostly prior to 2006. This result highlights the urgent need to locate and quantify the numbers of mature male and female whale sharks in order to ascertain the conservation status and ensure persistence of the species.
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Affiliation(s)
- Ana M. M. Sequeira
- IOMRC and The UWA Oceans Institute, School of Animal Biology and Centre for Marine Futures, University of Western Australia (M470), 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Michele Thums
- School of Civil, Environmental and Mining Engineering and UWA Oceans Institute, University of Western Australia (M470), 35 Stirling Highway, Crawley, Western Australia 6009, Australia
- Australian Institute of Marine Science, c/o UWA Oceans Institute (MO96), 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Kim Brooks
- Australian Institute of Marine Science, c/o UWA Oceans Institute (MO96), 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Mark G. Meekan
- Australian Institute of Marine Science, c/o UWA Oceans Institute (MO96), 35 Stirling Highway, Crawley, Western Australia 6009, Australia
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Díaz-Jaimes P, Bayona-Vásquez NJ, Adams DH, Uribe-Alcocer M. Complete mitochondrial DNA genome of bonnethead shark, Sphyrna tiburo, and phylogenetic relationships among main superorders of modern elasmobranchs. Meta Gene 2016; 7:48-55. [PMID: 27014583 PMCID: PMC4794228 DOI: 10.1016/j.mgene.2015.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 11/30/2022] Open
Abstract
Elasmobranchs are one of the most diverse groups in the marine realm represented by 18 orders, 55 families and about 1200 species reported, but also one of the most vulnerable to exploitation and to climate change. Phylogenetic relationships among main orders have been controversial since the emergence of the Hypnosqualean hypothesis by Shirai (1992) that considered batoids as a sister group of sharks. The use of the complete mitochondrial DNA (mtDNA) may shed light to further validate this hypothesis by increasing the number of informative characters. We report the mtDNA genome of the bonnethead shark Sphyrna tiburo, and compare it with mitogenomes of other 48 species to assess phylogenetic relationships. The mtDNA genome of S. tiburo, is quite similar in size to that of congeneric species but also similar to the reported mtDNA genome of other Carcharhinidae species. Like most vertebrate mitochondrial genomes, it contained 13 protein coding genes, two rRNA genes and 22 tRNA genes and the control region of 1086 bp (D-loop). The Bayesian analysis of the 49 mitogenomes supported the view that sharks and batoids are separate groups.
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Key Words
- ATP, Adenosine triphosphate
- Bonnethead
- CO, Cytochrome oxidase
- Cytb, Cytochrome B
- D-loop, Control region
- Hypnosqualea hypothesis
- ML, Maximum likelihood
- Mitogenome
- ND, Nicotine adenine dehydrogenase
- PCR, Polymerase chain reaction
- Phylogeny
- bp, Base pairs
- mt, Mitochondrial
- myr, Million years
- rRNA, Ribosomal RNA
- tRNA, Transference RNA
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Affiliation(s)
- Píndaro Díaz-Jaimes
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
| | - Natalia J. Bayona-Vásquez
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
| | - Douglas H. Adams
- Florida Fish and Wildlife Conservation Commission, Fish and
Wildlife Research Institute, 1220 Prospect Avenue, Suite 285, Melbourne, FL
32901, USA
| | - Manuel Uribe-Alcocer
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
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Vargas SM, Jensen MP, Ho SYW, Mobaraki A, Broderick D, Mortimer JA, Whiting SD, Miller J, Prince RIT, Bell IP, Hoenner X, Limpus CJ, Santos FR, FitzSimmons NN. Phylogeography, Genetic Diversity, and Management Units of Hawksbill Turtles in the Indo-Pacific. J Hered 2015; 107:199-213. [PMID: 26615184 DOI: 10.1093/jhered/esv091] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/06/2015] [Indexed: 12/24/2022] Open
Abstract
Hawksbill turtle (Eretmochelys imbricata) populations have experienced global decline because of a history of intense commercial exploitation for shell and stuffed taxidermied whole animals, and harvest for eggs and meat. Improved understanding of genetic diversity and phylogeography is needed to aid conservation. In this study, we analyzed the most geographically comprehensive sample of hawksbill turtles from the Indo-Pacific Ocean, sequencing 766 bp of the mitochondrial control region from 13 locations (plus Aldabra, n = 4) spanning over 13500 km. Our analysis of 492 samples revealed 52 haplotypes distributed in 5 divergent clades. Diversification times differed between the Indo-Pacific and Atlantic lineages and appear to be related to the sea-level changes that occurred during the Last Glacial Maximum. We found signals of demographic expansion only for turtles from the Persian Gulf region, which can be tied to a more recent colonization event. Our analyses revealed evidence of transoceanic migration, including connections between feeding grounds from the Atlantic Ocean and Indo-Pacific rookeries. Hawksbill turtles appear to have a complex pattern of phylogeography, showing a weak isolation by distance and evidence of multiple colonization events. Our novel dataset will allow mixed-stock analyses of hawksbill turtle feeding grounds in the Indo-Pacific by providing baseline data needed for conservation efforts in the region. Eight management units are proposed in our study for the Indo-Pacific region that can be incorporated in conservation plans of this critically endangered species.
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Affiliation(s)
- Sarah M Vargas
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia.
| | - Michael P Jensen
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Simon Y W Ho
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Asghar Mobaraki
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Damien Broderick
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Jeanne A Mortimer
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Scott D Whiting
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Jeff Miller
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Robert I T Prince
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Ian P Bell
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Xavier Hoenner
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Colin J Limpus
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Fabrício R Santos
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
| | - Nancy N FitzSimmons
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil (Vargas); School of Biological Sciences, University of Sydney, Sydney, Australia (Vargas and Ho); National Research Council under contract to Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA (Jensen); Natural History Museum and Genetic Resources Bureau, Department of the Environment Pardisan Eco-Park, Hemmat Highway, Tehran, Iran (Mobaraki); Department of Zoology, The University of Queensland, St Lucia, Australia (Broderick); Department of Biology, University of Florida, Gainesville, FL (Mortimer); Department of Land Resource Management, Palmerston, Australia (Whiting); Biological Research and Education Consultants, Missoula, MT (Miller); Marine Science Program, Department of Parks and Wildlife, Kensington, Australia (Prince); Marine Turtle Conservation Threatened Species Unit, Department of Environment and Heritage Protection, Queensland, Australia (Bell); Integrated Marine Observing System (IMOS), University of Tasmania, Private Bag 110, Hobart, TAS 7001, Australia (Hoenner); Department of Environment and Heritage Protection, Brisbane, Australia (Limpus); Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil (Santos); and Natural Environments Program, Queensland Museum, South Brisbane, Australia (FitzSimmons). Damien Broderick is now at 247 Anne St, Brisbane, QLD 4000, Australia. Jeanne A. Mortimer is now at PO Box 1443, Victoria, Mahé, Seychelles. Scott Whiting is now at Marine Science Program, Department of Parks and Wildlife, 17 Dick Perry Ave, Kensington, WA 6151, Australia
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Sanzogni RL, Meekan MG, Meeuwig JJ. Multi-Year Impacts of Ecotourism on Whale Shark (Rhincodon typus) Visitation at Ningaloo Reef, Western Australia. PLoS One 2015; 10:e0127345. [PMID: 26398338 PMCID: PMC4580324 DOI: 10.1371/journal.pone.0127345] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/14/2015] [Indexed: 11/18/2022] Open
Abstract
In-water viewing of sharks by tourists has become a popular and lucrative industry. There is some concern that interactions with tourists with ecotourism operations might harm sharks through disruption of behaviours. Here, we analysed five years of whale shark (Rhincodon typus) encounter data by an ecotourism industry at Ningaloo Reef, Western Australia, to assess the impact of ecotourism interactions on shark visitation, within the context of the biological and physical oceanography of the region. Our data base consisted of 2823 encounter records for 951 individual whale sharks collected by ecotourism operators between 2007 and 2011. We found that total encounters per whale shark and encounters per boat trip increased through time. On average, whale sharks re-encountered in subsequent years were encountered earlier, stayed longer and tended to be encountered more often within a season than sharks that were only encountered in a single year. Sequential comparisons between years did not show any patterns consistent with disturbance and the rate of departure of whale sharks from the aggregation was negatively correlated to the number of operator trips. Overall, our analysis of this multi-year data base found no evidence that interactions with tourists affected the likelihood of whale shark re-encounters and that instead, physical and biological environmental factors had a far greater influence on whale shark visitation rates. Our approach provides a template for assessing the effects of ecotourism interactions and environmental factors on the visitation patterns of marine megafauna over multiple years.
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Affiliation(s)
- R. L. Sanzogni
- School of Animal Biology (Oceans Institute), the University of Western Australia, 35 Stirling Hwy, Crawley, Western Australia, 6009, Australia
- Australian Institute of Marine Science c/o UWA Oceans Institute (MO96), 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - M. G. Meekan
- Australian Institute of Marine Science c/o UWA Oceans Institute (MO96), 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
- * E-mail:
| | - J. J. Meeuwig
- School of Animal Biology (Oceans Institute), the University of Western Australia, 35 Stirling Hwy, Crawley, Western Australia, 6009, Australia
- Centre for Marine Futures (Oceans Institute), the University of Western Australia, 35 Stirling Hwy, Crawley, Western Australia, 6009, Australia
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43
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Gaither MR, Bernal MA, Fernandez-Silva I, Mwale M, Jones SA, Rocha C, Rocha LA. Two deep evolutionary lineages in the circumtropical glasseye Heteropriacanthus cruentatus (Teleostei, Priacanthidae) with admixture in the south-western Indian Ocean. JOURNAL OF FISH BIOLOGY 2015; 87:715-727. [PMID: 26333139 DOI: 10.1111/jfb.12754] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 06/19/2015] [Indexed: 06/05/2023]
Abstract
A phylogeographic study of the circumtropical glasseye Heteropriacanthus cruentatus was conducted. Molecular analyses indicate two mitochondrial cytochrome c oxidase subunit I (coI) lineages that are 10·4% divergent: one in the western Atlantic (Caribbean) and another that was detected across the Indo-Pacific. A fixed single nucleotide polymorphism (SNP) was detected at a nuclear locus (S7 ribosomal protein) and is consistent with this finding. There is evidence of recent dispersal from the Atlantic to the Indian Ocean with individuals of mixed lineages detected in South Africa and the Mozambique Channel. Using coalescent analyses of the mitochondrial dataset, time of divergence between lineages was estimated to be c. 15·3 million years. The deep divergence between these two lineages indicates distinct evolutionary units, however, due to the lack of morphological differences and evidence of hybridization between lineages, taxonomic revision is not suggested at this time.
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Affiliation(s)
- M R Gaither
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, U.K
| | - M A Bernal
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
- University of Texas Marine Science Institute, 750 Channel View Drive, Port Aransas, TX, 78373, U.S.A
| | - I Fernandez-Silva
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - M Mwale
- South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown, 6140, South Africa
- National Zoological Gardens of South Africa, P. O. Box 754, Pretoria, 001, South Africa
| | - S A Jones
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
| | - C Rocha
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
| | - L A Rocha
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
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44
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Chabot CL. Microsatellite loci confirm a lack of population connectivity among globally distributed populations of the tope shark Galeorhinus galeus (Triakidae). JOURNAL OF FISH BIOLOGY 2015; 87:371-385. [PMID: 26179946 DOI: 10.1111/jfb.12727] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 05/18/2015] [Indexed: 06/04/2023]
Abstract
This study used 11 polymorphic nuclear microsatellite loci to determine the population connectivity of five geographically isolated populations of tope shark Galeorhinus galeus (Africa, Australia, North America, South America and western Europe). Genetic analyses revealed significant structure among all populations indicating a lack of population connectivity. These findings indicate that globally distributed populations of G. galeus are isolated and should be managed as distinct, independent stocks.
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Affiliation(s)
- C L Chabot
- Department of Biology, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA, 91330, U.S.A
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45
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Martinez-Takeshita N, Purcell CM, Chabot CL, Craig MT, Paterson CN, Hyde JR, Allen LG. A Tale of Three Tails: Cryptic Speciation in a Globally Distributed Marine Fish of the GenusSeriola. COPEIA 2015. [DOI: 10.1643/ci-124-224] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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46
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Spaet JLY, Jabado RW, Henderson AC, Moore ABM, Berumen ML. Population genetics of four heavily exploited shark species around the Arabian Peninsula. Ecol Evol 2015; 5:2317-32. [PMID: 26120422 PMCID: PMC4475365 DOI: 10.1002/ece3.1515] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 01/31/2023] Open
Abstract
The northwestern Indian Ocean harbors a number of larger marine vertebrate taxa that warrant the investigation of genetic population structure given remarkable spatial heterogeneity in biological characteristics such as distribution, behavior, and morphology. Here, we investigate the genetic population structure of four commercially exploited shark species with different biological characteristics (Carcharhinus limbatus, Carcharhinus sorrah, Rhizoprionodon acutus, and Sphyrna lewini) between the Red Sea and all other water bodies surrounding the Arabian Peninsula. To assess intraspecific patterns of connectivity, we constructed statistical parsimony networks among haplotypes and estimated (1) population structure; and (2) time of most recent population expansion, based on mitochondrial control region DNA and a total of 20 microsatellites. Our analysis indicates that, even in smaller, less vagile shark species, there are no contemporary barriers to gene flow across the study region, while historical events, for example, Pleistocene glacial cycles, may have affected connectivity in C. sorrah and R. acutus. A parsimony network analysis provided evidence that Arabian S. lewini may represent a population segment that is distinct from other known stocks in the Indian Ocean, raising a new layer of conservation concern. Our results call for urgent regional cooperation to ensure the sustainable exploitation of sharks in the Arabian region.
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Affiliation(s)
- Julia L Y Spaet
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology23955-6900, Thuwal, Saudi Arabia
| | - Rima W Jabado
- Gulf Elasmo ProjectP.O. Box 29588, Dubai, United Arab Emirates
| | - Aaron C Henderson
- Department of Marine Science & Fisheries, College of Agricultural & Marine Sciences, Sultan Qaboos UniversityMuscat, Oman
| | - Alec B M Moore
- RSK Environment Ltd, Spring LodgeHelsby, Cheshire, WA6 0AR, UK
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology23955-6900, Thuwal, Saudi Arabia
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47
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Zhang H, Zhang X, Han Z, Gao T. AFLP markers suggest low population genetic differentiation of the black rockfish Sebastes schlegelii. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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48
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da Silva Ferrette BL, Mendonça FF, Coelho R, de Oliveira PGV, Hazin FHV, Romanov EV, Oliveira C, Santos MN, Foresti F. High connectivity of the crocodile shark between the Atlantic and Southwest Indian Oceans: highlights for conservation. PLoS One 2015; 10:e0117549. [PMID: 25689742 PMCID: PMC4331560 DOI: 10.1371/journal.pone.0117549] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 12/27/2014] [Indexed: 12/02/2022] Open
Abstract
Among the various shark species that are captured as bycatch in commercial fishing operations, the group of pelagic sharks is still one of the least studied and known. Within those, the crocodile shark, Pseudocarcharias kamoharai, a small-sized lamnid shark, is occasionally caught by longline vessels in certain regions of the tropical oceans worldwide. However, the population dynamics of this species, as well as the impact of fishing mortality on its stocks, are still unknown, with the crocodile shark currently one of the least studied of all pelagic sharks. Given this, the present study aimed to assess the population structure of P. kamoharai in several regions of the Atlantic and Indian Oceans using genetic molecular markers. The nucleotide composition of the mitochondrial DNA control region of 255 individuals was analyzed, and 31 haplotypes were found, with an estimated diversity Hd = 0.627, and a nucleotide diversity π = 0.00167. An analysis of molecular variance (AMOVA) revealed a fixation index ΦST = -0.01118, representing an absence of population structure among the sampled regions of the Atlantic Ocean, and between the Atlantic and Indian Oceans. These results show a high degree of gene flow between the studied areas, with a single genetic stock and reduced population variability. In panmictic populations, conservation efforts can be concentrated in more restricted areas, being these representative of the total biodiversity of the species. When necessary, this strategy could be applied to the genetic maintenance of P. kamoharai.
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Affiliation(s)
- Bruno Lopes da Silva Ferrette
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Brasil
| | - Fernando Fernandes Mendonça
- Departamento de Ciências do Mar, Instituto do Mar, Universidade Federal de São Paulo, UNIFESP, Santos, Brasil
- * E-mail:
| | - Rui Coelho
- Instituto Português do Mar e da Atmosfera, IPMA, IP, Olhão, Portugal
- Centro de Ciências do Mar, CCMAR, Universidade Algarve, Faro, Portugal
| | | | - Fábio Hissa Vieira Hazin
- Departamento de Pesca e Aquicultura, Universidade Federal Rural de Pernambuco, UFRPE, Pernambuco, Recife, Brasil
| | - Evgeny V. Romanov
- Centre Technique d'Appui à la Pêche RéUNionnaise (CAP RUN), Association Réunionnaise de Développement de l'Aquaculture (ARDA), Le Port, Île de la Réunion, France
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Brasil
| | | | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Brasil
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49
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Chen W, Du K, He S. Genetic structure and historical demography of Schizothorax nukiangensis (Cyprinidae) in continuous habitat. Ecol Evol 2015; 5:984-95. [PMID: 25750724 PMCID: PMC4338980 DOI: 10.1002/ece3.1413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 01/07/2015] [Accepted: 01/12/2015] [Indexed: 11/24/2022] Open
Abstract
Geographic distance, different living habitats or Pleistocene climatic oscillations have frequently been found to shape population genetic structure in many species. The genetic structure of Schizothorax nukiangensis, a high altitude, valuable fish species, which is distributed throughout the Nujiang River, was investigated by mitochondrial DNA sequence analysis. The cytochrome c oxidase subunit I (COI), cytochrome b (cytb), and the mitochondrial control region (MCR) of S. nukiangensis were concatenated for examination of population structure and demographic history. The concatenated data set (2405 bp) implied a pronounced genetic population structure (overall FST = 0.149) and defined two population units. Strong differentiation was detected between the Sanjiangkou (SJK) population and other populations due to environmental heterogeneity, dispersal ability, and/or glacial cycles. Additional DNA sequencing of the nuclear RAG2 gene also examined significant differentiation between two units and between SJK and the upstream populations (U-unit). Recent expansion events suggest that S. nukiangensis may have undergone a rapid increase during warm interglacial periods. Surprisingly, S. nukiangensis appears to have undergone an obvious expansion during the last glaciations (LG) for cold hardiness and a sharp contraction from 1.5 ka to the present. However, two population units exhibited different reflections during the LG, which might be closely related to their living habitats and cold hardiness. A clear pattern of isolation by distance was detected in S. nukiangensis due to feeding habits, limited dispersal ability, and/or philopatry. It is vitally important that more attention be given to S. nukiangensis due to low genetic diversity, lack of gene flow, and recent population contraction.
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Affiliation(s)
- Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan, Hubei, 430072, China ; University of Chinese Academy of Sciences Beijing, 100049, People's Republic of China
| | - Kang Du
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan, Hubei, 430072, China ; University of Chinese Academy of Sciences Beijing, 100049, People's Republic of China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan, Hubei, 430072, China
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Garrick RC, Kajdacsi B, Russello MA, Benavides E, Hyseni C, Gibbs JP, Tapia W, Caccone A. Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises. Ecol Evol 2015; 5:676-94. [PMID: 25691990 PMCID: PMC4328771 DOI: 10.1002/ece3.1388] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 02/05/2023] Open
Abstract
Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (N e ) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ∽100 generations, ∽2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical N e of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary N e were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, N e generally represented ∽0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.
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Affiliation(s)
- Ryan C Garrick
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - Brittney Kajdacsi
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Michael A Russello
- Department of Biology, University of British ColumbiaOkanagan Campus, Kelowna, British Columbia, V1V 1V7, Canada
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Chaz Hyseni
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - James P Gibbs
- College of Environmental Science and Forestry, State University of New YorkSyracuse, New York, 13210
| | - Washington Tapia
- Department of Applied Research, Galápagos National Park ServicePuerto Ayora, Galápagos, Ecuador
- Biodiver S.A. ConsultoresKm 5 Vía a Baltra, Isla Santa Cruz, Galápagos, Ecuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
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