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Vella A, Vella N. The First Report of Pennella (Crustacea: Copepoda) Infesting Stenella coeruleoalba Stranded in Malta: Morphological and Genetic Analyses. Animals (Basel) 2024; 14:1107. [PMID: 38612346 PMCID: PMC11010884 DOI: 10.3390/ani14071107] [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: 01/31/2024] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Here, we document the stranding of a striped dolphin Stenella coeruleoalba (Meyen, 1833) (Mammalia: Delphinidae), which was found dead in Maltese waters in July 2020. The stranded dolphin exhibited a severe infestation of the mesoparasitic copepod, Pennella balaenoptera Koren and Danielssen, 1877 (Copepoda: Pennelidae). Parasites of this genus represent the largest known mesoparasites to infest cetaceans. Under normal circumstances, cetaceans may have a few P. balaenoptera individuals attached to them, but cetaceans with compromised health are more prone to heavy infestations. The identification of the parasite was accomplished through morphological and genetic analyses. This incident highlights the significance of monitoring mesoparasitic infestations, offering valuable insights into the health of cetacean populations and emphasizing the potential implications for conservation efforts in the region.
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Affiliation(s)
- Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, MSD 2080 Msida, Malta
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Delgado-Cano D, Mariño-Ramírez L, Hernández-Fernández J. Detection of high heteroplasmy in complete loggerhead and hawksbill sea turtles mitochondrial genomes using RNAseq. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:106-114. [PMID: 33629889 DOI: 10.1080/24701394.2021.1885389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Sea turtle populations around the world face rapid decline due to the effect of anthropogenic and environmental factors. Among the affected populations are those of hawksbill turtles (Eretmochelys imbricata) and loggerhead turtles (Caretta caretta), which is why a greater effort is currently being made in their monitoring and tracing. The intragenic degree of heteroplasmic mutations, commonly associated with diseases of variable symptoms, has not been analyzed in these species. In this study, heteroplasmy in the complete mitogenome (mtDNA) of three loggerhead turtles and one hawksbill turtle was identified from data obtained by RNAseq. Individuals Cc3, Ei1, Cc1 and Cc2 presented 0.3, 1.7, 1.8 and 7.1% of heteroplasmic mutations in all their mtDNA, respectively. The protein-coding genes that presented the highest percentage of heteroplasmy were ND4 and ND5 in individual Cc2 with 16 and 38.6%, respectively. Of the tRNA genes, only tRNATyr was heteroplasmic in the four individuals with 5.63% (Cc1), 25.35% (Ei1 and Cc2) and 49.3% (Cc3). In this study, we identified the critical sites of heteroplasmy in each individual and the genetic variability of their mitogenomes. The data obtained represents the baseline for future projects that evaluate the population status of these species.
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Affiliation(s)
- David Delgado-Cano
- Department of Natural and Environmental Sciences, Faculty of Science and Engineering, Genetics, Molecular Biology and Bioinformatic Research Group -GENBIMOL, Jorge Tadeo Lozano University, Bogotá, South America
| | | | - Javier Hernández-Fernández
- Department of Natural and Environmental Sciences, Faculty of Science and Engineering, Genetics, Molecular Biology and Bioinformatic Research Group -GENBIMOL, Jorge Tadeo Lozano University, Bogotá, South America
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3
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Camacho-Sánchez FY, Aguirre AA, Narváez-Zapata JA, Zavala-Norzagaray AA, Ley-Quiñónez CP, Acosta-Sánchez HH, Rodriguez-González H, Delgado-Trejo C, Reyes-López MA. DNA barcode analysis of the endangered green turtle ( Chelonia mydas) in Mexico 1. Genome 2021; 64:879-891. [PMID: 33555972 DOI: 10.1139/gen-2019-0213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Technological and analytical advances to study evolutionary biology, ecology, and conservation of green turtles (Chelonia mydas) are realized through molecular approaches including DNA barcoding. We characterized the usefulness of COI DNA barcodes in green turtles in Mexico to better understand genetic divergence and other genetic parameters of this species. We analyzed 63 sequences, including 25 from green turtle field specimens collected from the Gulf of Mexico and from the Mexican Pacific and 38 already present in the Barcode of Life Data Systems (BOLD). A total of 13 haplotypes were identified with four novel haplotypes from the Pacific Ocean and three novel haplotypes from the Atlantic Ocean. Intraspecific distance values among COI gene sequences by two different models were 0.01, demonstrating that there is not a subdivision for green turtle species. Otherwise, the interspecific distance interval ranged from 0.07 to 0.13, supporting a clear subdivision among all sea turtle species. Haplotype and total nucleotide diversity values of the COI gene reflect a medium genetic diversity average. Green turtles of the Mexican Pacific showed common haplotypes to some Australian and Chinese turtles, but different from the haplotypes of the Mexican Atlantic. COI analysis revealed new haplotypes and confirmed that DNA barcodes were useful for evaluation of the population diversity of green turtles in Mexico.
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Affiliation(s)
- Fátima Yedith Camacho-Sánchez
- Conservation Medicine Lab, Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - A Alonso Aguirre
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - José Alberto Narváez-Zapata
- Laboratorio de Biotecnología Industrial, Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico
| | - Alan A Zavala-Norzagaray
- Laboratorio de Vida Silvestre, Departamento de Medio Ambiente, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - Cesar P Ley-Quiñónez
- Laboratorio de Vida Silvestre, Departamento de Medio Ambiente, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - H Hugo Acosta-Sánchez
- United Nations Development Programme-Comisión Nacional de Áreas Naturales Protegidas, Ciudad Victoria, Tamaulipas, Mexico
| | - Hervey Rodriguez-González
- Laboratorio Nutrición Acuícola, Departamento de Acuacultura, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - Carlos Delgado-Trejo
- Departamento de Ecología Marina, Proyecto Tortuga Negra, Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Miguel Angel Reyes-López
- Conservation Medicine Lab, Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico
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Gangloff EJ, Schwartz TS, Klabacka R, Huebschman N, Liu AY, Bronikowski AM. Mitochondria as central characters in a complex narrative: Linking genomics, energetics, pace-of-life, and aging in natural populations of garter snakes. Exp Gerontol 2020; 137:110967. [DOI: 10.1016/j.exger.2020.110967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/11/2020] [Accepted: 05/01/2020] [Indexed: 12/18/2022]
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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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Tikochinski Y, Carreras C, Tikochinski G, Vilaça ST. Population-specific signatures of intra-individual mitochondrial DNA heteroplasmy and their potential evolutionary advantages. Sci Rep 2020; 10:211. [PMID: 31937820 PMCID: PMC6959243 DOI: 10.1038/s41598-019-56918-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/03/2019] [Indexed: 01/16/2023] Open
Abstract
Heteroplasmy is the existence of more than one mitochondrial DNA (mtDNA) variant within a cell. The evolutionary mechanisms of heteroplasmy are not fully understood, despite being a very common phenomenon. Here we combined heteroplasmy measurements using high throughput sequencing on green turtles (Chelonia mydas) with simulations to understand how heteroplasmy modulates population diversity across generations and under different demographic scenarios. We found heteroplasmy to be widespread in all individuals analysed, with consistent signal in individuals across time and tissue. Significant shifts in haplotype composition were found from mother to offspring, signalling the effect of the cellular bottleneck during oogenesis as included in the model. Our model of mtDNA inheritance indicated that heteroplasmy favoured the increase of population diversity through time and buffered against population bottlenecks, thus indicating the importance of this phenomenon in species with reduced population sizes and frequent population bottlenecks like marine turtles. Individuals with recent haplotypes showed higher levels of heteroplasmy than the individuals with ancient haplotypes, suggesting a potential advantage of maintaining established copies when new mutations arise. We recommend using heteroplasmy through high throughput sequencing in marine turtles, as well as other wildlife populations, for diversity assessment, population genetics, and mixed stock analysis.
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Affiliation(s)
- Yaron Tikochinski
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
| | - Carlos Carreras
- Department of Genetics, Microbiology and Statistics and IRBio, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | | | - Sibelle T Vilaça
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany. .,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany. .,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
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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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