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Whitney JL, Coleman RR, Deakos MH. Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian reef Manta Rays. BMC Ecol Evol 2023; 23:31. [PMID: 37422622 PMCID: PMC10329317 DOI: 10.1186/s12862-023-02130-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 06/07/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Reef manta rays (Mobula alfredi) are globally distributed in tropical and subtropical seas. Their life history traits (slow growth, late maturity, low reproductive output) make them vulnerable to perturbations and therefore require informed management strategies. Previous studies have reported wide-spread genetic connectivity along continental shelves suggesting high gene flow along continuous habitats spanning hundreds of kilometers. However, in the Hawaiian Islands, tagging and photo-identification evidence suggest island populations are isolated despite proximity, a hypothesis that has not yet been evaluated with genetic data. RESULTS This island-resident hypothesis was tested by analyzing whole mitogenome haplotypes and 2048 nuclear single nucleotide polymorphisms (SNPs) between M. alfredi (n = 38) on Hawai'i Island and Maui Nui (the 4-island complex of Maui, Moloka'i, Lāna'i and Kaho'olawe). Strong divergence in the mitogenome (ΦST = 0.488) relative to nuclear genome-wide SNPs (neutral FST = 0.003; outlier FST = 0.186), and clustering of mitochondrial haplotypes among islands provides robust evidence that female reef manta rays are strongly philopatric and do not migrate between these two island groups. Combined with restricted male-mediated migration, equivalent to a single male moving between islands every 2.2 generations (~ 64 years), we provide evidence these populations are significantly demographically isolated. Estimates of contemporary effective population size (Ne) are 104 (95% CI: 99-110) in Hawai'i Island and 129 (95% CI: 122-136) in Maui Nui. CONCLUSIONS Concordant with evidence from photo identification and tagging studies, these genetic results indicate reef manta rays in Hawai'i have small, genetically-isolated resident island populations. We hypothesize that due to the Island Mass Effect, large islands provide sufficient resources to support resident populations, thereby making crossing deep channels separating island groups unnecessary. Small effective population size, low genetic diversity, and k-selected life history traits make these isolated populations vulnerable to region-specific anthropogenic threats, which include entanglement, boat strikes, and habitat degradation. The long-term persistence of reef manta rays in the Hawaiian Islands will require island-specific management strategies.
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Affiliation(s)
- Jonathan L Whitney
- National Oceanic and Atmospheric Administration, Pacific Islands Fisheries Science Center, Honolulu, Hawai'i, USA.
| | - Richard R Coleman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Sciences, University of Miami, Miami, FL, USA
| | - Mark H Deakos
- Hawai'i Association for Marine Education and Research, Lahaina, Maui, Hawai'i, USA
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Marshall AD, Flam AL, Cullain N, Carpenter M, Conradie J, Venables SK. Southward range extension and transboundary movements of reef manta rays Mobula alfredi along the east African coastline. JOURNAL OF FISH BIOLOGY 2023; 102:628-634. [PMID: 36514854 DOI: 10.1111/jfb.15290] [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: 06/29/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Opportunistic in-water and aerial surveys in South Africa and the analysis of contributed citizen science data have extended the known range of reef manta rays Mobula alfredi along the eastern coast of Africa by 140 km (to Mdumbi Beach) and verified the first transboundary movements for the species. Additionally, six new long-range dispersal records have provided evidence of connectivity with the M. alfredi population off the Inhambane coastline of Mozambique. Five of these records captured one-way movements, the longest of which was an individual that travelled 505 km from Praia do Tofo to Sodwana Bay with 301 days between sightings. A single individual made a return trip between Závora, Mozambique and Sodwana Bay, South Africa (a total distance of ~870 km). These findings support the Convention on Migratory Species listing for the species, suggesting regional transboundary management units are warranted for this wide-ranging elasmobranch.
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Affiliation(s)
| | - Anna L Flam
- Marine Megafauna Foundation, West Palm Beach, Florida, USA
| | - Nakia Cullain
- Marine Megafauna Foundation, West Palm Beach, Florida, USA
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Michelle Carpenter
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
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Harned SP, Bernard AM, Salinas‐de‐León P, Mehlrose MR, Suarez J, Robles Y, Bessudo S, Ladino F, López Garo A, Zanella I, Feldheim KA, Shivji MS. Genetic population dynamics of the critically endangered scalloped hammerhead shark ( Sphyrna lewini) in the Eastern Tropical Pacific. Ecol Evol 2022; 12:e9642. [PMID: 36619714 PMCID: PMC9797937 DOI: 10.1002/ece3.9642] [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: 06/14/2022] [Revised: 11/17/2022] [Accepted: 11/30/2022] [Indexed: 12/30/2022] Open
Abstract
The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young-of-year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure suggesting that scalloped hammerheads in this ETP region comprise a single genetic stock. Galápagos aggregations of adults were not comprised of related individuals, suggesting that kinship does not play a role in the formation of the repeated, annual gatherings at these remote offshore locations. Despite high levels of fisheries exploitation of this species in the ETP, the adult scalloped hammerheads here showed greater genetic diversity compared with adult conspecifics from other parts of the species' global distribution. A phylogeographic analysis of available, globally sourced, mitochondrial control region sequence data (n = 1818 sequences) revealed that scalloped hammerheads comprise three distinct matrilines corresponding to the three major world ocean basins, highlighting the need for conservation of these evolutionarily unique lineages. This study provides the first view of the genetic properties of a scalloped hammerhead aggregation, and the largest sample size-based investigation of population structure and phylogeography of this species in the ETP to date.
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Affiliation(s)
- Sydney P. Harned
- Save Our Seas Foundation Shark Research Center and Guy Harvey Research InstituteNova Southeastern UniversityDania BeachFloridaUSA
| | - Andrea M. Bernard
- Save Our Seas Foundation Shark Research Center and Guy Harvey Research InstituteNova Southeastern UniversityDania BeachFloridaUSA
| | - Pelayo Salinas‐de‐León
- Save Our Seas Foundation Shark Research Center and Guy Harvey Research InstituteNova Southeastern UniversityDania BeachFloridaUSA,Charles Darwin Research StationCharles Darwin FoundationGalápagos IslandsEcuador
| | - Marissa R. Mehlrose
- Save Our Seas Foundation Shark Research Center and Guy Harvey Research InstituteNova Southeastern UniversityDania BeachFloridaUSA
| | - Jenifer Suarez
- Direccion Parque Nacional GalápagosDepartamento de Ecosistemas MarinosIslas GalápagosEcuador
| | - Yolani Robles
- Universidad de Panamá, Centro Regional Universitario de VeraguasSan Martín de PorresPanama
| | - Sandra Bessudo
- Fundacion Malpelo y Otros Ecosistemas MarinosBogotáColombia
| | - Felipe Ladino
- Fundacion Malpelo y Otros Ecosistemas MarinosBogotáColombia
| | - Andrés López Garo
- Asociación Conservacionista Misión Tiburon, Playas del CocoCarrilloGuanacasteCosta Rica
| | - Ilena Zanella
- Asociación Conservacionista Misión Tiburon, Playas del CocoCarrilloGuanacasteCosta Rica
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and EvolutionField Museum of Natural HistoryChicagoIllinoisUSA
| | - Mahmood S. Shivji
- Save Our Seas Foundation Shark Research Center and Guy Harvey Research InstituteNova Southeastern UniversityDania BeachFloridaUSA
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Gordon L, Vierus T. First photographic evidence of oceanic manta rays ( Mobula birostris) at two locations in the Fiji islands. PeerJ 2022; 10:e13883. [PMID: 36097525 PMCID: PMC9463998 DOI: 10.7717/peerj.13883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/21/2022] [Indexed: 01/18/2023] Open
Abstract
Until the revision of the genus Manta in 2009, when a second manta species (Manta alfredi) was resurrected based on morphological and meristic data, all available records in Fijian literature were recorded as Manta birostris. Subsequently, documented sightings were recorded as M. alfredi. Another reclassification of the genus Manta was undertaken in 2018 when both manta ray species (Manta alfredi, Manta birostris) were moved to Mobula based on phylogenetic analysis. Here, we present the first unequivocal evidence of oceanic manta ray (Mobula birostris) occurrence in Fijian waters. In November 2018, two individuals were sighted foraging in Laucala Bay, a large lagoon adjacent to Suva, the capital city of Fiji. Subsequently, three more individuals were sighted in December 2018, two individuals in July 2020, at least six individuals were observed in November 2021, and eight individuals in May/June 2022, all foraging in the same geographical area. Unique ventral identification patterns could be obtained for nine individuals, and all nine individuals have been re-sighted since first identification, with one individual being documented in 2018, 2020, 2021 and 2022. Two additional individuals were recorded in the Yasawa Island Group in the west of Fiji while passing through and foraging in a channel between Drawaqa and Naviti Island in April and September 2020. We provide photographic identification of ten M. birostris individuals from two sites and discuss our findings in the context of local environmental parameters and other recorded sightings in the South Pacific region. In light of the global extinction risk of M. birostris and the recent reclassification from Vulnerable to Endangered on the Red List of Threatened Species, the expansion of their known distribution range to Fijian waters and the recurrence of individuals over consecutive years in the same location adds valuable information for the development of effective and data-driven conservation strategies.
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Carpenter M, Cullain N, Venables SK, Tibiriçá Y, Griffiths C, Marshall AD. Evidence of Závora Bay as a critical site for reef manta rays, Mobula alfredi, in southern Mozambique. JOURNAL OF FISH BIOLOGY 2022; 101:628-639. [PMID: 35691006 PMCID: PMC9544570 DOI: 10.1111/jfb.15132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
The largest known reef manta ray (Mobula alfredi) population in Africa has been monitored for more than 20 years at several locations on the coast of the Inhambane Province in southern Mozambique. Nonetheless, before this study, little had been reported on the population dynamics of M. alfredi from Závora, a remote bay in the region. Photographic mark-recapture was used to investigate the size and structure of M. alfredi that aggregate at "Red Sands," a reef cleaning station in Závora Bay. An 11 year photographic data set was used to identify 583 M. alfredi individuals between 2010 and 2021. More than half of M. alfredi individuals were resighted at least once, with most encounters (up to 18 for one individual) occurring during the peak sighting period in July-November each year. An even sex ratio was observed, 44% females and 50% males, with no significant difference in resightings between the sexes. Pollock's robust design population models were used to estimate annual abundance, emigration, annual apparent survival and capture probability at Red Sands from July to November over a 6 year period (2016-2021). Abundance estimates varied year to year, ranging from 35 (95% c.i. [30, 45]) up to 233 (95% c.i. [224, 249]) M. alfredi individuals. Given the seasonal affinity of M. alfredi observed at Red Sands, this study highlights the importance of understanding fine-scale site use within the larger home range of this population to develop local management strategies.
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Affiliation(s)
- Michelle Carpenter
- Department of Biological SciencesUniversity of Cape TownCape TownSouth Africa
| | - Nakia Cullain
- Marine Megafauna FoundationWest Palm BeachFloridaUSA
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | | | - Yara Tibiriçá
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizCádizSpain
| | - Charles Griffiths
- Department of Biological SciencesUniversity of Cape TownCape TownSouth Africa
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De Araujo Barbosa V, Graham SE, Smith BJ, Hogg ID, McGaughran A. Assessing population genetic structure of three New Zealand stream insects using mitochondrial and nuclear DNA markers. Genome 2022; 65:427-441. [PMID: 35785969 DOI: 10.1139/gen-2022-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Assessing genetic differentiation among natural populations can aid understanding of dispersal patterns and connectivity among habitats. Several molecular markers have become increasingly popular in determining population genetic structure for this purpose. Here, we compared the resolution of mitochondrial cytochrome c oxidase subunit I (COI) and nuclear single nucleotide polymorphism (SNP) markers for detecting population structure among stream insects at small spatial scales. Individuals of three endemic taxa - Coloburiscus humeralis (Ephemeroptera), Zelandobius confusus (Plecoptera), and Hydropsyche fimbriata (Trichoptera) - were collected from forested streams that flow across open pasture in the North Island of New Zealand. Both COI and SNP data indicated limited population structure across the study area, and small differences observed among these species were likely related to their putative dispersal abilities. For example, fine-scale genetic differentiation between and among neighbouring stream populations for H. fimbriata suggests that gene flow, and hence dispersal, may be more limited for this species relative to the others. Based on the generally similar results provided by both types of markers, we suggest that either COI or SNP markers can provide suitable initial estimates of fine-scale population genetic differentiation in stream insects.
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Affiliation(s)
| | - S Elizabeth Graham
- National Institute of Water and Atmospheric Research Hamilton, 418394, Hamilton, Waikato, New Zealand;
| | - Brian J Smith
- National Institute of Water and Atmospheric Research Hamilton, 418394, Hamilton, New Zealand;
| | - Ian D Hogg
- University of Waikato, 3717, Department of Science, Hamilton, New Zealand.,Polar Knowledge Canada, 513970, Canadian High Arctic Research Station, Cambridge Bay, Nunavut, Canada;
| | - Angela McGaughran
- University of Waikato, 3717, School of Science, Hamilton, Waikato, New Zealand;
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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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