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Luna-Ortiz A, Marín-Capuz G, Abella E, Crespo-Picazo JL, Escribano F, Félix G, Giralt S, Tomás J, Pegueroles C, Pascual M, Carreras C. New colonisers drive the increase of the emerging loggerhead turtle nesting in Western Mediterranean. Sci Rep 2024; 14:1506. [PMID: 38233518 PMCID: PMC10794258 DOI: 10.1038/s41598-024-51664-w] [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: 08/04/2023] [Accepted: 01/06/2024] [Indexed: 01/19/2024] Open
Abstract
The loggerhead sea turtle (Caretta caretta) is sensitive to climate change and is responding by colonising the Western Mediterranean. To understand the rapid nesting increase in recent years in Spain, we sampled 45 hatchlings from 8 nests between 2016 and 2019. We sequenced a mtDNA D-loop region, genotyped 2291 SNPs using 2bRAD and collected data on clutch size, hatching success, and incubation duration. We confirmed that the colonisation has a Mediterranean and Atlantic mixed origin and we detected that these nests were laid by different females, except for two nests within the same season. Our results suggest that the recent increase in nesting is due to an increase in the number of colonising individuals rather than females born in the same area returning to breed. We hypothesize that this increase in the number of colonisers results from successful conservation efforts, feminisation of the populations of origin and earlier sexual maturation. However, the percentage of offspring females produced in Spain suggests that future returning individuals will aid to the settlement of the new population. These results allow defining the current status of this colonisation although future efforts are needed to detect remigrants to confirm the establishment of a resident population.
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Affiliation(s)
- Astrid Luna-Ortiz
- Department of Genetics, Microbiology and Statistics and IrBio, University of Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
| | - Gisela Marín-Capuz
- Department of Genetics, Microbiology and Statistics and IrBio, University of Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
| | - Elena Abella
- BETA Technological Center, University of Vic - Central University of Catalonia, Carretera Roda 70, 08500, Vic, Spain
| | - José Luis Crespo-Picazo
- Fundació Oceanogràfic de la Comunitat Valenciana, Ciutat de les Arts i les Ciències, 46013, Valencia, Spain
| | - Fernando Escribano
- Centro de Recuperación de Fauna Silvestre "El Valle", Ctra. Subida a El Valle, 62, 30150, La Alberca de las Torres, Murcia, Spain
| | - Guillem Félix
- Consorci per a la Recuperació de la Fauna de les Illes Balears (COFIB), Servei de Protecció d'Espècies. Conselleria Agricultura, Pesca i Medi Natural. Govern de les Illes Balears, Carretera Palma- Sineu, Km 15,400, 07142, Santa Eugènia, Balearic Islands, Spain
| | - Silvia Giralt
- Fundación para la Conservación y la Recuperación de Animales Marinos (CRAM), 08820, El Prat de Llobregat, Barcelona, Spain
| | - Jesús Tomás
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, University of Valencia, Apdo, 22085, 46071, Valencia, Spain
| | - Cinta Pegueroles
- Department of Genetics, Microbiology and Statistics and IrBio, University of Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
| | - Marta Pascual
- Department of Genetics, Microbiology and Statistics and IrBio, University of Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
| | - Carlos Carreras
- Department of Genetics, Microbiology and Statistics and IrBio, University of Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain.
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2
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Vella A, Vella N. Conservation Genetics of the Loggerhead Sea Turtle, Caretta caretta, from the Central Mediterranean: An Insight into the Species' Reproductive Behaviour in Maltese Waters. Animals (Basel) 2023; 14:137. [PMID: 38200868 PMCID: PMC10778046 DOI: 10.3390/ani14010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Loggerhead sea turtle, Caretta caretta (Linnaeus, 1758), nestlings were investigated through specimens found dead either after hatching or unhatched (n = 120) from eight nests around the Maltese islands (Central Mediterranean). Molecular genetics was used to conduct maternity and paternity tests of the collected specimens utilizing expanded mitochondrial DNA sequences from the control region (858 bp) and 25 microsatellite loci (12 dinucleotide loci and 13 tetranucleotide loci). Mitochondrial data produced two haplotypes, CC-A2.1 and CC-A3.1, with the most common haplotype being present in seven nests. Microsatellite data revealed the identity of six different females that were involved in the deposition of the eggs in the eight turtle nests analysed. This confirms that two females laid multiple nests. Additionally, microsatellite data allowed for the determination of multiple paternity, with one clutch being sired by two fathers. These results are useful for monitoring the genetic diversity of loggerhead sea turtle nestlings and of the turtle mothers and fathers contributing to future turtle offspring, which rely on Maltese sandy beaches for their successful start to life. Effective conservation management benefits from merging scientific knowledge with effective measures at potential nesting sites to avoid losses of nestlings caused by human negligence.
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Affiliation(s)
- Adriana Vella
- Conservation Biology Research Group, Department of Biology, Faculty of Science, University of Malta, MSD 2080 Msida, Malta
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3
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Lasala JA, Macksey MC, Mazzarella KT, Main KL, Foote JJ, Tucker AD. Forty years of monitoring increasing sea turtle relative abundance in the Gulf of Mexico. Sci Rep 2023; 13:17213. [PMID: 37821522 PMCID: PMC10567714 DOI: 10.1038/s41598-023-43651-4] [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: 06/08/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023] Open
Abstract
Longitudinal data sets for population abundance are essential for studies of imperiled organisms with long life spans or migratory movements, such as marine turtles. Population status trends are crucial for conservation managers to assess recovery effectiveness. A direct assessment of population growth is the enumeration of nesting numbers and quantifying nesting attempts (successful nests/unsuccessful attempts) and emergence success (number of hatchlings leaving the nest) because of the substantial annual variations due to nest placement, predation, and storm activity. We documented over 133,000 sea turtle crawls for 50.9 km of Florida Gulf of Mexico coastline from 1982 to 2021 for a large loggerhead turtle nesting aggregation and a recovering remnant population of green sea turtles. Over time both species have emerged to nest significantly earlier in the year and green sea turtle nesting seasons have extended. Nest counts and hatchling production for both species have significantly increased, but the rate of emergence success of hatchlings leaving nests has not changed for loggerheads and has declined for green sea turtles. Sea level rise and coastal developments undoubtedly influence coastal habitats in the long-term, impacting nest site selection and potential recruitment from the loss of emerged hatchlings. However, the present indications for steady Gulf of Mexico recovery of loggerhead and green sea turtles counter findings of the Florida Atlantic coasts. This study indicates that effective conservation practices can be detected within time scales of 1-2 turtle generations.
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Affiliation(s)
- Jacob Andrew Lasala
- Sea Turtle Conservation and Research Program, Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA.
| | - Melissa C Macksey
- Sea Turtle Conservation and Research Program, Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
| | - Kristen T Mazzarella
- Sea Turtle Conservation and Research Program, Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
| | - Kevan L Main
- Sea Turtle Conservation and Research Program, Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
| | - Jerris J Foote
- Sea Turtle Conservation and Research Program, Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
- Parks, Recreation and Natural Resources, Sarasota County, 1660 Ringling Boulevard, Sarasota, FL, 34236, USA
| | - Anton D Tucker
- Sea Turtle Conservation and Research Program, Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
- Marine Science Program, Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA, Australia
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4
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Chang G, Jones S, Leelakumari S, Ashkani J, Culibrk L, O'Neill K, Tse K, Cheng D, Chuah E, McDonald H, Kirk H, Pandoh P, Pari S, Angelini V, Kyle C, Bertorelle G, Zhao Y, Mungall A, Moore R, Vilaça S, Jones S. The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758. F1000Res 2023; 12:336. [PMID: 37455852 PMCID: PMC10338980 DOI: 10.12688/f1000research.131283.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
We present a genome assembly of Caretta caretta (the Loggerhead sea turtle; Chordata, Testudines, Cheloniidae), generated from genomic data from two unrelated females. The genome sequence is 2.13 gigabases in size. The assembly has a busco completion score of 96.1% and N50 of 130.95 Mb. The majority of the assembly is scaffolded into 28 chromosomal representations with a remaining 2% of the assembly being excluded from these.
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Affiliation(s)
- Glenn Chang
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Samantha Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Sreeja Leelakumari
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Jahanshah Ashkani
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Kane Tse
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Helen McDonald
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Heather Kirk
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Sauro Pari
- Fondazione Cetacea Onlus, Riccione, RN, 47838, Italy
| | | | - Christopher Kyle
- Forensic Science Department, Trent University, Peterborough, Ontario, K9L 0G2, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, K9L 0G2, Canada
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, FE, 44121, Italy
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Andrew Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Sibelle Vilaça
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, K9L 0G2, Canada
| | - Steven Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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5
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Buss DL, Atmore LM, Zicos MH, Goodall-Copestake WP, Brace S, Archer FI, Baker CS, Barnes I, Carroll EL, Hart T, Kitchener AC, Sabin R, Sremba AL, Weir CR, Jackson JA. Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales. Genes (Basel) 2023; 14:1038. [PMID: 37239398 PMCID: PMC10218396 DOI: 10.3390/genes14051038] [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: 03/31/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.
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Affiliation(s)
- Danielle L. Buss
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
| | - Lane M. Atmore
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Maria H. Zicos
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - William P. Goodall-Copestake
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
- Scottish Association for Marine Science, Oban PA37 1QA, UK
| | - Selina Brace
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Frederick I. Archer
- National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - C. Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Ian Barnes
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Emma L. Carroll
- Te Kura Mātauranga Koiora—School of Biological Sciences, University of Auckland Waipapa Taumata Rau, Auckland 1010, New Zealand
| | - Tom Hart
- Department of Zoology, University of Oxford, Mansfield Road, Oxford OX1 3SZ, UK
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Richard Sabin
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Angela L. Sremba
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Caroline R. Weir
- Falklands Conservation, Ross Road, Stanley F1QQ 1ZZ, Falkland Islands
| | - Jennifer A. Jackson
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
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Vélez-Rubio GM, Prosdocimi L, López-Mendilaharsu M, Caraccio MN, Fallabrino A, LaCasella EL, Dutton PH. Natal Origin and Spatiotemporal Distribution of Leatherback Turtle ( Dermochelys coriacea) Strandings at a Foraging Hotspot in Temperate Waters of the Southwest Atlantic Ocean. Animals (Basel) 2023; 13:ani13081285. [PMID: 37106848 PMCID: PMC10134985 DOI: 10.3390/ani13081285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Leatherback turtles migrate long distances between nesting beaches and distant foraging areas worldwide. This study analyzes the genetic diversity, life history stage, spatiotemporal distribution, and associated threats of a foraging aggregation in the Southwest Atlantic Ocean. A total of 242 leatherbacks stranded or bycaught by artisanal fisheries were recorded from 1997 to 2021 in Uruguay, with sizes ranging from 110.0 to 170.0 cm carapace lengths, indicating that the aggregation is composed of large juveniles and adults. Results of Bayesian mixed-stock analysis show that leatherbacks come primarily from the West African rookeries, based on mitochondrial DNA sequences obtained from 59 of the turtles representing seven haplotypes, including a novel one (Dc1.7). The main threat identified in the area is the fisheries bycatch but most of the carcasses observed were badly decomposed. There was significant seasonal and interannual variability in strandings that is likely associated with the availability of prey and the intensity of the fishing effort. Taken together, these findings reinforce the importance of these South American foraging areas for leatherbacks and the need to determine regional habitat use and migratory routes across the broader Atlantic region, in order to develop effective conservation measures to mitigate threats both at nesting beaches and foraging areas.
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Affiliation(s)
- Gabriela M Vélez-Rubio
- Karumbé NGO, Av. Rivera 3245, Montevideo 11600, Uruguay
- Sección Oceanografía y Ecología Marina, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
- Departamento MEDIA, Centro Universitario Regional del Este (CURE), Universidad de la República, Ruta 9 Intersección con Ruta 15, Rocha 27000, Uruguay
| | - Laura Prosdocimi
- Karumbé NGO, Av. Rivera 3245, Montevideo 11600, Uruguay
- Laboratorio de Ecología, Comportamiento y Mamíferos Marinos (LECyMM), Museo Argentino de Ciencias Naturales (MACN-CONICET), Av. Ángel Gallardo 470, CABA, Buenos Aires C1405DJR, Argentina
| | | | | | | | - Erin L LaCasella
- NOAA-National Marine Fisheries Service, Southwest Fisheries Science Center, 8901 La Jolla Shores Dr, La Jolla, CA 92037, USA
| | - Peter H Dutton
- NOAA-National Marine Fisheries Service, Southwest Fisheries Science Center, 8901 La Jolla Shores Dr, La Jolla, CA 92037, USA
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7
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Vilaça ST, Maroso F, Lara P, de Thoisy B, Chevallier D, Arantes LS, Santos FR, Bertorelle G, Mazzoni CJ. Evidence of backcross inviability and mitochondrial DNA paternal leakage in sea turtle hybrids. Mol Ecol 2023; 32:628-643. [PMID: 36336814 DOI: 10.1111/mec.16773] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
Hybridization is known to be part of many species' evolutionary history. Sea turtles have a fascinating hybridization system in which species separated by as much as 43 million years are still capable of hybridizing. Indeed, the largest nesting populations in Brazil of loggerheads (Caretta caretta) and hawksbills (Eretmochelys imbricata) have a high incidence of hybrids between these two species. A third species, olive ridleys (Lepidochelys olivacea), is also known to hybridize although at a smaller scale. Here, we used restriction site-associated DNA sequencing (RAD-Seq) markers, mitogenomes, and satellite-telemetry to investigate the patterns of hybridization and introgression in the Brazilian sea turtle population and their relationship with the migratory behaviours between feeding and nesting aggregations. We also explicitly test if the mixing of two divergent genomes in sea turtle hybrids causes mitochondrial paternal leakage. We developed a new species-specific PCR-assay capable of detecting mitochondrial DNA (mtDNA) inheritance from both parental species and performed ultra-deep sequencing to estimate the abundance of each mtDNA type. Our results show that all adult hybrids are first generation (F1) and most display a loggerhead migratory behaviour. We detected paternal leakage in F1 hybrids and different proportions of mitochondria from maternal and paternal species. Although previous studies showed no significant fitness decrease in hatchlings, our results support genetically-related hybrid breakdown possibly caused by cytonuclear incompatibility. Further research on hybrids from other populations in addition to Brazil and between different species will show if backcross inviability and mitochondrial paternal leakage is observed across sea turtle species.
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Affiliation(s)
- Sibelle T Vilaça
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany.,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Francesco Maroso
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Paulo Lara
- Fundação Projeto Tamar, Mata de São João, Bahia, Brazil
| | | | - Damien Chevallier
- BOREA, National Museum of Natural History (MNHN), CNRS 8067, SU, IRD 207, UCN, UA, Martinique, France
| | - Larissa Souza Arantes
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Fabricio R Santos
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Camila J Mazzoni
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
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8
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Incorporating distance metrics and temporal trends to refine mixed stock analysis. Sci Rep 2022; 12:20569. [PMID: 36446818 PMCID: PMC9709048 DOI: 10.1038/s41598-022-24279-2] [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: 07/26/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
The distribution of marine organisms is shaped by geographic distance and oceanographic features like currents. Among migratory species, individuals from multiple populations may share feeding habitats seasonally or across life stages. Here, we introduce a modification for many-to-many mixed stock models to include distance between breeding and foraging sites as an ecological covariate and evaluate how the composition of green turtle, Chelonia mydas, juvenile mixed stock aggregations changed in response to population growth over time. Our modified many-to-many model is more informative and generally tightens credible intervals over models that do not incorporate distance. Moreover, we identified a decrease in genetic diversity in a Florida nesting site and two juvenile aggregations. Mixed stock aggregations in central Florida have changed from multiple sources to fewer dominant source populations over the past ~ 20 years. We demonstrate that shifts in contributions from source populations to mixed stock aggregations are likely associated with nesting population growth. Furthermore, our results highlight the importance of long-term monitoring and the need for periodical reassessment of reproductive populations and juvenile aggregations. Understanding how mixed stock aggregations change over time and how different life stages are connected is fundamental for the development of successful conservation plans for imperiled species.
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9
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Phillips KF, Martin KR, Stahelin GD, Savage AE, Mansfield KL. Genetic variation among sea turtle life stages and species suggests connectivity among ocean basins. Ecol Evol 2022; 12:e9426. [PMID: 36329816 PMCID: PMC9618668 DOI: 10.1002/ece3.9426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
Regional genetic differentiation of mitochondrial lineages occurs in migratory species with natal philopatry such as sea turtles. However, early juvenile dispersal represents a key opportunity for gene flow and colonization of new regions through founder events, making it an important yet under-studied life stage. To assess connectivity among sea turtle life stages and ocean basins, we sequenced mitochondrial DNA (mtDNA) fragments from 35 juveniles sampled in the Gulf of Mexico from the rarely observed dispersal stage across three species: green turtles (Chelonia mydas; n = 30), hawksbills (Eretmochelys imbricata; n = 3), and loggerheads (Caretta caretta; n = 2). We estimated green turtle rookery contributions using a many-to-many Bayesian mixed stock analysis that incorporated dispersal probabilities based on rookery size and transport via ocean currents. We assembled a gene tree including 709 distinct mtDNA control region haplotypes from the literature for all seven extant sea turtle species to assess gaps in life-stage data across ocean basins, as well as contextualize the lineages we sampled from dispersing juveniles. Our results indicate a high likelihood that green turtles sampled in the Gulf of Mexico originated from rookeries along the coast of Mexico, with smaller contributions from Costa Rica and Suriname. The gene tree analysis yielded species-level relationships consistent with those presented previously, while intra-species relationships between lineages and ocean basins differed, particularly within loggerhead and green turtle clades. Our results highlight the lack of genetic data from juvenile sea turtles, especially the early dispersal stage, and the potential for these data to answer broader questions of connectivity and diversification across species and lineages.
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Affiliation(s)
| | | | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaOrlandoFloridaUSA
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10
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Hochscheid S, Maffucci F, Abella E, Bradai MN, Camedda A, Carreras C, Claro F, de Lucia GA, Jribi I, Mancusi C, Marco A, Marrone N, Papetti L, Revuelta O, Urso S, Tomás J. Nesting range expansion of loggerhead turtles in the Mediterranean: Phenology, spatial distribution, and conservation implications. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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11
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Global phylogeography of ridley sea turtles (Lepidochelys spp.): evolution, demography, connectivity, and conservation. CONSERV GENET 2022; 23:995-1010. [PMID: 36397975 PMCID: PMC9659502 DOI: 10.1007/s10592-022-01465-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 07/15/2022] [Indexed: 11/29/2022]
Abstract
Globally distributed marine taxa are well suited for investigations of biogeographic impacts on genetic diversity, connectivity, and population demography. The sea turtle genus Lepidochelys includes the wide-ranging and abundant olive ridley (L. olivacea), and the geographically restricted and ‘Critically Endangered’ Kemp’s ridley (L. kempii). To investigate their historical biogeography, we analyzed a large dataset of mitochondrial DNA (mtDNA) sequences from olive (n = 943) and Kemp’s (n = 287) ridleys, and genotyped 15 nuclear microsatellite loci in a global sample of olive ridleys (n = 285). We found that the ridley species split ~ 7.5 million years ago, before the Panama Isthmus closure. The most ancient mitochondrial olive ridley lineage, located in the Indian Ocean, was dated to ~ 2.2 Mya. Both mitochondrial and nuclear markers revealed significant structure for olive ridleys between Atlantic (ATL), East Pacific (EP), and Indo-West Pacific (IWP) areas. However, the divergence of mtDNA clades was very recent (< 1 Mya) with low within- clade diversity, supporting a recurrent extinction-recolonization model for these ocean regions. All data showed that ATL and IWP groups were more closely related than those in the EP, with mtDNA data supporting recent recolonization of the ATL from the IWP. Individual olive ridley dispersal between the ATL, EP, and IN/IWP could be interpreted as more male- than female-biased, and genetic diversity was lowest in the Atlantic Ocean. All populations showed signs of recent expansion, and estimated time frames were concordant with their recent colonization history. Investigating species abundance and distribution changes over time is central to evolutionary biology, and this study provides a historical biogeographic context for marine vertebrate conservation and management.
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12
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Farrell JA, Whitmore L, Mashkour N, Rollinson Ramia DR, Thomas RS, Eastman CB, Burkhalter B, Yetsko K, Mott C, Wood L, Zirkelbach B, Meers L, Kleinsasser P, Stock S, Libert E, Herren R, Eastman S, Crowder W, Bovery C, Anderson D, Godfrey D, Condron N, Duffy DJ. Detection and population genomics of sea turtle species via non-invasive environmental DNA analysis of nesting beach sand tracks and oceanic water. Mol Ecol Resour 2022; 22:2471-2493. [PMID: 35377560 DOI: 10.1111/1755-0998.13617] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/12/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022]
Abstract
Elusive aquatic wildlife, such as endangered sea turtles, are difficult to monitor and conserve. As novel molecular and genetic technologies develop, it is possible to adapt and optimize them for wildlife conservation. One such technology is environmental (e)DNA - the detection of DNA shed from organisms into their surrounding environments. We developed species-specific green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtle probe-based qPCR assays, which can detect and quantify sea turtle eDNA in controlled (captive tank water and sand samples) and free ranging (oceanic water samples and nesting beach sand) settings. eDNA detection complemented traditional in-water sea turtle monitoring by enabling detection even when turtles were not visually observed. Furthermore, we report that high throughput shotgun sequencing of eDNA sand samples enabled sea turtle population genetic studies and pathogen monitoring, demonstrating that non-invasive eDNA techniques are viable and efficient alternatives to biological sampling (e.g. biopsies and blood draws). Genetic information was obtained from sand many hours after nesting events, without having to observe or interact with the target individual. This greatly reduces the sampling stress experienced by nesting mothers and emerging hatchlings, and avoids sacrificing viable eggs for genetic analysis. The detection of pathogens from sand indicates significant potential for increased wildlife disease monitoring capacity and viral variant surveillance. Together, these results demonstrate the potential of eDNA approaches to ultimately help understand and conserve threatened species such as sea turtles.
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Affiliation(s)
- Jessica A Farrell
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Liam Whitmore
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - Narges Mashkour
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Devon R Rollinson Ramia
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Rachel S Thomas
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Catherine B Eastman
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Brooke Burkhalter
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Kelsey Yetsko
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biological Sciences, Florida International University, Miami, FL, 33181, USA
| | - Cody Mott
- Inwater Research Group Inc, Jensen Beach, FL, 34957, USA
| | - Larry Wood
- Florida Hawksbill Project, National Save The Sea Turtle Foundation, Ft. Lauderdale, FL, 33308, USA
| | - Bette Zirkelbach
- The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Lucas Meers
- Mickler's Landing Turtle Patrol, Ponte Vedra Beach, FL, 32082, USA
| | - Pat Kleinsasser
- Crescent Beach Turtle Patrol, Crescent Beach, FL, 32080, USA
| | - Sharon Stock
- Flagler Turtle Patrol, Marineland Beach, FL, 32080, USA
| | | | | | - Scott Eastman
- Florida Department of Environmental Protection, St Augustine, FL, 32080, USA
| | | | | | | | - David Godfrey
- The Sea Turtle Conservancy, Gainesville, FL, 32609, USA
| | - Nancy Condron
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Mickler's Landing Turtle Patrol, Ponte Vedra Beach, FL, 32082, USA
| | - David J Duffy
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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13
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Martin KR, Mansfield KL, Savage AE. Adaptive evolution of major histocompatibility complex class I immune genes and disease associations in coastal juvenile sea turtles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211190. [PMID: 35154791 PMCID: PMC8825991 DOI: 10.1098/rsos.211190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/06/2022] [Indexed: 05/12/2023]
Abstract
Characterizing polymorphism at the major histocompatibility complex (MHC) genes is key to understanding the vertebrate immune response to disease. Despite being globally afflicted by the infectious tumour disease fibropapillomatosis (FP), immunogenetic variation in sea turtles is minimally explored. We sequenced the α 1 peptide-binding region of MHC class I genes (162 bp) from 268 juvenile green (Chelonia mydas) and 88 loggerhead (Caretta caretta) sea turtles in Florida, USA. We recovered extensive variation (116 alleles) and trans-species polymorphism. Supertyping analysis uncovered three functional MHC supertypes corresponding to the three well-supported clades in the phylogeny. We found significant evidence of positive selection at seven amino acid sites in the class I exon. Random forest modelling and risk ratio analysis of Ch. mydas alleles uncovered one allele weakly associated with smooth FP tumour texture, which may be associated with disease outcome. Our study represents the first characterization of MHC class I diversity in Ch. mydas and the largest sample of sea turtles used to date in any study of adaptive genetic variation, revealing tremendous genetic variation and high adaptive potential to viral pathogen threats. The novel associations we identified between MHC diversity and FP outcomes in sea turtles further highlight the importance of evaluating genetic predictors of disease, including MHC and other functional markers.
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Affiliation(s)
- Katherine R. Martin
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
| | - Katherine L. Mansfield
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
| | - Anna E. Savage
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
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14
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van de Geer CH, Bourjea J, Broderick AC, Dalleau M, Fernandes RS, Harris LR, Inteca GE, Kiponda FK, Louro CMM, Mortimer JA, Msangameno D, Mwasi LD, Nel R, Okemwa GM, Olendo M, Pereira MAM, Rees AF, Silva I, Singh S, West L, Williams JL, Godley BJ. Marine turtles of the African east coast: current knowledge and priorities for conservation and research. ENDANGER SPECIES RES 2022. [DOI: 10.3354/esr01180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Tissue and Temperature-Specific RNA-Seq Analysis Reveals Genomic Versatility and Adaptive Potential in Wild Sea Turtle Hatchlings ( Caretta caretta). Animals (Basel) 2021; 11:ani11113013. [PMID: 34827746 PMCID: PMC8614379 DOI: 10.3390/ani11113013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 10/18/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Digital transcriptomics is rapidly emerging as a powerful new technology for modelling the environmental dynamics of the adaptive landscape in diverse lineages. This is particularly valuable in taxa such as turtles and tortoises (order Testudines) which contain a large fraction of endangered species at risk due to anthropogenic impacts on the environment, including pollution, overharvest, habitat degradation, and climate change. Sea turtles (family Cheloniidae) in particular invite a genomics-enabled approach to investigating their remarkable portfolio of adaptive evolution. Our de novo transcriptome assemblies and measurements of tissue- and temperature- specific global gene expression in the loggerhead sea turtle (Caretta caretta) reveal the genomic basis for potential resiliency in this endangered flagship species, and are crucial to future management and conservation strategies with attention to changing climates. We summarize the interactions among differentially expressed genes by producing network visualizations, and highlight the shared biological pathways related to development, migration, immunity, and longevity reported in the avian and reptilian literature. Our original results for loggerhead sea turtles provide a large, new comparative genomic resource for the investigation of genotype–phenotype relationships in amniotes. Abstract Background: Digital transcriptomics is rapidly emerging as a powerful new technology for modelling the environmental dynamics of the adaptive landscape in diverse lineages. This is particularly valuable in taxa such as turtles and tortoises (order Testudines) which contain a large fraction of endangered species at risk due to anthropogenic impacts on the environment, including pollution, overharvest, habitat degradation, and climate change. Sea turtles (family Cheloniidae) in particular invite a genomics-enabled approach to investigating their remarkable portfolio of adaptive evolution. The sex of the endangered loggerhead sea turtle (Caretta caretta) is subject to temperature-dependent sex determination (TSD), a mechanism by which exposure to temperatures during embryonic development irreversibly determines sex. Higher temperatures produce mainly female turtles and lower temperatures produce mainly male turtles. Incubation temperature can have long term effects on the immunity, migratory ability, and ultimately longevity of hatchlings. We perform RNA-seq differential expression analysis to investigate tissue- and temperature-specific gene expression within brain (n = 7) and gonadal (n = 4) tissue of male and female loggerhead hatchlings. Results: We assemble tissue- and temperature-specific transcriptomes and identify differentially expressed genes relevant to sexual development and life history traits of broad adaptive interest to turtles and other amniotic species. We summarize interactions among differentially expressed genes by producing network visualizations, and highlight shared biological pathways related to migration, immunity, and longevity reported in the avian and reptile literature. Conclusions: The measurement of tissue- and temperature-specific global gene expression of an endangered, flagship species such as the loggerhead sea turtle (Caretta caretta) reveals the genomic basis for potential resiliency and is crucial to future management and conservation strategies with attention to changing climates. Brain and gonadal tissue collected from experimentally reared loggerhead male and female hatchlings comprise an exceedingly rare dataset that permits the identification of genes enriched in functions related to sexual development, immunity, longevity, and migratory behavior and will serve as a large, new genomic resource for the investigation of genotype–phenotype relationships in amniotes.
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16
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Distribution of genetic diversity reveals colonization patterns and philopatry of the loggerhead sea turtles across geographic scales. Sci Rep 2020; 10:18001. [PMID: 33093463 PMCID: PMC7583243 DOI: 10.1038/s41598-020-74141-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/21/2020] [Indexed: 12/23/2022] Open
Abstract
Understanding the processes that underlie the current distribution of genetic diversity in endangered species is a goal of modern conservation biology. Specifically, the role of colonization and dispersal events throughout a species' evolutionary history often remains elusive. The loggerhead sea turtle (Caretta caretta) faces multiple conservation challenges due to its migratory nature and philopatric behaviour. Here, using 4207 mtDNA sequences, we analysed the colonisation patterns and distribution of genetic diversity within a major ocean basin (the Atlantic), a regional rookery (Cabo Verde Archipelago) and a local island (Island of Boa Vista, Cabo Verde). Data analysis using hypothesis-driven population genetic models suggests the colonization of the Atlantic has occurred in two distinct waves, each corresponding to a major mtDNA lineage. We propose the oldest lineage entered the basin via the isthmus of Panama and sequentially established aggregations in Brazil, Cabo Verde and in the area of USA and Mexico. The second lineage entered the Atlantic via the Cape of Good Hope, establishing colonies in the Mediterranean Sea, and from then on, re-colonized the already existing rookeries of the Atlantic. At the Cabo Verde level, we reveal an asymmetric gene flow maintaining links across island-specific nesting groups, despite significant genetic structure. This structure stems from female philopatric behaviours, which could further be detected by weak but significant differentiation amongst beaches separated by only a few kilometres on the island of Boa Vista. Exploring biogeographic processes at diverse geographic scales improves our understanding of the complex evolutionary history of highly migratory philopatric species. Unveiling the past facilitates the design of conservation programmes targeting the right management scale to maintain a species' evolutionary potential.
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17
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Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output. Sci Rep 2020; 10:12847. [PMID: 32733067 PMCID: PMC7393485 DOI: 10.1038/s41598-020-69613-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 07/15/2020] [Indexed: 11/24/2022] Open
Abstract
Hybridization between sea turtle species occurs with particularly high frequency at two adjacent nesting areas in northeastern Brazil. To understand the outcomes of hybridization and their consequences for sea turtle conservation, we need to evaluate the extent of hybridization occurrence and possible deleterious effects in the hybrid progeny. Thus, we investigated the hypothesis of the existence of a new hybrid spot offshore of Brazil’s northeastern coast. The Abrolhos Archipelago is surrounded by the largest and richest coral reefs in the South Atlantic and is known to be a nesting site for loggerhead turtles (Carettacaretta). In this study, we performed a multidisciplinary investigation into levels of hybridization in sea turtles and their reproductive output in the Abrolhos beaches. Genetic data from mitochondrial DNA (mtDNA) and six autosomal markers showed that there are first-generation hybrid females nesting in Abrolhos, resulting from crossings between hawksbill males (Eretmochelysimbricata) and loggerhead females, and backcrossed hatchlings from both parental species. The type and extent of hybridization were characterized using genomic data obtained with the 3RAD method, which confirmed backcrossing between F1 hybrids and loggerhead turtles. The reproductive output data of Abrolhos nests suggests a disadvantage of hybrids when compared to loggerheads. For the first time, we have shown the association between hybridization and low reproductive success, which may represent a threat to sea turtle conservation.
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18
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Arantes LS, Vilaça ST, Mazzoni CJ, Santos FR. New Genetic Insights About Hybridization and Population Structure of Hawksbill and Loggerhead Turtles From Brazil. J Hered 2020; 111:444-456. [DOI: 10.1093/jhered/esaa024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022] Open
Abstract
Abstract
An extremely high incidence of hybridization among sea turtles is found along the Brazilian coast. This atypical phenomenon and its impact on sea turtle conservation can be elucidated through research focused on the evolutionary history of sea turtles. We assessed high-quality multilocus haplotypes of 143 samples of the 5 species of sea turtles that occur along the Brazilian coast to investigate the hybridization process and the population structure of hawksbill (Eretmochelys imbricata) and loggerhead turtles (Caretta caretta). The multilocus data were initially used to characterize interspecific hybrids. Introgression (F2 hybrids) was only confirmed in hatchlings of F1 hybrid females (hawksbill × loggerhead), indicating that introgression was either previously overestimated and F2 hybrids may not survive to adulthood, or the first-generation hybrid females nesting in Brazil were born as recent as few decades ago. Phylogenetic analyses using nuclear markers recovered the mtDNA-based Indo-Pacific and Atlantic lineages for hawksbill turtles, demonstrating a deep genetic divergence dating from the early Pliocene. In addition, loggerhead turtles that share a common feeding area and belong to distinct Indo-Pacific and Atlantic mtDNA clades present no clear genetic differentiation at the nuclear level. Finally, our results indicate that hawksbill and loggerhead rookeries along the Brazilian coast are likely connected by male-mediated gene flow.
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Affiliation(s)
- Larissa S Arantes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Avenida Antônio Carlos, Belo Horizonte - MG, Brazil
| | - Sibelle T Vilaça
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6–8, Berlin, Germany (Vilaça and Mazzoni)
- Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, Berlin, Germany
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6–8, Berlin, Germany (Vilaça and Mazzoni)
- Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, Berlin, Germany
| | - Fabrício R Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Avenida Antônio Carlos, Belo Horizonte - MG, Brazil
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19
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Arantes LS, Vargas SM, Santos FR. Global phylogeography of the critically endangered hawksbill turtle (Eretmochelys imbricata). Genet Mol Biol 2020; 43:e20190264. [PMID: 32555943 PMCID: PMC7288670 DOI: 10.1590/1678-4685-gmb-2019-0264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/11/2020] [Indexed: 11/22/2022] Open
Abstract
The hawksbill turtle is a broadly distributed, highly migratory and critically endangered sea turtle species. The paucity of studies restricts the comprehension of its behavior and life history. In this work, we performed a global phylogeographic analysis using a compilation of previously published mitochondrial haplotype data to understand the dynamics and diversity of hawksbill populations worldwide. Our results revealed a complex demographic pattern associated to hawksbill phylogeography since the Pliocene. Isolation by distance is not enough to explain distinct demographic units of hawksbill turtles, which are also influenced by other factors as oceanic currents, coral reef distribution and nesting timing. The foraging aggregations are typically mixed stocks of individuals originating from multiple nesting areas, but there is also a trend of foragers coming from nearby natal beaches. Phylogenetic analysis indicates two highly divergent major lineages split between Atlantic and Indo-Pacific rookeries, but there is also a more recent Atlantic Ocean colonization from the Indo-Pacific Ocean. Long-distance dispersal events are likely responsible for homogenization between distant populations within oceans. Our findings provided new insights about population connectivity, identified gaps that should be prioritized in future research and highlighted the need for international efforts aiming at hawksbill's conservation.
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Affiliation(s)
- Larissa S Arantes
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte, MG, Brazil
| | - Sarah M Vargas
- Universidade Federal do Espírito Santo (UFES), Instituto de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Vitória, ES, Brazil
| | - Fabrício R Santos
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte, MG, Brazil
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20
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Meiofauna Life on Loggerhead Sea Turtles-Diversely Structured Abundance and Biodiversity Hotspots That Challenge the Meiofauna Paradox. DIVERSITY 2020. [DOI: 10.3390/d12050203] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sea turtles migrate thousands of miles annually between foraging and breeding areas, carrying dozens of epibiont species with them on their journeys. Most sea turtle epibiont studies have focused on large-sized organisms, those visible to the naked eye. Here, we report previously undocumented levels of epibiont abundance and biodiversity for loggerhead sea turtles (Caretta caretta), by focusing on the microscopic meiofauna. During the peak of the 2018 loggerhead nesting season at St. George Island, Florida, USA, we sampled all epibionts from 24 carapaces. From the subsamples, we identified 38,874 meiofauna individuals belonging to 20 higher taxa. This means 810,753 individuals were recovered in our survey, with an average of 33,781 individuals per carapace. Of 6992 identified nematodes, 111 different genera were observed. To our knowledge, such levels of sea turtle epibiont abundance and diversity have never been recorded. Loggerhead carapaces are without doubt hotspots of meiofaunal and nematode diversity, especially compared to other non-sedimentary substrates. The posterior carapace sections harbored higher diversity and evenness compared to the anterior and middle sections, suggesting increased colonization and potentially facilitation favoring posterior carapace epibiosis, or increased disturbance on the anterior and middle carapace sections. Our findings also shed new light on the meiofauna paradox: “How do small, benthic meiofauna organisms become cosmopolitan over large geographic ranges?” Considering high loggerhead epibiont colonization, the large distances loggerheads migrate for reproduction and feeding, and the evolutionary age and sheer numbers of sea turtles worldwide, potentially large-scale exchange and dispersal for meiofauna through phoresis is implied. We distinguished different groups of loggerhead carapaces based on divergent epibiont communities, suggesting distinct epibiont colonization processes. These epibiont observations hold potential for investigating loggerhead movements and, hence, their conservation.
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21
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Brito C, Vilaça ST, Lacerda AL, Maggioni R, Marcovaldi MÂ, Vélez-Rubio G, Proietti MC. Combined use of mitochondrial and nuclear genetic markers further reveal immature marine turtle hybrids along the South Western Atlantic. Genet Mol Biol 2020; 43:e20190098. [PMID: 32353097 PMCID: PMC7199923 DOI: 10.1590/1678-4685-gmb-2019-0098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 01/16/2020] [Indexed: 11/22/2022] Open
Abstract
Marine turtle hybridization is usually sporadic and involves reports of only a few individuals; however, Brazilian populations have high hybridization rates. Here we investigated the presence of hybrids in morphologically identified immature hawksbills (Eretmochelys imbricata) along the South Western Atlantic (SWA). We sequenced one mitochondrial (D-Loop) and three nuclear DNA (RAG1, RAG2, and CMOS) markers to better understand the patterns and characteristics of hybrids. We identified 22 hybrids (n = 270), 11 of them at the extreme South of the SWA. Uruguay had the highest hybrid frequency in the SWA (~37.5%) followed by southern Brazil with 30%. These are common areas for loggerheads (Caretta caretta) but uncommon for hawksbills, and these hybrids may be adopting the behavior of loggerheads. By analyzing nuclear markers, we can infer that 50% of the sampled hybrids are first generation (F1) and 36% are the result of backcrosses between hybrids and pure E. imbricata (> F1). We also report for the first time immature E. imbricata x Lepidochelys olivacea hybrids at the Brazilian coast. Considering the high frequency of hybrids in the SWA, continuous monitoring should be performed to assess the fitness, genetic integrity, and extent of changes in the gene pools of involved populations.
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Affiliation(s)
- Cíntia Brito
- Universidade Federal do Rio Grande (FURG), Instituto de Oceanografia (IO), Laboratório de Ecologia Molecular Marinha, Rio Grande, RS, Brazil
| | - Sibelle Torres Vilaça
- Trent University, Environmental and Life Sciences Graduate Program, Peterborough, Canada.,Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ana Luzia Lacerda
- Universidade Federal do Rio Grande (FURG), Instituto de Oceanografia (IO), Laboratório de Ecologia Molecular Marinha, Rio Grande, RS, Brazil
| | - Rodrigo Maggioni
- Universidade Federal do Ceará (UFC), Instituto de Ciências do Mar (LABOMAR), Fortaleza, CE, Brazil
| | - Maria Ângela Marcovaldi
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Projeto TAMAR, Salvador, BA, Brazil.,Fundação Pró-TAMAR, Salvador, BA, Brazil
| | - Gabriela Vélez-Rubio
- Asociación Civil Karumbé, Montevideo, Uruguay.,Universidade de la República, Centro Universitario Regional del Este (CURE), Rocha, Uruguay
| | - Maíra Carneiro Proietti
- Universidade Federal do Rio Grande (FURG), Instituto de Oceanografia (IO), Laboratório de Ecologia Molecular Marinha, Rio Grande, RS, Brazil
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22
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Identifying patterns in foraging-area origins in breeding aggregations of migratory species: Loggerhead turtles in the Northwest Atlantic. PLoS One 2020; 15:e0231325. [PMID: 32282844 PMCID: PMC7153900 DOI: 10.1371/journal.pone.0231325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/20/2020] [Indexed: 11/20/2022] Open
Abstract
Population assessments conducted at reproductive sites of migratory species necessitate understanding the foraging-area origins of breeding individuals. Without this information, efforts to contextualize changes in breeding populations and develop effective management strategies are compromised. We used stable isotope analysis of tissue samples collected from loggerhead sea turtles (Caretta caretta) nesting at seven sites in the Northern Recovery Unit (NRU) of the eastern United States (North Carolina, South Carolina and Georgia) to assign females to three separate foraging areas in the Northwest Atlantic Ocean (NWA). We found that the majority of the females at NRU nesting sites (84.4%) use more northern foraging areas in the Mid-Atlantic Bight, while fewer females use more proximate foraging areas in the South Atlantic Bight (13.4%) and more southerly foraging areas in the Subtropical Northwest Atlantic (2.2%). We did not find significant latitudinal or temporal trends in the proportions of NRU females originating from different foraging areas. Combining these findings with previous data from stable isotope and satellite tracking studies across NWA nesting sites showed that variation in the proportion of adult loggerheads originating from different foraging areas is primarily related differences between recovery units: individuals in the NRU primarily use the Mid-Atlantic Bight foraging area, while individuals from the three Florida recovery units primarily use the Subtropical Northwest Atlantic and Eastern Gulf of Mexico foraging areas. Because each foraging area is associated with its own distinct ecological characteristics, environmental fluctuations and anthropogenic threats that affect the abundance and productivity of individuals at nesting sites, this information is critical for accurately evaluating population trends and developing effective region-specific management strategies.
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23
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Chow JC, Anderson PE, Shedlock AM. Sea Turtle Population Genomic Discovery: Global and Locus-Specific Signatures of Polymorphism, Selection, and Adaptive Potential. Genome Biol Evol 2020; 11:2797-2806. [PMID: 31504487 PMCID: PMC6786478 DOI: 10.1093/gbe/evz190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2019] [Indexed: 12/21/2022] Open
Abstract
In the era of genomics, single-nucleotide polymorphisms (SNPs) have become a preferred molecular marker to study signatures of selection and population structure and to enable improved population monitoring and conservation of vulnerable populations. We apply a SNP calling pipeline to assess population differentiation, visualize linkage disequilibrium, and identify loci with sex-specific genotypes of 45 loggerhead sea turtles (Caretta caretta) sampled from the southeastern coast of the United States, including 42 individuals experimentally confirmed for gonadal sex. By performing reference-based SNP calling in independent runs of Stacks, 3,901–6,998 SNPs and up to 30 potentially sex-specific genotypes were identified. Up to 68 pairs of loci were found to be in complete linkage disequilibrium, potentially indicating regions of natural selection and adaptive evolution. This study provides a valuable SNP diagnostic workflow and a large body of new biomarkers for guiding targeted studies of sea turtle genome evolution and for managing legally protected nonmodel iconic species that have high economic and ecological importance but limited genomic resources.
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Affiliation(s)
- Julie C Chow
- Integrative Genetics and Genomics Graduate Group, University of California, Davis
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, Charleston, South Carolina.,Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA 93407
| | - Andrew M Shedlock
- Department of Biology, College of Charleston, Charleston, South Carolina.,College of Graduate Studies, Medical University of South Carolina.,Marine Genomics Division, Hollings Marine Laboratory, Charleston, South Carolina
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24
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López-Mendilaharsu M, Giffoni B, Monteiro D, Prosdocimi L, Vélez-Rubio GM, Fallabrino A, Estrades A, Santos AS, Lara PH, Pires T, Tiwari M, Bolten AB, Marcovaldi MÂ. Multiple-threats analysis for loggerhead sea turtles in the southwest Atlantic Ocean. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Priority-setting approaches for widely distributed and long-lived species can be challenging. This is especially true for sea turtles, which are species of conservation concern. The aim of this study was to conduct a detailed analysis of threats to identify, quantify and prioritize the main impacts to the loggerhead Caretta caretta population in the southwest Atlantic (SWA) region. A matrix of relative threats was constructed. Threats were identified and classified for 8 different life stages (nesting females, eggs, hatchlings, swim-frenzy transitional stage, juveniles-neritic, juveniles-oceanic, adults-neritic, adults-oceanic) and for 3 ecosystems inhabited by sea turtles (terrestrial, neritic and oceanic). Results indicated that fisheries bycatch represents a major threat for loggerheads in the SWA. The trawl fishery was identified as the main source of mortality for neritic juvenile and adult turtles, whereas juveniles in oceanic areas are mostly impacted by surface longlines. In terrestrial environments, eggs and hatchlings are mainly affected by habitat alteration and by native and exotic predators. Loggerheads have shown a positive nesting trend at their main nesting beaches in the SWA, probably due to long-term conservation efforts to reduce mortality of the different life stages within the terrestrial zone. However, the high mortality rates of juveniles and sub-adults documented at some known foraging grounds represent a reason for concern, as this may affect the overall population trend in the future. This threat analysis provides a tool to review the goals of national action plans, prioritize actions and optimize the allocation of management resources.
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Affiliation(s)
- M López-Mendilaharsu
- Fundação Pró-Tamar, Rua Rubens Guelli 134/ 307, Itaigara - Salvador, CEP: 41815-135 Bahia, Brazil
| | - B Giffoni
- Fundação Pró-Tamar, Rua Rubens Guelli 134/ 307, Itaigara - Salvador, CEP: 41815-135 Bahia, Brazil
| | - D Monteiro
- Núcleo de Educação e Monitoramento Ambiental - NEMA, Rua Maria Araújo 450, 96207-480 Rio Grande, RS, Brazil
- Laboratório de Ecologia e Conservação da Megafauna Marinha, EcoMega, Universidade Federal do Rio Grande, FURG, 96203-900 Rio Grande, RS, Brazil
| | - L Prosdocimi
- Programa Regional de Investigación y Conservación de Tortugas Marinas de la Argentina (PRICTMA), 1609 Buenos Aires, Argentina
| | - GM Vélez-Rubio
- Karumbé NGO, Zoo Villa Dolores, 11600 Montevideo, Uruguay
- Centro Universitario Regional del Este (CURE), Universidad de la República, 27000 Rocha, Uruguay
| | - A Fallabrino
- Karumbé NGO, Zoo Villa Dolores, 11600 Montevideo, Uruguay
| | - A Estrades
- Karumbé NGO, Zoo Villa Dolores, 11600 Montevideo, Uruguay
| | - AS Santos
- Fundação Pró-Tamar, Rua Rubens Guelli 134/ 307, Itaigara - Salvador, CEP: 41815-135 Bahia, Brazil
| | - PH Lara
- Fundação Pró-Tamar, Rua Rubens Guelli 134/ 307, Itaigara - Salvador, CEP: 41815-135 Bahia, Brazil
| | - T Pires
- Fundação Pró-Tamar, Rua Rubens Guelli 134/ 307, Itaigara - Salvador, CEP: 41815-135 Bahia, Brazil
| | - M Tiwari
- NOAA-National Marine Fisheries Service, Marine Turtle Ecology & Assessment Program, Southwest Fisheries Science Center, La Jolla, California 92034, USA
| | - AB Bolten
- Archie Carr Center for Sea Turtle Research and Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - MÂ Marcovaldi
- Fundação Pró-Tamar, Rua Rubens Guelli 134/ 307, Itaigara - Salvador, CEP: 41815-135 Bahia, Brazil
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Windsor AM, Moore MK, Warner KA, Stadig SR, Deeds JR. Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin. PeerJ 2019; 7:e7827. [PMID: 31720100 DOI: 10.7717/peerj.7827] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/03/2019] [Indexed: 11/20/2022] Open
Abstract
Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as "blue crab" and "Product of the USA" may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as "Product of the USA" and "Product of Venezuela." In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise F st values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances were 0.45%, 0.19%, and 0.07% for Lineages 1, 2, and 3, respectively. Among all vouchered reference specimens collected from the continental United States, Mexico, Puerto Rico, and Venezuela, we identified 22 phylogenetically informative sites that drive observed lineage divergences. Haplotypes identified from barcode COI sequences from commercial C. sapidus products labeled as originating from the US all aligned with haplotypes from Lineage 1 reference specimens and haplotypes from commercial products labeled as originating from Venezuela all aligned with Lineage 2, suggesting that these lineages may be useful for indicating whether products originate from the continental US or are imported when package labeling is in question.
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Affiliation(s)
- Amanda M Windsor
- Office of Regulatory Science, United States Food and Drug Administration, College Park, MD, USA
| | - M Katherine Moore
- Conservation Biology Division, Forensic Laboratory, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Charleston, SC, USA
| | | | - Sarah R Stadig
- Office of Regulatory Science, United States Food and Drug Administration, College Park, MD, USA
| | - Jonathan R Deeds
- Office of Regulatory Science, United States Food and Drug Administration, College Park, MD, USA
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Reid BN, Naro-Maciel E, Hahn AT, FitzSimmons NN, Gehara M. Geography best explains global patterns of genetic diversity and postglacial co-expansion in marine turtles. Mol Ecol 2019; 28:3358-3370. [PMID: 31264298 DOI: 10.1111/mec.15165] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 01/07/2023]
Abstract
For many species, climate oscillations drove cycles of population contraction during cool glacial periods followed by expansion during interglacials. Some groups, however, show evidence of uniform and synchronous expansion, while others display differences in the timing and extent of demographic change. We compared demographic histories inferred from genetic data across marine turtle species to identify responses to postglacial warming shared across taxa and to examine drivers of past demographic change at the global scale. Using coalescent simulations and approximate Bayesian computation (ABC), we estimated demographic parameters, including the likelihood of past population expansion, from a mitochondrial data set encompassing 23 previously identified lineages from all seven marine turtle species. For lineages with a high posterior probability of expansion, we conducted a hierarchical ABC analysis to estimate the proportion of lineages expanding synchronously and the timing of synchronous expansion. We used Bayesian model averaging to identify variables associated with expansion and genetic diversity. Approximately 60% of extant marine turtle lineages showed evidence of expansion, with the rest mainly exhibiting patterns of genetic diversity most consistent with population stability. For lineages showing expansion, there was a strong signal of synchronous expansion after the Last Glacial Maximum. Expansion and genetic diversity were best explained by ocean basin and the degree of endemism for a given lineage. Geographic differences in sensitivity to climate change have implications for prioritizing conservation actions in marine turtles as well as for identifying areas of past demographic stability and potential resilience to future climate change for broadly distributed taxa.
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Affiliation(s)
- Brendan N Reid
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
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Komoroske LM, Miller MR, O'Rourke SM, Stewart KR, Jensen MP, Dutton PH. A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles. Mol Ecol Resour 2019; 19:497-511. [DOI: 10.1111/1755-0998.12980] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/21/2018] [Accepted: 11/27/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Lisa M. Komoroske
- Department of Environmental Conservation University of Massachusetts Amherst Amherst Massachusetts
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Michael R. Miller
- Department of Animal Science University of California, Davis Davis California
| | - Sean M. O'Rourke
- Department of Animal Science University of California, Davis Davis California
| | - Kelly R. Stewart
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
- The Ocean Foundation Washington District of Columbia
| | - Michael P. Jensen
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Peter H. Dutton
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
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Usategui-Martín A, Liria-Loza A, Miller JD, Medina-Suárez M, Jiménez-Bordón S, Pérez-Mellado V, Montero D. Effects of incubation temperature on hatchling performance and phenotype in loggerhead sea turtle Caretta caretta. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Pfaller JB, Payton AC, Bjorndal KA, Bolten AB, McDaniel SF. Hitchhiking the high seas: Global genomics of rafting crabs. Ecol Evol 2019; 9:957-974. [PMID: 30805133 PMCID: PMC6374717 DOI: 10.1002/ece3.4694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/04/2022] Open
Abstract
Population differentiation and diversification depend in large part on the ability and propensity of organisms to successfully disperse. However, our understanding of these processes in organisms with high dispersal ability is biased by the limited genetic resolution offered by traditional genotypic markers. Many neustonic animals disperse not only as pelagic larvae, but also as juveniles and adults while drifting or rafting at the surface of the open ocean. In theory, the heightened dispersal ability of these animals should limit opportunities for species diversification and population differentiation. To test these predictions, we used next-generation sequencing of genomewide restriction-site-associated DNA tags (RADseq) and traditional mitochondrial DNA sequencing, to investigate the species-level relationships and global population structure of Planes crabs collected from oceanic flotsam and sea turtles. Our results indicate that species diversity in this clade is low-likely three closely related species-with no evidence of cryptic or undescribed species. Moreover, our results indicate weak population differentiation among widely separated aggregations with genetic indices showing only subtle genetic discontinuities across all oceans of the world (RADseq F ST = 0.08-0.16). The results of this study provide unprecedented resolution of the systematics and global biogeography of this group and contribute valuable information to our understanding of how theoretical dispersal potential relates to actual population differentiation and diversification among marine organisms. Moreover, these results demonstrate the limitations of single gene analyses and the value of genomic-level resolution for estimating contemporary population structure in organisms with large, highly connected populations.
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Affiliation(s)
- Joseph B. Pfaller
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
- Caretta Research ProjectSavannahGeorgia
| | - Adam C. Payton
- Department of BiologyUniversity of FloridaGainesvilleFlorida
| | - Karen A. Bjorndal
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
| | - Alan B. Bolten
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
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Casale P, Broderick AC, Camiñas JA, Cardona L, Carreras C, Demetropoulos A, Fuller WJ, Godley BJ, Hochscheid S, Kaska Y, Lazar B, Margaritoulis D, Panagopoulou A, Rees AF, Tomás J, Türkozan O. Mediterranean sea turtles: current knowledge and priorities for conservation and research. ENDANGER SPECIES RES 2018. [DOI: 10.3354/esr00901] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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31
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Carreras C, Pascual M, Tomás J, Marco A, Hochscheid S, Castillo JJ, Gozalbes P, Parga M, Piovano S, Cardona L. Sporadic nesting reveals long distance colonisation in the philopatric loggerhead sea turtle (Caretta caretta). Sci Rep 2018; 8:1435. [PMID: 29362421 PMCID: PMC5780500 DOI: 10.1038/s41598-018-19887-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/10/2018] [Indexed: 11/08/2022] Open
Abstract
The colonisation of new suitable habitats is crucial for species survival at evolutionary scale under changing environmental conditions. However, colonisation potential may be limited by philopatry that facilitates exploiting successful habitats across generations. We examine the mechanisms of long distance dispersal of the philopatric loggerhead sea turtle (Caretta caretta) by analysing 40 sporadic nesting events in the western Mediterranean. The analysis of a fragment of the mitochondrial DNA and 7 microsatellites of 121 samples from 18 of these nesting events revealed that these nests were colonising events associated with juveniles from distant populations feeding in nearby foraging grounds. Considering the temperature-dependent sex determination of the species, we simulated the effect of the incubation temperature and propagule pressure on a potential colonisation scenario. Our results indicated that colonisation will succeed if warm temperature conditions, already existing in some of the beaches in the area, extend to the whole western Mediterranean. We hypothesize that the sporadic nesting events in developmental foraging grounds may be a mechanism to overcome philopatry limitations thus increasing the dispersal capabilities of the species and the adaptability to changing environments. Sporadic nesting in the western Mediterranean can be viewed as potential new populations in a scenario of rising temperatures.
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Affiliation(s)
- Carlos Carreras
- Department of Genetics, Microbiology and Statistics and IRBio, University of Barcelona, Av.Diagonal 643, E-08028, Barcelona, Spain.
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, TR10 9EZ, UK.
| | - Marta Pascual
- Department of Genetics, Microbiology and Statistics and IRBio, University of Barcelona, Av.Diagonal 643, E-08028, Barcelona, Spain
| | - Jesús Tomás
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Apdo. 22085, E-46071, Valencia, Spain
| | - Adolfo Marco
- Estación Biológica de Doñana, CSIC, c/ Américo Vespucio s/n, E-41092, Sevilla, Spain
| | - Sandra Hochscheid
- Marine Turtle Research Centre, Department RIMAR, Stazione Zoologica Anton Dohrn, Via Nuova Macello, 80055, Portici, Italy
| | - Juan José Castillo
- CREMA (Centro de Recuperación de Especies Marinas Amenazadas), Aula del Mar de Málaga-Consejería de Medio Ambiente de la Junta de Andalucía, c/Pacífico 80, E-29004, Málaga, Spain
| | - Patricia Gozalbes
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Apdo. 22085, E-46071, Valencia, Spain
| | - Mariluz Parga
- Submon Marine Conservation, Rabassa 49, E-08024, Barcelona, Spain
- Marine Animal Rescue Center (CRAM), Passeig de la Platja 28-30, E-08820, El Prat de Llobregat, Spain
| | - Susanna Piovano
- Dipartimento di Biologia Animale e dell'Uomo, University of Torino, Via Accademia Albertina 13, 10123, Turin, Italy
- School of Marine Studies, The University of the South Pacific, Laucala Campus, Prive Mail Bag, Suva, Fiji
| | - Luis Cardona
- Department of Evolutionary Biology, Ecology and Environmental Sciences and IRBIo, University of Barcelona, Avda. Diagonal 643, E-08028, Barcelona, Spain
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Splendiani A, Fioravanti T, Giovannotti M, D’Amore A, Furii G, Totaro G, Nisi Cerioni P, Lucchetti A, Caputo Barucchi V. Mitochondrial DNA reveals the natal origin of Caretta caretta (Testudines: Cheloniidae) stranded or bycaught along the Southwestern Adriatic coasts. THE EUROPEAN ZOOLOGICAL JOURNAL 2017. [DOI: 10.1080/24750263.2017.1400597] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- A. Splendiani
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
| | - T. Fioravanti
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
| | - M. Giovannotti
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
| | - A. D’Amore
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
| | - G. Furii
- Centro Recupero Tartarughe Marine di Legambiente (CRTM) , Manfredonia, Italy
| | - G. Totaro
- Centro Recupero Tartarughe Marine di Legambiente (CRTM) , Manfredonia, Italy
| | - P. Nisi Cerioni
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
| | - A. Lucchetti
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine Sezione Pesca Marittima , Ancona, Italy
| | - V. Caputo Barucchi
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine Sezione Pesca Marittima , Ancona, Italy
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Marchiori E, Negrisolo E, Cassini R, Garofalo L, Poppi L, Tessarin C, Marcer F. Cardiovascular flukes (Trematoda: Spirorchiidae) in Caretta caretta Linnaeus, 1758 from the Mediterranean Sea. Parasit Vectors 2017; 10:467. [PMID: 29017541 PMCID: PMC5633879 DOI: 10.1186/s13071-017-2396-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 09/20/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The northern Adriatic Sea represents one of the most important neritic foraging grounds for the loggerhead sea turtle Caretta caretta L. in the Mediterranean Sea. Four genera of blood flukes with variable prevalence and pathogenic impact have been reported worldwide in this species. Hapalotrema Looss, 1899 and Amphiorchis Price, 1934 are the only two genera reported in Mediterranean waters; however, updated data describing spirorchiidiasis in the central and eastern Mediterranean and infection prevalence are still lacking. This work aimed to investigate the presence and pathology of spirorchiidiasis in C. caretta in the Mediterranean Sea. METHODS One hundred sixty-eight animals stranded along the northwestern Adriatic coast between 2009 and 2015 were submitted to necropsy and subsequent analyses for the detection of adult flukes, detection of eggs in the faeces and spleen and histopathology. Molecular analyses were carried out on hosts (mitochondrial D-loop) and parasites (28S gene and ITS2 spacer) to trace the turtle origins and identify the fluke phylogenetic relationships. RESULTS Spirorchiidiasis was detected in 16.7% of the animals. Hapalotrema mistroides (Monticelli, 1899) and Neospirorchis sp. were found in twenty-six and ten cases, respectively. Adult flukes were found in six cases, while eggs were detectable through copromicroscopic examination for all infected turtles, and the results for the detection of eggs in the spleen agreed with the copromicroscopic analysis. Only mild lesions were observed. Eggs of types 1 and 3 were grossly visible in the gastrointestinal mucosa, vasculitis was rarely observed in the heart and great vessels, and multifocal granulomas were widespread in the tissues. Molecular identification unambiguously assigned the spirorchiid samples to H. mistroides and Neospirorchis sp. Genetic characterization of loggerhead mtDNA pointed to a Mediterranean origin of the turtle hosts. CONCLUSION This survey provides new data on the spread of spirorchiidiasis in the Mediterranean loggerhead sea turtle population and reports for the first time the presence of Neospirorchis spp. in this basin. The infections did not have a causal effect on the death nor a strong impact on the general health status of the animals.
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Affiliation(s)
- Erica Marchiori
- Department of Animal Medicine, Production and Health, University of Padova, Viale dell'Università, Legnaro, Italy.
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, Legnaro, Italy
| | - Rudi Cassini
- Department of Animal Medicine, Production and Health, University of Padova, Viale dell'Università, Legnaro, Italy
| | - Luisa Garofalo
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana, Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Rieti, Italy
| | - Lisa Poppi
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, Legnaro, Italy
| | - Cinzia Tessarin
- Department of Animal Medicine, Production and Health, University of Padova, Viale dell'Università, Legnaro, Italy
| | - Federica Marcer
- Department of Animal Medicine, Production and Health, University of Padova, Viale dell'Università, Legnaro, Italy
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Santoro M, Di Nocera F, Iaccarino D, Lawton SP, Cerrone A, Degli Uberti B, D'Amore M, Affuso A, Hochscheid S, Maffucci F, Galiero G. Pathology and molecular analysis of Hapalotrema mistroides (Digenea: Spirorchiidae) infecting a Mediterranean loggerhead turtle Caretta caretta. DISEASES OF AQUATIC ORGANISMS 2017; 124:101-108. [PMID: 28425423 DOI: 10.3354/dao03117] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Turtle blood flukes belonging to the family Spirorchiidae (Digenea) represent a major threat for sea turtle health and are considered the most important parasitic cause of turtle stranding and mortality worldwide. Despite the large diversity of spirorchiid species found globally, there are only 2 records for free-ranging Mediterranean sea turtles that date back to the late 1800s involving just Hapalotrema mistroides Monticelli, 1896. This study describes the first fatal confirmed case of spirorchiidiasis in a free-ranging Mediterranean loggerhead turtle Caretta caretta (Linnaeus) and, owing to the complexities of taxonomic identification of these parasites, provides the first molecular characterization and phylogenetic analysis of H. mistroides from the Mediterranean Sea. The loggerhead turtle showed cachexia and digestive disorders associated with severe damage to the pancreas and intestinal ganglia, caused by deposition of Hapalotrema eggs forming granulomas. Massive Hapalotrema egg emboli in several tissues and organs and encephalitis were the most probable contributions to the death of the turtle. The congruence between the phylogenetic analysis of both the ITS2 and 28S rDNA resolved the Italian and USA H. mistroides as the same species, confirming the parasite identification. The case here described clearly indicates that the blood flukes should be considered in the differential diagnosis of Mediterranean sea turtle diseases.
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Affiliation(s)
- M Santoro
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute n. 2, 80055 Portici, Italy
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Rees ALF, Carreras C, Broderick AC, Margaritoulis D, Stringell TB, Godley BJ. Linking loggerhead locations: using multiple methods to determine the origin of sea turtles in feeding grounds. MARINE BIOLOGY 2017; 164:30. [PMID: 28133395 PMCID: PMC5236075 DOI: 10.1007/s00227-016-3055-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/05/2016] [Indexed: 06/06/2023]
Abstract
Many marine megavertebrate taxa, including sea turtles, disperse widely from their hatching or birthing locations but display natal homing as adults. We used flipper tagging, satellite tracking and genetics to identify the origin of loggerhead turtles living in Amvrakikos Gulf, Greece. This location has been identified as hosting regionally important numbers of large-juvenile to adult sized turtles that display long-term residency and/or association to the area, and also presents a male biased sex ratio for adults. A total of 20 individuals were linked to nesting areas in Greece through flipper tagging and satellite telemetry, with the majority (16) associated with Zakynthos Island. One additional female was tracked from Amvrakikos Gulf to Turkey where she likely nested. Mitochondrial DNA mixed stock analyses of turtles captured in Amvrakikos Gulf (n = 95) indicated 82% of individuals originated from Greek nesting stocks, mainly from Zakynthos Island (63%), with lesser contributions from central Turkey, Cyprus and Libya. These results suggest that the male-biased sex ratio found in Amvrakikos Gulf may be driven by the fact that males breed twice as frequently on Zakynthos, resulting in their using foraging grounds of greater proximity to the breeding site. Conservation measures in localised foraging habitats for the protection of marine vertebrates, such as sea turtles, may have positive impacts on several disparate breeding stocks and the use of multiple methods to determine source populations can indicate the relative effectiveness of these measures.
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Affiliation(s)
- ALan F. Rees
- ARCHELON, the Sea Turtle Protection Society of Greece, Solomou 57, 104 32 Athens, Greece
- Marine Turtle Research Group, Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE UK
| | - Carlos Carreras
- Marine Turtle Research Group, Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE UK
- Department of Genetics, Microbiology and Statistics and IRBio, University of Barcelona, Av.Diagonal 643, 08028 Barcelona, Spain
| | - Annette C. Broderick
- Marine Turtle Research Group, Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE UK
| | - Dimitris Margaritoulis
- ARCHELON, the Sea Turtle Protection Society of Greece, Solomou 57, 104 32 Athens, Greece
| | - Thomas B. Stringell
- Marine Turtle Research Group, Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE UK
| | - Brendan J. Godley
- Marine Turtle Research Group, Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE UK
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Rees AF, Alfaro-Shigueto J, Barata PCR, Bjorndal KA, Bolten AB, Bourjea J, Broderick AC, Campbell LM, Cardona L, Carreras C, Casale P, Ceriani SA, Dutton PH, Eguchi T, Formia A, Fuentes MMPB, Fuller WJ, Girondot M, Godfrey MH, Hamann M, Hart KM, Hays GC, Hochscheid S, Kaska Y, Jensen MP, Mangel JC, Mortimer JA, Naro-Maciel E, Ng CKY, Nichols WJ, Phillott AD, Reina RD, Revuelta O, Schofield G, Seminoff JA, Shanker K, Tomás J, van de Merwe JP, Van Houtan KS, Vander Zanden HB, Wallace BP, Wedemeyer-Strombel KR, Work TM, Godley BJ. Are we working towards global research priorities for management and conservation of sea turtles? ENDANGER SPECIES RES 2016. [DOI: 10.3354/esr00801] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Novelletto A, Testa L, Iacovelli F, Blasi P, Garofalo L, Mingozzi T, Falconi M. Polymorphism in Mitochondrial Coding Regions of Mediterranean Loggerhead Turtles: Evolutionary Relevance and Structural Effects. Physiol Biochem Zool 2016; 89:473-486. [DOI: 10.1086/688679] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Matsuzawa Y, Kamezaki N, Ishihara T, Omuta K, Takeshita H, Goto K, Arata T, Honda H, Kameda K, Kashima Y, Kayo M, Kawazu I, Kodama J, Kumazawa Y, Kuroyanagi K, Mizobuchi K, Mizuno K, Oki K, Watanabe KK, Yamamoto A, Yamashita Y, Yamato T, Hamabata T, Ishizaki A, Dutton PH. Fine-scale genetic population structure of loggerhead turtles in the Northwest Pacific. ENDANGER SPECIES RES 2016. [DOI: 10.3354/esr00724] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Maffucci F, Corrado R, Palatella L, Borra M, Marullo S, Hochscheid S, Lacorata G, Iudicone D. Seasonal heterogeneity of ocean warming: a mortality sink for ectotherm colonizers. Sci Rep 2016; 6:23983. [PMID: 27044321 PMCID: PMC4820753 DOI: 10.1038/srep23983] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 03/11/2016] [Indexed: 11/09/2022] Open
Abstract
Distribution shifts are a common adaptive response of marine ectotherms to climate change but the pace of redistribution depends on species-specific traits that may promote or hamper expansion to northern habitats. Here we show that recently, the loggerhead turtle (Caretta caretta) has begun to nest steadily beyond the northern edge of the species' range in the Mediterranean basin. This range expansion is associated with a significant warming of spring and summer sea surface temperature (SST) that offers a wider thermal window suitable for nesting. However, we found that post-hatchlings departing from this location experience low winter SST that may affect their survival and thus hamper the stabilization of the site by self-recruitment. The inspection of the Intergovernmental Panel on Climate Change model projections and observational data on SST trends shows that, despite the annual warming for this century, winter SST show little or no trends. Therefore, thermal constraints during the early developmental phase may limit the chance of population growth at this location also in the near future, despite increasingly favourable conditions at the nesting sites. Quantifying and understanding the interplay between dispersal and environmental changes at all life stages is critical for predicting ectotherm range expansion with climate warming.
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Affiliation(s)
- Fulvio Maffucci
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.,Dipartimento di Scienze, Università Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy
| | - Raffaele Corrado
- Consiglio Nazionale delle Ricerche, Istituto di Scienze dell'Atmosfera e del Clima, Str. Lecce-Monteroni, 73100, Lecce, Italy
| | - Luigi Palatella
- Consiglio Nazionale delle Ricerche, Istituto di Scienze dell'Atmosfera e del Clima, Str. Lecce-Monteroni, 73100, Lecce, Italy
| | - Marco Borra
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Salvatore Marullo
- Dipartimento di Scienze, Università Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy
| | - Sandra Hochscheid
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Guglielmo Lacorata
- Consiglio Nazionale delle Ricerche, Istituto di Scienze dell'Atmosfera e del Clima, Str. Lecce-Monteroni, 73100, Lecce, Italy
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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Gaos AR, Lewison RL, Liles MJ, Gadea V, Altamirano E, Henríquez AV, Torres P, Urteaga J, Vallejo F, Baquero A, LeMarie C, Muñoz JP, Chaves JA, Hart CE, Peña de Niz A, Chácon D, Fonseca L, Otterstrom S, Yañez IL, LaCasella EL, Frey A, Jensen MP, Dutton PH. Hawksbill turtle terra incognita: conservation genetics of eastern Pacific rookeries. Ecol Evol 2016; 6:1251-64. [PMID: 26941950 PMCID: PMC4761781 DOI: 10.1002/ece3.1897] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/21/2015] [Accepted: 11/26/2015] [Indexed: 11/05/2022] Open
Abstract
Prior to 2008 and the discovery of several important hawksbill turtle (Eretmochelys imbricata) nesting colonies in the EP (Eastern Pacific), the species was considered virtually absent from the region. Research since that time has yielded new insights into EP hawksbills, salient among them being the use of mangrove estuaries for nesting. These recent revelations have raised interest in the genetic characterization of hawksbills in the EP, studies of which have remained lacking to date. Between 2008 and 2014, we collected tissue samples from 269 nesting hawksbills at nine rookeries across the EP and used mitochondrial DNA sequences (766 bp) to generate the first genetic characterization of rookeries in the region. Our results inform genetic diversity, population differentiation, and phylogeography of the species. Hawksbills in the EP demonstrate low genetic diversity: We identified a total of only seven haplotypes across the region, including five new and two previously identified nesting haplotypes (pooled frequencies of 58.4% and 41.6%, respectively), the former only evident in Central American rookeries. Despite low genetic diversity, we found strong stock structure between the four principal rookeries, suggesting the existence of multiple populations and warranting their recognition as distinct management units. Furthermore, haplotypes EiIP106 and EiIP108 are unique to hawksbills that nest in mangrove estuaries, a behavior found only in hawksbills along Pacific Central America. The detected genetic differentiation supports the existence of a novel mangrove estuary "reproductive ecotype" that may warrant additional conservation attention. From a phylogeographic perspective, our research indicates hawksbills colonized the EP via the Indo-Pacific, and do not represent relict populations isolated from the Atlantic by the rising of the Panama Isthmus. Low overall genetic diversity in the EP is likely the combined result of few rookeries, extremely small reproductive populations and evolutionarily recent colonization events. Additional research with larger sample sizes and variable markers will help further genetic understanding of hawksbill turtles in the EP.
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Shamblin BM, Dutton PH, Bjorndal KA, Bolten AB, Naro-Maciel E, Santos AJB, Bellini C, Baptistotte C, Marcovaldi MÂ, Nairn CJ. Deeper Mitochondrial Sequencing Reveals Cryptic Diversity and Structure in Brazilian Green Turtle Rookeries. CHELONIAN CONSERVATION AND BIOLOGY 2015. [DOI: 10.2744/ccb-1152.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Brian M. Shamblin
- Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602 USA [ ; ]
| | - Peter H. Dutton
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, California 92037 USA [ ]
| | - Karen A. Bjorndal
- Archie Carr Center for Sea Turtle Research and Department of Biology, University of Florida, Gainesville, Florida 32611 USA [ ; ]
| | - Alan B. Bolten
- Archie Carr Center for Sea Turtle Research and Department of Biology, University of Florida, Gainesville, Florida 32611 USA [ ; ]
| | - Eugenia Naro-Maciel
- College of Staten Island, City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314 USA [ ]
| | | | - Claudio Bellini
- Centro Nacional de Conservação e Manejo de Tartarugas Marinhas, TAMAR-ICMBio, Caixa Postal 2219 Rio Vermelho, CEP 41950-970, Salvador, BA, Brazil [ ; ]
| | - Cecilia Baptistotte
- Centro Nacional de Conservação e Manejo de Tartarugas Marinhas, TAMAR-ICMBio, Caixa Postal 2219 Rio Vermelho, CEP 41950-970, Salvador, BA, Brazil [ ; ]
| | | | - Campbell J. Nairn
- Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602 USA [ ; ]
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Identification of Diagnostic Mitochondrial DNA Single Nucleotide Polymorphisms Specific to Sumatran Orangutan (Pongo abelii) Populations. HAYATI JOURNAL OF BIOSCIENCES 2015. [DOI: 10.1016/j.hjb.2015.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Zanden HBV, Tucker AD, Hart KM, Lamont MM, Fuisaki I, Addison D, Mansfield KL, Phillips KF, Wunder MB, Bowen GJ, Pajuelo M, Bolten AB, Bjorndal KA. Determining origin in a migratory marine vertebrate: a novel method to integrate stable isotopes and satellite tracking. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2015; 25:320-335. [PMID: 26263657 DOI: 10.1890/14-0581.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Stable isotope analysis is a useful tool to track animal movements in both terrestrial and marine environments. These intrinsic markers are assimilated through the diet and may exhibit spatial gradients as a result of biogeochemical processes at the base of the food web. In the marine environment, maps to predict the spatial distribution of stable isotopes are limited, and thus determining geographic origin has been reliant upon integrating satellite telemetry and stable isotope data. Migratory sea turtles regularly move between foraging and reproductive areas. Whereas most nesting populations can be easily accessed and regularly monitored, little is known about the demographic trends in foraging populations. The purpose of the present study was to examine migration patterns of loggerhead nesting aggregations in the Gulf of Mexico (GoM), where sea turtles have been historically understudied. Two methods of geographic assignment using stable isotope values in known-origin samples from satellite telemetry were compared: (1) a nominal approach through discriminant analysis and (2) a novel continuous-surface approach using bivariate carbon and nitrogen isoscapes (isotopic landscapes) developed for this study. Tissue samples for stable isotope analysis were obtained from 60 satellite-tracked individuals at five nesting beaches within the GoM. Both methodological approaches for assignment resulted in high accuracy of foraging area determination, though each has advantages and disadvantages. The nominal approach is more appropriate when defined boundaries are necessary, but up to 42% of the individuals could not be considered in this approach. All individuals can be included in the continuous-surface approach, and individual results can be aggregated to identify geographic hotspots of foraging area use, though the accuracy rate was lower than nominal assignment. The methodological validation provides a foundation for future sea turtle studies in the region to inexpensively determine geographic origin for large numbers of untracked individuals. Regular monitoring of sea turtle nesting aggregations with stable isotope sampling can be used to fill critical data gaps regarding habitat use and migration patterns. Probabilistic assignment to origin with isoscapes has not been previously used in the marine environment, but the methods presented here could also be applied to other migratory marine species.
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Alfaro-Núñez A, Frost Bertelsen M, Bojesen AM, Rasmussen I, Zepeda-Mendoza L, Tange Olsen M, Gilbert MTP. Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles. BMC Evol Biol 2014; 14:206. [PMID: 25342462 PMCID: PMC4219010 DOI: 10.1186/s12862-014-0206-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/21/2014] [Indexed: 01/09/2023] Open
Abstract
Background Fibropapillomatosis (FP) is a neoplastic disease characterized by cutaneous tumours that has been documented to infect all sea turtle species. Chelonid fibropapilloma-associated herpesvirus (CFPHV) is believed to be the aetiological agent of FP, based principally on consistent PCR-based detection of herpesvirus DNA sequences from FP tumours. We used a recently described PCR-based assay that targets 3 conserved CFPHV genes, to survey 208 green turtles (Chelonia mydas). This included both FP tumour exhibiting and clinically healthy individuals. An additional 129 globally distributed clinically healthy individual sea turtles; representing four other species were also screened. Results CFPHV DNA sequences were obtained from 37/37 (100%) FP exhibiting green turtles, and 45/300 (15%) clinically healthy animals spanning all five species. Although the frequency of infected individuals per turtle population varied considerably, most global populations contained at least one CFPHV positive individual, with the exception of various turtle species from the Arabian Gulf, Northern Indian Ocean and Puerto Rico. Haplotype analysis of the different gene markers clustered the CFPHV DNA sequences for two of the markers (UL18 and UL22) in turtles from Turks and Caicos separate to all others, regardless of host species or geographic origin. Conclusion Presence of CFPHV DNA within globally distributed samples for all five species of sea turtle was confirmed. While 100% of the FP exhibiting green turtles yielded CFPHV sequences, surprisingly, so did 15% of the clinically healthy turtles. We hypothesize that turtle populations with zero (0%) CFPHV frequency may be attributed to possible environmental differences, diet and/or genetic resistance in these individuals. Our results provide first data on the prevalence of CFPHV among seemingly healthy turtles; a factor that may not be directly correlated to the disease incidence, but may suggest of a long-term co-evolutionary latent infection interaction between CFPHV and its turtle-host across species. Finally, computational analysis of amino acid variants within the Turks and Caicos samples suggest potential functional importance in a substitution for marker UL18 that encodes the major capsid protein gene, which potentially could explain differences in pathogenicity. Nevertheless, such a theory remains to be validated by further research. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0206-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alonzo Alfaro-Núñez
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | | | - Anders Miki Bojesen
- Department of Veterinary Disease Biology, Veterinary Clinical Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Isabel Rasmussen
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Lisandra Zepeda-Mendoza
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Morten Tange Olsen
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Marcus Thomas Pius Gilbert
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark. .,Trace and Environmental DNA Laboratory, School of Environment and Agriculture, Curtin University, Perth, Western Australia, 6845, Australia.
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Anastácio R, Santos C, Lopes C, Moreira H, Souto L, Ferrão J, Garnier J, Pereira MJ. Reproductive biology and genetic diversity of the green turtle (Chelonia mydas) in Vamizi island, Mozambique. SPRINGERPLUS 2014; 3:540. [PMID: 26034669 PMCID: PMC4447848 DOI: 10.1186/2193-1801-3-540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 09/08/2014] [Indexed: 12/04/2022]
Abstract
Introduction Vamizi, an Island located in the Western Indian Ocean, is visited by a small and not fully characterized green turtle (Chelonia mydas (L.)) population. This population is threatened by natural hazards and several human activities, which are used to identify conservation priorities for marine turtles. It was our aim to contribute to the knowledge of marine turtles that nest in Vamizi, with respect to its regional management, and to an area that may possibly be included on the UNESCO World Heritage List due to its potential Outstanding Universal Value. Case description Here, we evaluate the nesting parameters (incubation period, clutch size, hatching and emergence successes rates) and patterns over an 8-year (2003 – 2010) conservation program. We also present the results of genetic diversity based on the analysis of approximately an 850 pb fragment of the mitochondrial DNA control region. Discussion and evaluation We found that Vamizi beaches host a small number of nesting females, approximately 52 per year, but these have shown a reduction in their length. High hatching success (88.5 ± SD 17.2%, N = 649), emergence success rates (84.5 ± SD 20.4%, N = 649) were observed, and genetic diversity (N = 135), with 11 haplotypes found (7 new). It was also observed, in the later years of this study, a reduction in the incubation period, a dislocation of the nesting peak activity and an increase in the number of flooded nests and an increase of the number of nests in areas with lower human activity. Conclusions Some resilience and behavioral plasticity seems to occur regarding human territory occupancy and climate changes. However, regardless of the results, aspects like what seems to be the reduction of some cohorts, the number of flooded nests and the diminishing of the incubation period (East and South facing beaches), show that conservation efforts have to be improved. Electronic supplementary material The online version of this article (doi:10.1186/2193-1801-3-540) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rita Anastácio
- Departamento de Biologia e CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Camila Santos
- Departamento de Biologia e CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Cardoso Lopes
- Maluane - Cabo Delgado Conservation and Tourism, Pemba, Mozambique
| | - Helena Moreira
- Departamento de Biologia e CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Luis Souto
- Departamento de Biologia e CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Jorge Ferrão
- Maluane - Cabo Delgado Conservation and Tourism, Pemba, Mozambique ; Lúrio University, Nampula, Mozambique
| | - Julie Garnier
- The Zological Society of London, Regent's Park, London, NW1 4RY UK
| | - Mário J Pereira
- Departamento de Biologia e CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal ; AFPR - A For Plankton Research, 3800-365 Aveiro, Portugal
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