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Chevallier D, Fretey J, Lescure J, Girondot M. First Record of Kemp's Ridley Sea Turtle, Lepidochelys kempii (Garman, 1880), in the Waters of Martinique Island (Lesser Antilles). Animals (Basel) 2024; 14:596. [PMID: 38396564 PMCID: PMC10886026 DOI: 10.3390/ani14040596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/22/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
An adult female Lepidochelys kempii was found trapped in drifting sargassum south of Martinique; this is the southernmost report of this taxon in the Lesser Antilles arc. Determining the limits of distribution and the existence of possible sympatry between L. kempii and L. olivacea in certain subregions of the Caribbean has been hindered by numerous misidentifications. We review the available data and propose a new distribution map in the Caribbean, which can serve as a basis for future studies.
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Affiliation(s)
- Damien Chevallier
- Unité de Recherche BOREA, MNHN, CNRS 8067, SU, IRD 207, UCN, UA, Station de Recherche Marine de Martinique, Quartier Degras, Petite Anse, 97217 Les Anses d’Arlet, France
| | - Jacques Fretey
- Sea Turtle Research Center—Chélonée, 46260 Beauregard, France;
| | - Jean Lescure
- National Museum of Natural History, Institute of Systematics, Evolution and Biodiversity–CP 30, 57 rue Cuvier, 75005 Paris, France;
| | - Marc Girondot
- Laboratoire Ecologie, Systématique et Évolution, Équipe de Processus Écologiques et Pressions Anthropiques, CNRS, AgroParisTech et Université Paris-Saclay, UMR 8079, 91190 Gif-sur-Yvette, France;
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2
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Genetic Evidence for Indo-Western Pacific Olive Ridley Sea Turtles in Mexican Waters. DIVERSITY 2023. [DOI: 10.3390/d15030430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
The olive ridley sea turtle is predominantly an epipelagic species with no apparent migration corridors. Research in feeding areas in other sea turtle species has identified aggregations of individuals from diverse backgrounds; however, no specific feeding areas have been identified for the olive ridley. We used mtDNA control region sequencing to identify the haplotype composition of 85 olive ridley turtles (adult and immature turtles from both sexes) captured and released in Central Mexican Pacific waters. Amplified fragments of the control region (751 bp) revealed the presence of 17 haplotypes (h = 0.5877 ± 0.0622 and π = 0.001698 ± 0.001185), and 16 of them were phylogenetically grouped within the lineage of the Eastern Pacific, but the haplotype Lo37 showed close evolutionary relationships with the lineage of the East Coast of India. Lagrangian drifter data showed that West–East transport from the Indo-Pacific to the tropical Eastern Pacific might be possible through passive drift. These results highlight the importance of more genetic studies offshore and the role of the ocean currents in the migratory behavior of olive ridleys, as well as the need to establish multinational strategies for the conservation and management of the species in international waters.
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Ashworth MP, Majewska R, Frankovich TA, Sullivan M, Bosak S, Filek K, Van de Vijver B, Arendt M, Schwenter J, Nel R, Robinson NJ, Gary MP, Theriot EC, Stacy NI, Lam DW, Perrault JR, Manire CA, Manning SR. Cultivating epizoic diatoms provides insights into the evolution and ecology of both epibionts and hosts. Sci Rep 2022; 12:15116. [PMID: 36068258 PMCID: PMC9448772 DOI: 10.1038/s41598-022-19064-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Our understanding of the importance of microbiomes on large aquatic animals—such as whales, sea turtles and manatees—has advanced considerably in recent years. The latest observations indicate that epibiotic diatom communities constitute diverse, polyphyletic, and compositionally stable assemblages that include both putatively obligate epizoic and generalist species. Here, we outline a successful approach to culture putatively obligate epizoic diatoms without their hosts. That some taxa can be cultured independently from their epizoic habitat raises several questions about the nature of the interaction between these animals and their epibionts. This insight allows us to propose further applications and research avenues in this growing area of study. Analyzing the DNA sequences of these cultured strains, we found that several unique diatom taxa have evolved independently to occupy epibiotic habitats. We created a library of reference sequence data for use in metabarcoding surveys of sea turtle and manatee microbiomes that will further facilitate the use of environmental DNA for studying host specificity in epizoic diatoms and the utility of diatoms as indicators of host ecology and health. We encourage the interdisciplinary community working with marine megafauna to consider including diatom sampling and diatom analysis into their routine practices.
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Affiliation(s)
- Matt P Ashworth
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA.
| | - Roksana Majewska
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa.,Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, 2520, South Africa
| | - Thomas A Frankovich
- Institute of Environment, Florida International University, 11200 SW 8th St., Miami, FL, 33037, USA
| | | | - Sunčica Bosak
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - Klara Filek
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - Bart Van de Vijver
- Research Department, Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium.,Department of Biology, University of Antwerp, ECOSPHERE, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Michael Arendt
- Department of Natural Resources, Marine Resources Division, Charleston, SC, USA
| | - Jeffrey Schwenter
- Department of Natural Resources, Marine Resources Division, Charleston, SC, USA
| | - Ronel Nel
- Department of Zoology, Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha, 6031, South Africa
| | - Nathan J Robinson
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Barcelona, Spain
| | - Meagan P Gary
- Santa Cruz, Institute of Marine Sciences, University of California, Santa Cruz, CA, 95060, USA
| | - Edward C Theriot
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
| | - Nicole I Stacy
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32608, USA
| | - Daryl W Lam
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA
| | | | | | - Schonna R Manning
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
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4
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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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Cáceres-Farias L, Reséndiz E, Espinoza J, Fernández-Sanz H, Alfaro-Núñez A. Threats and Vulnerabilities for the Globally Distributed Olive Ridley (Lepidochelys olivacea) Sea Turtle: A Historical and Current Status Evaluation. Animals (Basel) 2022; 12:ani12141837. [PMID: 35883384 PMCID: PMC9311662 DOI: 10.3390/ani12141837] [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: 05/23/2022] [Revised: 07/08/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
The olive ridley (Lepidochelys olivacea) is the most abundant of all seven sea turtles, found across the tropical regions of the Atlantic, Pacific, and Indian Oceans in over 80 different countries all around the globe. Despite being the most common and widely distributed sea turtle, olive ridley populations have been declining substantially for decades. Worldwide, olive ridleys have experienced a 30–50% decline, putting their populations at risk and being considered an Endangered Species by the IUCN. Natural habitat degradation, pollution, bycatch, climate change, predation by humans and animals, infectious diseases and illegal trade are the most notorious threats to explain olive ridley populations rapidly decline. The present review assesses the numerous dangers that the olive ridley turtle has historically faced and currently faces. To preserve olive ridleys, stronger conservation initiatives and strategies must continue to be undertaken. Policies and law enforcement for the protection of natural environments and reduction in the effects of climate change should be implemented worldwide to protect this turtle species.
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Affiliation(s)
- Lenin Cáceres-Farias
- AquaCEAL Corporation, Urb. Las Palmeras, Ave. Capitán Byron Palacios & General Quisquis, Santo Domingo de los Colorados 230101, Ecuador;
- Grupo de Investigación en Biología y Cultivo de Moluscos, Departamento de Acuicultura, Pesca y Recursos Naturales Renovables, Facultad de Ciencias Veterinarias, Universidad Técnica de Manabí, Bahía de Caráquez, Manabí 131101, Ecuador
| | - Eduardo Reséndiz
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz 23080, Mexico; (E.R.); (J.E.); (H.F.-S.)
- Health Assessments in Sea Turtles from BCS, La Paz 23085, Mexico
| | - Joelly Espinoza
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz 23080, Mexico; (E.R.); (J.E.); (H.F.-S.)
- Health Assessments in Sea Turtles from BCS, La Paz 23085, Mexico
| | - Helena Fernández-Sanz
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz 23080, Mexico; (E.R.); (J.E.); (H.F.-S.)
- Health Assessments in Sea Turtles from BCS, La Paz 23085, Mexico
| | - Alonzo Alfaro-Núñez
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
- Department of Clinical Biochemistry, Naestved Hospital, Ringstedgade 57a, 4700 Naestved, Denmark
- Correspondence:
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Santhanam H, Kundu SK. Assessment of Socio-technical Constraints of Marine Fishers in the Utilisation of Marine Fishery Advisories in Southern Odisha, India. ANTHROPOCENE SCIENCE 2022. [PMCID: PMC8907898 DOI: 10.1007/s44177-022-00014-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Sustainable marine fishing practices are often hindered by local-level factors in areas with high fishery potentials, such as Odisha, India. Scientific services to fishing, such as Marine Fishery Advisories (MFAs) on the Potential Fishing Zone (PFZ) and weather information in the form of Ocean State Forecast (OSF) advisories provided by INCOIS, India, are valuable knowledge products which can help the fishers to overcome several socio-technical constraints (STCs) to effective fishing practices. The present investigation provides a critical analysis of five STCs prevailing in 4 districts (Kendrapara, Jagatsinghpur, Puri and Ganjam) of Southern Odisha which can possibly hinder the effective assimilation of the MFAs. These five STCs are the hierarchy of fishers in fishing operations, pathways of transition to new fishing technologies, the adaptive capacity of the fishers to use scientific advisories, the need to achieve economic resilience from fishing as well as the contribution to the preservation of ecosystem sustainability. Stakeholder mapping based on the ground-based observations revealed that inadequate transitions pathways, varying hierarchical positions and low adaptive capacities contributed to higher STCs in general. Sensitivity of the fishers to achieving economic as well as environmental sustainability in their enterprise leads to lower STCs and greater assimilation capacities. The analyses of STCs presented here provide a robust methodology to manage the social cost of carbon which can be useful to achieve sustainability targets with respect to marine fisheries by adopting regular use of MFAs.
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Cunha RL, Costa A, Godinho F, Santos C, Castilho R. Hidden diversity of the olive ridley sea turtle (Lepidochelys olivacea) from Angola, West Africa. CONSERV GENET 2022. [DOI: 10.1007/s10592-021-01422-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Silver‐Gorges I, Koval J, Rodriguez‐Zarate CJ, Paladino FV, Jordan M. Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific Olive ridley sea turtles ( Lepidochelys olivacea). Ecol Evol 2020; 10:8688-8704. [PMID: 32884651 PMCID: PMC7452818 DOI: 10.1002/ece3.6564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 06/04/2020] [Accepted: 06/15/2020] [Indexed: 12/29/2022] Open
Abstract
Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial control region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (F ST = 0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and preexisting microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (F ST = 0.08, p < .001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (F ST = 0.103, p < .001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p < .001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life history, particularly in light of the natal-homing paradigm.
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Affiliation(s)
- Ian Silver‐Gorges
- Department of BiologyCenter for Marine Conservation and BiologyPurdue University‐Fort WayneFort WayneINUSA
| | - Julianne Koval
- Department of BiologyCenter for Marine Conservation and BiologyPurdue University‐Fort WayneFort WayneINUSA
| | - Clara J. Rodriguez‐Zarate
- Marine Turtle Conservation ProgrammeEmirates Nature in Association with World Wide Fund for Nature (WWF)DubaiUnited Arab Emirates
| | - Frank V. Paladino
- Department of BiologyCenter for Marine Conservation and BiologyPurdue University‐Fort WayneFort WayneINUSA
| | - Mark Jordan
- Department of BiologyCenter for Marine Conservation and BiologyPurdue University‐Fort WayneFort WayneINUSA
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9
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Infante-Rojas H, Marino-Ramirez L, Hernández-Fernández J. Structural analysis of leucine, lysine and tryptophan mitochondrial tRNA of nesting turtles Caretta caretta (Testudines: Chelonioidea) in the Colombian Caribbean. PeerJ 2020; 8:e9204. [PMID: 32596037 PMCID: PMC7306221 DOI: 10.7717/peerj.9204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/25/2020] [Indexed: 11/20/2022] Open
Abstract
The understanding of the functional properties of mitochondrial transfer RNA (mt tRNAs) depend on the knowledge of its structure. tRNA acts as an interface between polynucleotides and polypeptides thus, they are key molecules in protein biosynthesis. The tRNA molecule has a functional design and, given its importance in the translation of mitochondrial genes, it is plausible that modifications of the structure can affect the synthesis of proteins and the functional properties of the mitochondria. In a previous work, the mitochondrial genome of an individual of the nesting Caretta caretta of the Colombian Caribbean was obtained, where specific mutations were identified in the only tRNALeu (CUN), tRNATrp and tRNALys genes. In order to analyze the effect of these mutations on these three mt tRNAs, the prediction of 2D and 3D structures was performed. Genes were sequenced in 11 nesting loggerhead turtles from the Colombian Caribbean. Two-dimensional structures were inferred using the ARWEN program, and three-dimensional structures were obtained with the RNA Composer 3D program. Two polymorphisms were identified in tRNATrp and another one was located in tRNALys, both specific to C. caretta. The thymine substitution in nucleotide position 14 of tRNATrp could constitute an endemic polymorphism of the nesting colony of the Colombian Caribbean. Two 2D and three 3D patterns were obtained for tRNATrp. In the case of tRNALys and tRNALeu 2D and 3D structures were obtained respectively, which showed compliance to canonical structures, with 4 bp in the D-arm, 4-5 bp in the T-arm, and 5 bp in the anticodon arm. Moderate deviations were found, such as a change in the number of nucleotides, elongation in loops or stems and non-Watson-Crick base pairing: adenine-adenine in stem D of tRNATrp, uracil-uracil and adenine-cytosine in the acceptor arm of the tRNALys and cytosine-cytosine in the anticodon stem of the tRNALeu. In addition, distortions or lack of typical interactions in 3D structures gave them unique characteristics. According to the size of the variable region (4-5 nt), the three analyzed tRNAs belong to class I. The interactions in the three studied tRNAs occur mainly between D loop-variable region, and between spacer bases-variable region, which classifies them as tRNA of typology II. The polymorphisms and structural changes described can, apparently, be post-transcriptionally stabilized. It will be crucial to perform studies at the population and functional levels to elucidate the synthetic pathways affected by these genes. This article analyses for the first time the 1D, 2D and 3D structures of the mitochondrial tRNALys, tRNATrp and tRNALeu in the loggerhead turtle.
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Affiliation(s)
- Harvey Infante-Rojas
- Department of Natural and Environmental Sciences, Genetics, Molecular Biology and Bioinformatics Lab, Jorge Tadeo Lozano University, Bogotá, Cundinamarca, Colombia
| | | | - Javier Hernández-Fernández
- Department of Natural and Environmental Sciences, Genetics, Molecular Biology and Bioinformatics Lab, Jorge Tadeo Lozano University, Bogotá, Cundinamarca, Colombia
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10
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Hebbar P, Ravikanth G, Aravind NA. A review on the conservation genetic studies of Indian amphibians and their implications on developing strategies for conservation†. J Genet 2019. [DOI: 10.1007/s12041-019-1159-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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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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12
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Work TM, Dagenais J, Stacy BA, Ladner JT, Lorch JM, Balazs GH, Barquero-Calvo E, Berlowski-Zier BM, Breeden R, Corrales-Gómez N, Gonzalez-Barrientos R, Harris HS, Hernández-Mora G, Herrera-Ulloa Á, Hesami S, Jones TT, Morales JA, Norton TM, Rameyer RA, Taylor DR, Waltzek TB. A novel host-adapted strain of Salmonella Typhimurium causes renal disease in olive ridley turtles (Lepidochelys olivacea) in the Pacific. Sci Rep 2019; 9:9313. [PMID: 31249336 PMCID: PMC6597722 DOI: 10.1038/s41598-019-45752-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/14/2019] [Indexed: 01/01/2023] Open
Abstract
Salmonella spp. are frequently shed by wildlife including turtles, but S. enterica subsp. enterica serovar Typhimurium or lesions associated with Salmonella are rare in turtles. Between 1996 and 2016, we necropsied 127 apparently healthy pelagic olive ridley turtles (Lepidochelys olivacea) that died from drowning bycatch in fisheries and 44 live or freshly dead stranded turtles from the west coast of North and Central America and Hawaii. Seven percent (9/127) of pelagic and 47% (21/44) of stranded turtles had renal granulomas associated with S. Typhimurium. Stranded animals were 12 times more likely than pelagic animals to have Salmonella-induced nephritis suggesting that Salmonella may have been a contributing cause of stranding. S. Typhimurium was the only Salmonella serovar detected in L. olivacea, and phylogenetic analysis from whole genome sequencing showed that the isolates from L. olivacea formed a single clade distinct from other S. Typhimurium. Molecular clock analysis revealed that this novel clade may have originated as recently as a few decades ago. The phylogenetic lineage leading to this group is enriched for non-synonymous changes within the genomic area of Salmonella pathogenicity island 1 suggesting that these genes are important for host adaptation.
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Affiliation(s)
- Thierry M Work
- US Geological Survey, National Wildlife Health Center, Honolulu Field Station, Honolulu, Hawaii, 96850, United States of America.
| | - Julie Dagenais
- US Geological Survey, National Wildlife Health Center, Honolulu Field Station, Honolulu, Hawaii, 96850, United States of America
| | - Brian A Stacy
- NOAA Fisheries, Office of Protected Resources, University of Florida, Gainesville, Florida, 32603, United States of America
| | - Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, 86011, United States of America
| | - Jeffrey M Lorch
- US Geological Survey, National Wildlife Health Center, Madison, Wisconsin, 53711, United States of America
| | - George H Balazs
- Golden Honu Services of Oceania, Honolulu, Hawaii, 96825, United States of America
| | - Elías Barquero-Calvo
- Escuela de Medicina Veterinaria (EMV), Universidad Nacional Costa Rica, Heredia, 3000, Costa Rica
| | - Brenda M Berlowski-Zier
- US Geological Survey, National Wildlife Health Center, Madison, Wisconsin, 53711, United States of America
| | - Renee Breeden
- US Geological Survey, National Wildlife Health Center, Honolulu Field Station, Honolulu, Hawaii, 96850, United States of America
| | | | - Rocio Gonzalez-Barrientos
- Pathology Area National Service of Animal Health (SENASA), Ministry of Agriculture and Livestock, Heredia, 3000, Costa Rica
| | - Heather S Harris
- NOAA Fisheries West Coast Region, Morro Bay, California, United States of America
| | - Gabriela Hernández-Mora
- Pathology Area National Service of Animal Health (SENASA), Ministry of Agriculture and Livestock, Heredia, 3000, Costa Rica
| | - Ángel Herrera-Ulloa
- Bacteriology Area, National Service of Animal Health (SENASA), Ministry of Agriculture and Livestock, Heredia, 3000, Costa Rica
| | - Shoreh Hesami
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, 32603, United States of America
| | - T Todd Jones
- NOAA Fisheries, Pacific Islands Fisheries Science Center, Honolulu, Hawaii, 96818, United States of America
| | - Juan Alberto Morales
- Escuela de Medicina Veterinaria (EMV), Universidad Nacional Costa Rica, Heredia, 3000, Costa Rica
| | - Terry M Norton
- Georgia Sea Turtle Center/Jekyll Island Authority, Jekyll Island, Georgia, 31527, United States of America
| | - Robert A Rameyer
- US Geological Survey, National Wildlife Health Center, Honolulu Field Station, Honolulu, Hawaii, 96850, United States of America
| | - Daniel R Taylor
- US Geological Survey, National Wildlife Health Center, Madison, Wisconsin, 53711, United States of America
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, 32603, United States of America
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Rodríguez-Zárate CJ, Sandoval-Castillo J, van Sebille E, Keane RG, Rocha-Olivares A, Urteaga J, Beheregaray LB. Isolation by environment in the highly mobile olive ridley turtle ( Lepidochelys olivacea) in the eastern Pacific. Proc Biol Sci 2019; 285:rspb.2018.0264. [PMID: 29720414 DOI: 10.1098/rspb.2018.0264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/10/2018] [Indexed: 11/12/2022] Open
Abstract
Spatial and temporal scales at which processes modulate genetic diversity over the landscape are usually overlooked, impacting the design of conservation management practices for widely distributed species. We examine processes shaping population divergence in highly mobile species by re-assessing the case of panmixia in the iconic olive ridley turtle from the eastern Pacific. We implemented a biophysical model of connectivity and a seascape genetic analysis based on nuclear DNA variation of 634 samples collected from 27 nesting areas. Two genetically distinct populations largely isolated during reproductive migrations and mating were detected, each composed of multiple nesting sites linked by high connectivity. This pattern was strongly associated with a steep environmental gradient and also influenced by ocean currents. These findings relate to meso-scale features of a dynamic oceanographic interface in the eastern tropical Pacific (ETP) region, a scenario that possibly provides different cost-benefit solutions and selective pressures for sea turtles during both the mating and migration periods. We reject panmixia and propose a new paradigm for olive ridley turtles where reproductive isolation due to assortative mating is linked to its environment. Our study demonstrates the relevance of integrative approaches for assessing the role of environmental gradients and oceanographic currents as drivers of genetic differentiation in widely distributed marine species. This is relevant for the conservation management of species of highly mobile behaviour, and assists the planning and development of large-scale conservation strategies for the threatened olive ridley turtles in the ETP.
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Affiliation(s)
| | | | - Erik van Sebille
- Institute for Marine and Atmospheric Research, Utrecht University, 3584 CC, The Netherlands.,Grantham Institute and Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Robert G Keane
- Geographic Information Systems, Flinders University, Adelaide, South Adelaide 5001, Australia
| | - Axayácatl Rocha-Olivares
- Laboratorio de Ecología Molecular, Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada Baja California 22860, Mexico
| | | | - Luciano B Beheregaray
- Molecular Ecology Laboratory, Flinders University, Adelaide, South Adelaide 5001, Australia
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Pinou T, Prunier R, Bresson M, Padilla IE, Javier Perez JF, Robles JAT, DiGiovanni RA, Robinson NJ. Repeated sampling adds to the genetic diversity of Lepidochelys olivacea (Eschscholtz 1829) olive ridley sea turtle. J NAT HIST 2019. [DOI: 10.1080/00222933.2018.1557755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Theodora Pinou
- Department of Biological and Environmental Sciences, Western Connecticut State University, Danbury, USA
| | - Rachel Prunier
- Centro Universitario De La Costa Sur, Universidad de Guadalajara, Jalisco, Mexico
| | - Meghan Bresson
- Riverhead Foundation for Marine Research and Preservation, Riverhead, USA
| | | | | | | | - Robert A. DiGiovanni
- Departamento de Ecología, Universidad de Guadalajara, Centro Universitario de Ciencias Biológicas y Agropecuarias, Zapopan, México
| | - Nathan J. Robinson
- Cape Eleuthera Institute, Cape Eleuthera Island School, Cape Eleuthera, Eleuthera, The Bahamas
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15
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Shamblin BM, Bolten AB, Abreu-Grobois FA, Bjorndal KA, Cardona L, Carreras C, Clusa M, Monzón-Argüello C, Nairn CJ, Nielsen JT, Nel R, Soares LS, Stewart KR, Vilaça ST, Türkozan O, Yilmaz C, Dutton PH. Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences. PLoS One 2014; 9:e85956. [PMID: 24465810 PMCID: PMC3900438 DOI: 10.1371/journal.pone.0085956] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/04/2013] [Indexed: 11/24/2022] Open
Abstract
Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (∼800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.
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Affiliation(s)
- Brian M. Shamblin
- National Research Council Research Associateship Program, Washington, D.C., United States of America
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Atmospheric and Oceanic Administration Fisheries, La Jolla, California, United States of America
| | - Alan B. Bolten
- Archie Carr Center for Sea Turtle Research and Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - F. Alberto Abreu-Grobois
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán, Sinaloa, México
| | - Karen A. Bjorndal
- Archie Carr Center for Sea Turtle Research and Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Luis Cardona
- Department of Animal Biology and IRBio, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Carlos Carreras
- Department of Animal Biology and IRBio, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Marine Turtle Research Group, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Peryn, Cornwall, United Kingdom
| | - Marcel Clusa
- Department of Animal Biology and IRBio, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Catalina Monzón-Argüello
- Departamento de Biología, Universidad de Las Palmas de Gran Canaria, Campus de Tafira, Las Palmas de Gran Canaria, Spain
| | - Campbell J. Nairn
- Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Janne T. Nielsen
- Department of Biology, University of Miami, Coral Gables, Florida, United States of America
| | - Ronel Nel
- Zoology Department, Nelson Mandela Metropolitan University, Summerstrand Campus South, University Way, Summerstrand, Port Elizabeth, South Africa
| | - Luciano S. Soares
- Archie Carr Center for Sea Turtle Research and Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Projeto TAMAR-ICMBio, Salvador, BA, Brazil
| | - Kelly R. Stewart
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Atmospheric and Oceanic Administration Fisheries, La Jolla, California, United States of America
- The Ocean Foundation, Washington, D.C., United States of America
| | - Sibelle T. Vilaça
- Laboratório de Biodiversidade e Evolução Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Oguz Türkozan
- Adnan Menderes University, Faculty of Science and Arts, Department of Biology, Aydin, Turkey
| | - Can Yilmaz
- Adnan Menderes University, Faculty of Science and Arts, Department of Biology, Aydin, Turkey
| | - Peter H. Dutton
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Atmospheric and Oceanic Administration Fisheries, La Jolla, California, United States of America
- * E-mail:
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Jensen MP, Limpus CJ, Whiting SD, Guinea M, Prince RIT, Dethmers KEM, Adnyana IBW, Kennett R, FitzSimmons NN. Defining olive ridley turtle Lepidochelys olivacea management units in Australia and assessing the potential impact of mortality in ghost nets. ENDANGER SPECIES RES 2013. [DOI: 10.3354/esr00521] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Natal Homing and Imprinting in Sea Turtles. THE BIOLOGY OF SEA TURTLES, VOLUME III 2013. [DOI: 10.1201/b13895-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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18
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Leroux RA, Dutton PH, Abreu-Grobois FA, Lagueux CJ, Campbell CL, Delcroix E, Chevalier J, Horrocks JA, Hillis-Starr Z, Troëng S, Harrison E, Stapleton S. Re-examination of population structure and phylogeography of hawksbill turtles in the wider Caribbean using longer mtDNA sequences. ACTA ACUST UNITED AC 2012; 103:806-20. [PMID: 23045611 DOI: 10.1093/jhered/ess055] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Management of the critically endangered hawksbill turtle in the Wider Caribbean (WC) has been hampered by knowledge gaps regarding stock structure. We carried out a comprehensive stock structure re-assessment of 11 WC hawksbill rookeries using longer mtDNA sequences, larger sample sizes (N = 647), and additional rookeries compared to previous surveys. Additional variation detected by 740 bp sequences between populations allowed us to differentiate populations such as Barbados-Windward and Guadeloupe (F (st) = 0.683, P < 0.05) that appeared genetically indistinguishable based on shorter 380 bp sequences. POWSIM analysis showed that longer sequences improved power to detect population structure and that when N < 30, increasing the variation detected was as effective in increasing power as increasing sample size. Geographic patterns of genetic variation suggest a model of periodic long-distance colonization coupled with region-wide dispersal and subsequent secondary contact within the WC. Mismatch analysis results for individual clades suggest a general population expansion in the WC following a historic bottleneck about 100 000-300 000 years ago. We estimated an effective female population size (N (ef)) of 6000-9000 for the WC, similar to the current estimated numbers of breeding females, highlighting the importance of these regional rookeries to maintaining genetic diversity in hawksbills. Our results provide a basis for standardizing future work to 740 bp sequence reads and establish a more complete baseline for determining stock boundaries in this migratory marine species. Finally, our findings illustrate the value of maintaining an archive of specimens for re-analysis as new markers become available.
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Affiliation(s)
- Robin A Leroux
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
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19
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Moura CCDM, Guimarães EDS, Moura GJBD, Amaral GJAD, Silva ACD. Distribuição espaço-temporal e sucesso reprodutivo de Eretmochelys imbricata nas praias do Ipojuca, Pernambuco, Brasil. ACTA ACUST UNITED AC 2012. [DOI: 10.1590/s0073-47212012005000003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Este estudo objetivou verificar a distribuição temporal e espacial de Eretmochelys imbricata (Linnaeus, 1766) e aspectos de sua biologia reprodutiva, tais como tempo de incubação, sucesso reprodutivo, biometria das fêmeas, número de ninhos e fecundidade. Os dados foram coletados de 2007 a 2010 nas praias de Muro Alto, Cupe, Merepe, Porto de Galinhas e Maracaípe, todas elas localizadas no município do Ipojuca, estado de Pernambuco, Brasil. Foram analisados comparativamente parâmetros relativos à biologia reprodutiva e áreas de nidificação da espécie. Eretmochelys imbricata foi registrada nidificando entre os meses de outubro a maio, totalizando 350 ninhos monitorados em três temporadas. Os picos de desova ocorreram de janeiro a março, revelando um padrão sazonal das desovas. Houve diferença significativa entre o número de ninhos nas temporadas. A praia de Merepe apresentou uma ocorrência elevada de ninhos (46 ninhos/km) em relação às demais praias monitoradas. Quanto aos aspectos da biologia reprodutiva, o sucesso reprodutivo foi 65,6%, e o intervalo do tempo de incubação de 54 a 56 dias. As medidas biométricas foram coletadas de 59 espécimes, e apresentaram média de 92,5 cm ± 4,5 para o comprimento curvilíneo da carapaça e de 83,4 cm ± 5 para a largura curvilínea da carapaça. Os resultados podem ser utilizados para subsidiar planos de conservação e demonstram que as praias registradas neste estudo têm relevância como áreas de nidificação para E. imbricata.
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20
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Marine turtle mitogenome phylogenetics and evolution. Mol Phylogenet Evol 2012; 65:241-50. [PMID: 22750111 DOI: 10.1016/j.ympev.2012.06.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 11/21/2022]
Abstract
The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution.
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21
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Plot V, de Thoisy B, Blanc S, Kelle L, Lavergne A, Roger-Bérubet H, Tremblay Y, Fossette S, Georges JY. Reproductive synchrony in a recovering bottlenecked sea turtle population. J Anim Ecol 2011; 81:341-51. [PMID: 22007680 DOI: 10.1111/j.1365-2656.2011.01915.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
1. The assessment of species extinction risk has been well established for some time now. Assessing the potential for recovery in endangered species is however much more challenging, because complementary approaches are required to detect reliable signals of positive trends. 2. This study combines genetics, demography and behavioural data at three different time-scales to assess historical and recent population changes and evidence of reproductive synchrony in a small population of olive ridley sea turtle Lepidochelys olivacea. Lepidochelys is considered as the most extraordinary example of reproductive synchrony in reptiles, yet to date, it has only been reported in large populations. 3. Using Bayesian coalescent-based models on microsatellite nuclear DNA variability, we demonstrate that effective population size in olive ridleys nesting in French Guiana has dramatically declined by 99% over the last 20 centuries. This low current population size is further illustrated by the absence of genetic mitochondrial DNA diversity in the present nesting population. Yet, monitoring of nesting sites in French Guiana suggests a possible recovery of the population over the last decade. 4. Satellite telemetry shows that over the first 14 days of their 28-days inter-nesting interval, i.e. when eggs maturation is likely to occur, gravid females disperse over the continental shelf. They then gather together with a striking spatiotemporal consistency close to the nesting site, where they later emerge for their second nesting event. 5. Our results therefore suggest that reproductive synchrony also occurs in small populations. Olive ridleys may ensure this synchrony by adjusting the duration of the second half of their inter-nesting interval prior to landing, possibly through social mediation. 6. Such reproductive synchrony may be related to the maintenance of some species-specific strategy despite former collapse and may contribute to the present population recovery. The gregarious behaviour of reproductive individuals close to shore where human-induced perturbations occur is however a cause for conservation concern for this still poorly known species.
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Affiliation(s)
- Virginie Plot
- Université de Strasbourg, IPHC, 23 rue Becquerel, 67087 Strasbourg, France
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22
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Burbrink FT, Pyron RA. THE IMPACT OF GENE-TREE/SPECIES-TREE DISCORDANCE ON DIVERSIFICATION-RATE ESTIMATION. Evolution 2011; 65:1851-61. [PMID: 21729043 DOI: 10.1111/j.1558-5646.2011.01260.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frank T Burbrink
- Department of Biology, The College of Staten Island, The City University of New York, Staten Island, New York 10314, USA
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23
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NARO‐MACIEL EUGENIA, REID BRENDAN, FITZSIMMONS NANCYN, LE MINH, DESALLE ROB, AMATO GEORGE. DNA barcodes for globally threatened marine turtles: a registry approach to documenting biodiversity. Mol Ecol Resour 2010; 10:252-63. [DOI: 10.1111/j.1755-0998.2009.02747.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- EUGENIA NARO‐MACIEL
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
| | - BRENDAN REID
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
| | - NANCY N. FITZSIMMONS
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - MINH LE
- Center for Natural Resources and Environmental Studies, Vietnam National University, 19 Le Thanh Tong St., Hanoi, Vietnam
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - ROB DESALLE
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - GEORGE AMATO
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
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24
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Reis EC, Soares LS, Vargas SM, Santos FR, Young RJ, Bjorndal KA, Bolten AB, Lôbo-Hajdu G. Genetic composition, population structure and phylogeography of the loggerhead sea turtle: colonization hypothesis for the Brazilian rookeries. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9975-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Singh L. Development and exploitation of DNA fingerprinting technology in India. Biotechnol J 2009; 4:335-41. [DOI: 10.1002/biot.200900015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Abstract
The seven species of sea turtles occupy a diversity of niches, and have a history tracing back over 100 million years, yet all share basic life-history features, including exceptional navigation skills and periodic migrations from feeding to breeding habitats. Here, we review the biogeographic, behavioural, and ecological factors that shape the distribution of genetic diversity in sea turtles. Natal homing, wherein turtles return to their region of origin for mating and nesting, has been demonstrated with mtDNA sequences. These maternally inherited markers show strong population structure among nesting colonies while nuclear loci reveal a contrasting pattern of male-mediated gene flow, a phenomenon termed 'complex population structure'. Mixed-stock analyses indicate that multiple nesting colonies can contribute to feeding aggregates, such that exploitation of turtles in these habitats can reduce breeding populations across the region. The mtDNA data also demonstrate migrations across entire ocean basins, some of the longest movements of marine vertebrates. Multiple paternity occurs at reported rates of 0-100%, and can vary by as much as 9-100% within species. Hybridization in almost every combination among members of the Cheloniidae has been documented but the frequency and ultimate ramifications of hybridization are not clear. The global phylogeography of sea turtles reveals a gradient based on habitat preference and thermal regime. The cold-tolerant leatherback turtle (Dermochelys coriacea) shows no evolutionary partitions between Indo-Pacific and Atlantic populations, while the tropical green (Chelonia mydas), hawksbill (Eretmochelys imbricata), and ridleys (Lepidochelys olivacea vs. L. kempi) have ancient separations between oceans. Ridleys and loggerhead (Caretta caretta) also show more recent colonization between ocean basins, probably mediated by warm-water gyres that occasionally traverse the frigid upwelling zone in southern Africa. These rare events may be sufficient to prevent allopatric speciation under contemporary geographic and climatic conditions. Genetic studies have advanced our understanding of marine turtle biology and evolution, but significant gaps persist and provide challenges for the next generation of sea turtle geneticists.
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Affiliation(s)
- B W Bowen
- Hawaii Institute of Marine Biology, University of Hawaii, PO Box 1346, Kaneohe, HI 96744, USA.
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27
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Aggarwal RK, Lalremruata A, Velavan TP, Pavani Sowjanya A, Singh L. Development and characterization of ten novel microsatellite markers from olive ridley sea turtle (Lepidochelys olivacea). CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9421-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Gururaja KV, Aravind NA, Ali S, Ramachandra TV, Velavan TP, Krishnakumar V, Aggarwal RK. A new frog species from the central western Ghats of India, and its phylogenetic position. Zoolog Sci 2007; 24:525-34. [PMID: 17867853 DOI: 10.2108/zsj.24.525] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Accepted: 12/01/2006] [Indexed: 11/17/2022]
Abstract
Tropical evergreen forests of Indian subcontinent, especially of the Western Ghats, are known hot spots of amphibian diversity, where many new anuran species await to be identified. Here we describe from the Sharavathi River basin of central Western Ghats a new shrub-frog taxon related to the anuran family Rhacophoridae. The new frog possesses the characteristic features of rhacophorids (dilated digit tips with differentiated pads circumscribed by a complete groove, intercalary cartilages on digits, T-shaped terminal phalanges and granular belly, the adaptive characters for arboreal life forms), but also a suite of unique features that distinguish it from all known congeners in the region. Morphogenetic analysis based on morphological characteristics and diversity in the mitochondrial 12S and 16S rRNA genes revealed it to be a new Philautus species that we named Philautus neelanethrus sp. nov. The phylogenetic analysis suggests the new frog to represent a relatively early Philautus species lineage recorded from the region. The distribution pattern of the species suggests its importance as a bioindicator of habitat health. In general, this relatively widespread species was found distributed only in non-overlapping small stretches, which indirectly indicates the fragmentation of the evergreen to moist deciduous forests that characterize the Western Ghats. Thus the discovery of the new rhacophorid species described here not only further reinforces the significance of the Western Ghats as a major hotspot of amphibian biodiversity, but also brings into focus the deterioration of forest habitats in the region and the need for prioritization of their conservation.
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Affiliation(s)
- Kotambylu Vasudeva Gururaja
- Energy and Wetlands Research Group, Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
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29
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Aggarwal RK, Kivisild T, Ramadevi J, Singh L. Mitochondrial DNA coding region sequences support the phylogenetic distinction of two Indian wolf species. J ZOOL SYST EVOL RES 2007. [DOI: 10.1111/j.1439-0469.2006.00400.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Lee PLM, Luschi P, Hays GC. Detecting female precise natal philopatry in green turtles using assignment methods. Mol Ecol 2007; 16:61-74. [PMID: 17181721 DOI: 10.1111/j.1365-294x.2006.03115.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
It is well established that sea turtles return to natal rookeries to mate and lay their eggs, and that individual females are faithful to particular nesting sites within the rookery. Less certain is whether females are precisely returning to their natal beach. Attempts to demonstrate such precise natal philopatry with genetic data have had mixed success. Here we focused on the green turtles of three nesting sites in the Ascension Island rookery, separated by 5-15 km. Our approach differed from previous work in two key areas. First, we used male microsatellite data (five loci) reconstructed from samples collected from their offspring (N = 17) in addition to data for samples taken directly from females (N = 139). Second, we employed assignment methods in addition to the more traditional F-statistics. No significant genetic structure could be demonstrated with F(ST). However, when average assignment probabilities of females were examined, those for nesting populations in which they were sampled were indeed significantly higher than their probabilities for other populations (Mann-Whitney U-test: P < 0.001). Further evidence was provided by a significant result for the mAI(C) test (P < 0.001), supporting greater natal philopatry for females compared with males. The results suggest that female natal site fidelity was not sufficient for significant genetic differentiation among the nesting populations within the rookery, but detectable with assignment tests.
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Affiliation(s)
- Patricia L M Lee
- Institute of Environmental Sustainability, Department of Biological Sciences, University of Wales Swansea, Swansea SA2 8PP, UK.
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31
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The genetic structure of the loggerhead sea turtle (Caretta caretta) in the Mediterranean as revealed by nuclear and mitochondrial DNA and its conservation implications. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9224-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Pearce JM. Minding the gap: frequency of indels in mtDNA control region sequence data and influence on population genetic analyses. Mol Ecol 2006; 15:333-41. [PMID: 16448404 DOI: 10.1111/j.1365-294x.2005.02781.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Insertions and deletions (indels) result in sequences of various lengths when homologous gene regions are compared among individuals or species. Although indels are typically phylogenetically informative, occurrence and incorporation of these characters as gaps in intraspecific population genetic data sets are rarely discussed. Moreover, the impact of gaps on estimates of fixation indices, such as F(ST), has not been reviewed. Here, I summarize the occurrence and population genetic signal of indels among 60 published studies that involved alignments of multiple sequences from the mitochondrial DNA (mtDNA) control region of vertebrate taxa. Among 30 studies observing indels, an average of 12% of both variable and parsimony-informative sites were composed of these sites. There was no consistent trend between levels of population differentiation and the number of gap characters in a data block. Across all studies, the average influence on estimates of PhiST was small, explaining only an additional 1.8% of among population variance (range 0.0-8.0%). Studies most likely to observe an increase in PhiST with the inclusion of gap characters were those with < 20 variable sites, but a near equal number of studies with few variable sites did not show an increase. In contrast to studies at interspecific levels, the influence of indels for intraspecific population genetic analyses of control region DNA appears small, dependent upon total number of variable sites in the data block, and related to species-specific characteristics and the spatial distribution of mtDNA lineages that contain indels.
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Affiliation(s)
- John M Pearce
- Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska, Fairbanks, AK 99775, USA.
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López-Castro MC, Rocha-Olivares A. The panmixia paradigm of eastern Pacific olive ridley turtles revised: consequences for their conservation and evolutionary biology. Mol Ecol 2006; 14:3325-34. [PMID: 16156806 DOI: 10.1111/j.1365-294x.2005.02652.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous studies of the olive ridley Lepidochelys olivacea population structure in the tropical eastern Pacific have indicated the existence of a single panmictic population ranging from Costa Rica to Mexico. This information has been used to design specific management measures to conserve primary nesting beaches in Mexico. However, little is known about olive ridleys in the Baja California Peninsula, their northernmost reproductive limit, where recent observations have shown differences in nesting female behaviour and size of hatchlings relative to other continental rookeries. We used mtDNA control region sequences from 137 turtles from five continental and four peninsular nesting sites to determine whether such differences correspond to a genetic distinction of Baja California olive ridleys or to phenotypic plasticity associated with the extreme environmental nesting conditions of this region. We found that genetic diversity in peninsular turtles was significantly lower than in continental nesting colonies. Analysis of molecular variance revealed a significant population structure (Phi ST = 0.048, P = 0.006) with the inclusion of peninsular samples. Our results: (i) suggest that the observed phenotypic variation may be associated with genetic differentiation and reproductive isolation; (ii) support the recent colonization of the eastern Pacific by Lepidochelys; (iii) reveal genetic signatures of historical expansion and colonization events; and (iv) significantly challenge the notion of a single genetic and conservation unit of olive ridleys in the eastern Pacific. We conclude that conservation measures for olive ridleys in Mexico should be revised to grant peninsular beaches special attention.
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Affiliation(s)
- M C López-Castro
- Laboratorio de Ecología Molecular, Departamento de Oceanografía Biológica, División de Oceanología, Centro de Investigación Científica y de Educación Superior de Ensenada, Km 107 carretera Tijuana-Ensenada, Ensenada Baja California 22860, México
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Abstract
The Ashoka Trust for Research in Ecology and the Environment was established in 1996 to curtail the rapid loss of India's biological resources and natural ecosystems.
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Affiliation(s)
- Kartik Shanker
- Ashoka Trust for Research in Ecology and the Environment, Bangalore, India.
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