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4. Three disputes and three objectives: China and the South China Sea

Author

Dutton, Peter

Subjects
SOUTH CHINA SEA - Strategic Importance, CHINA (PEOPLE'S REPUBLIC) - Foreign Policy, TERRITORIAL WATERS - Laws and Regulations, ASSOCIATION OF SOUTHEAST ASIAN NATIONS - Politics and Government, PACIFIC REGION - Politics and Government
Abstract

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Published
2011

6. Carving up the East China Sea

Author

Dutton, Peter, CDR, Ret

Subjects
CHINA (PEOPLE'S REPUBLIC) - Foreign Relations - Asia, Southeastern, ASIA, SOUTHEASTERN - Foreign Relations - China (People's Republic), TREATIES AND ALLIANCES, BALANCE OF POWER - Asia, Eastern, SOUTH CHINA SEA - Strategic Importance
Abstract

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Published
2007

9. Species and population specific gene expression in blood transcriptomes of marine turtles

Author

Banerjee, Shreya M, Stoll, Jamie Adkins, Allen, Camryn D, Lynch, Jennifer M, Harris, Heather S, Kenyon, Lauren, Connon, Richard E, Sterling, Eleanor J, Naro-Maciel, Eugenia, McFadden, Kathryn, Lamont, Margaret M, Benge, James, Fernandez, Nadia B, Seminoff, Jeffrey A, Benson, Scott R, Lewison, Rebecca L, Eguchi, Tomoharu, Summers, Tammy M, Hapdei, Jessy R, Rice, Marc R, Martin, Summer, Jones, T Todd, Dutton, Peter H, Balazs, George H, and Komoroske, Lisa M

Subjects
Human Genome, Genetics, Biotechnology, Life Below Water, Life on Land, Animals, Base Sequence, Species Specificity, Transcriptome, Turtles, Comparative transcriptomics, Sea turtle, Minimally invasive sampling, Conservation physiology, RNA-sequencing, Ortholog, Biological Sciences, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics
Abstract

BackgroundTranscriptomic data has demonstrated utility to advance the study of physiological diversity and organisms' responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations.ResultsWe generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance.ConclusionsObtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles.

Published
2021

12. Long-term trends in the foraging ecology and habitat use of an endangered species: an isotopic perspective

Author

Hetherington, Elizabeth D, Seminoff, Jeffrey A, Dutton, Peter H, Robison, Lisa C, Popp, Brian N, and Kurle, Carolyn M

Subjects
Biological Sciences, Ecology, Life on Land, Animals, Ecosystem, Endangered Species, Oceans and Seas, Turtles, United States Virgin Islands, N-15, Foraging ecology, Leatherback turtle, Trophic position, δ15N, Evolutionary biology, Zoology
Abstract

Evaluating long-term drivers of foraging ecology and population productivity is crucial for providing ecological baselines and forecasting species responses to future environmental conditions. Here, we examine the trophic ecology and habitat use of North Atlantic leatherback turtles (St. Croix nesting population) and investigate the effects of large-scale oceanographic conditions on leatherback foraging dynamics. We used bulk and compound-specific nitrogen isotope analysis of amino acids (CSIA-AA) to estimate leatherback trophic position (TP) over an 18-year period, compare these estimates with TP estimates from a Pacific leatherback population, and elucidate the pre-nesting habitat use patterns of leatherbacks. Our secondary objective was to use oceanographic indices and nesting information from St. Croix leatherbacks to evaluate relationships between trophic ecology, nesting parameters, and regional environmental conditions measured by the North Atlantic Oscillation (NAO) and Atlantic Multidecadal Oscillation. We found no change in leatherback TP over time and no difference in TP between Atlantic and Pacific leatherbacks, indicating that differences in trophic ecology between populations are an unlikely driver of the population dichotomy between Pacific and Atlantic leatherbacks. Isotope data suggested that St. Croix leatherbacks inhabit multiple oceanic regions prior to nesting, although, like their conspecifics in the Pacific, individuals exhibit fidelity to specific foraging regions. Leatherback nesting parameters were weakly related to the NAO, which may suggest that positive NAO phases benefit St. Croix leatherbacks, potentially through increases in resource availability in their foraging areas. Our data contribute to the understanding of leatherback turtle ecology and potential mechanistic drivers of the dichotomy between populations of this protected species.

Published
2018

13. Outcomes from a mechanistic biomarker multi-arm and randomised study of liposomal MTP-PE (Mifamurtide) in metastatic and/or recurrent osteosarcoma (EuroSarc-Memos trial)

Author

Barnes, David J., Dutton, Peter, Bruland, Øyvind, Gelderblom, Hans, Faleti, Ade, Bühnemann, Claudia, van Maldegem, Annemiek, Johnson, Hannah, Poulton, Lisa, Love, Sharon, Tiemeier, Gesa, van Beelen, Els, Herbschleb, Karin, Haddon, Caroline, Billingham, Lucinda, Bradley, Kevin, Ferrari, Stefano, Palmerini, Emanuela, Picci, Piero, Dirksen, Uta, Strauss, Sandra J., Hogendoorn, Pancras C. W., Buddingh, Emmeline, Blay, Jean-Yves, Cleton-Jansen, Anne Marie, and Hassan, Andrew Bassim

Published
2022
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19. Translating Marine Animal Tracking Data into Conservation Policy and Management

Author

Hays, Graeme C., Bailey, Helen, Bograd, Steven J., Bowen, W. Don, Campagna, Claudio, Carmichael, Ruth H., Casale, Paolo, Chiaradia, Andre, Costa, Daniel P., Cuevas, Eduardo, Nico de Bruyn, P.J., Dias, Maria P., Duarte, Carlos M., Dunn, Daniel C., Dutton, Peter H., Esteban, Nicole, Friedlaender, Ari, Goetz, Kimberly T., Godley, Brendan J., Halpin, Patrick N., Hamann, Mark, Hammerschlag, Neil, Harcourt, Robert, Harrison, Autumn-Lynn, Hazen, Elliott L., Heupel, Michelle R., Hoyt, Erich, Humphries, Nicolas E., Kot, Connie Y., Lea, James S.E., Marsh, Helene, Maxwell, Sara M., McMahon, Clive R., Notarbartolo di Sciara, Giuseppe, Palacios, Daniel M., Phillips, Richard A., Righton, David, Schofield, Gail, Seminoff, Jeffrey A., Simpfendorfer, Colin A., Sims, David W., Takahashi, Akinori, Tetley, Michael J., Thums, Michele, Trathan, Philip N., Villegas-Amtmann, Stella, Wells, Randall S., Whiting, Scott D., Wildermann, Natalie E., and Sequeira, Ana M.M.

Published
2019
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21. Genetic characteristics of loggerhead turtles in the coastal corridor of the North West Pacific, around the Cape Muroto, Japan.

Author

Takashi Ishihara, Naoki Kamezaki, Saya Hirai, Yoshimasa Matsuzawa, Tomoko Hamabata, Asuka Ishizaki, and Dutton, Peter H.

Subjects
LOGGERHEAD turtle, HAPLOTYPES, MITOCHONDRIAL DNA, PUBERTY, ANIMAL migration, TURTLES
Abstract

Genetic characteristics of North Pacific loggerhead turtles captured as bycatch in pound nets operating inMuroto, Kochi, Japan were sampled to identify and estimate stock structure of coastal foraging aggregations. Tissue samples were obtained from juvenile, subadult and adult turtles from 2005-2006 and 2008-2010. For each of the years, 100 samples were processed and approximately 820 bp of mitochondrial DNA control region were sequenced. Straight carapace length of the turtles ranged from 56.3-99.1 cmand their life stages were identified based on previous estimates of the size at puberty (66.0cm) and maturity (82.1cm). A total of 487 out of the 500 samples yielded sequences of sufficient quality to identify five different haplotypes. We conducted mixed stock analysis (MSA) using Bayesian approaches to estimate the contributions of three potential source nesting Management Units (MU) to the Muroto foraging aggregation. There were no significant differences between haplotype frequencies among the different size classes and life stages, nor among the different years, thus the haplotype frequencies were combined for the MSA. The MSA was runwith and without consideration of MUsize and distance, which resulted in similar MSA estimates. A >50% contribution was estimated from the Yakushima MU, and 40% from the Mainland MU, with only minor contribution from the Ryukyu MU. The estimated contribution from Mainland MU and Yakushima MU were disproportionately larger than the relative abundance of nesting at these MUs compared with Ryukyu MU, demonstrating that closer MUs had a greater contribution than those from further away. The lack of differences found in haplotype frequency among life stages, suggests that both juvenile and mature loggerhead turtles that remigrate to Japanese waters have the tendency to utilize foraging grounds and migration routes near their natal waters. [ABSTRACT FROM AUTHOR]

Published
2024
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25. Rookery contributions, movements and conservation needs of hawksbill turtles at foraging grounds in the eastern Pacific Ocean

Author

Gaos, Alexander R., Lewison, Rebecca L., Jensen, Michael P., Liles, Michael J., Henriquez, Ana, Chavarria, Sofia, Pacheco, Carlos Mario, Valle, Melissa, Melero, David, Gadea, Velkiss, Altamirano, Eduardo, Torres, Perla, Vallejo, Felipe, Miranda, Cristina, LeMarie, Carolina, Lucero, Jesus, Oceguera, Karen, Chácon, Didiher, Fonseca, Luis, Abrego, Marino, Seminoff, Jeffrey A., Flores, Eric E., Llamas, Israel, Donadi, Rodrigo, Peña, Bernardo, Muñoz, Juan Pablo, Ruales, Daniela Alarcòn, Chaves, Jaime A., Otterstrom, Sarah, Zavala, Alan, Hart, Catherine E., Brittain, Rachel, Alfaro-Shigueto, Joanna, Mangel, Jeffrey, Yañez, Ingrid L., and Dutton, Peter H.

Published
2018

27. First-line selective internal radiotherapy plus chemotherapy versus chemotherapy alone in patients with liver metastases from colorectal cancer (FOXFIRE, SIRFLOX, and FOXFIRE-Global): a combined analysis of three multicentre, randomised, phase 3 trials

Author

Adams, Richard, Bateman, Andrew, Blesing, Claire, Brown, Ewan, Chau, Ian, Cummins, Sebastian, Cunningham, David, Falk, Stephen, Hadaki, Maher, Hall, Marcia, Hickish, Tamas, Hornbuckle, Joanne, Lofts, Fiona, Lowndes, Sarah, Mayer, Astrid, Metcalfe, Matthew, Middleton, Gary, Mills, Jamie, Montazeri, Amir, Muirhead, Rebecca, Polychronis, Andreas, Purcell, Colin, Ross, Paul, Sharma, Ricky A, Sherwin, Liz, Smith, David, Soomal, Rubin, Swinson, Daniel, Walther, Axel, Wasan, Harpreet, Weaver, Andrew, Wilson, Charles, Wilson, Greg, Amin, Pradip, Angelelli, Bruna, Balosso, Jacques, Beny, Alex, Bloomgarden, Daniel, Boucher, Evelyn, Brown, Michael, Bruch, Harald-Robert, Bui, James, Burge, Matthew, Cardaci, Giuseppe, Carlisle, James, Chai, Seungjean, Chen, Yi-Jen, Chevallier, Patrick, Chuong, Michael, Clarke, Stephen, Coveler, Andrew, Craninx, Michael, Delanoit, Thierry, Deleporte, Amélie, Eliadis, Paul, Facchini, Francis, Ferguson, Thomas, Ferrante, Michel, Findlay, Michael, Frenette, Gary, Frick, Jacob, Ganju, Vinod, Garofalo, Michael, Geboes, Karen, Gehbauer, Gerald, George, Benjamin, Geva, Ravit, Gibbs, Peter, Gordon, Michael, Gregory, Kate, Gulec, Seza, Hannigan, James, van Hazel, Guy, Heching, Norman, Heinemann, Volker, Helmberger, Thomas, Hendlisz, Alain, Hendrickx, Koen, Holtzman, Matthew, Isaacs, Richard, Jackson, Christopher, James, Philip, Kaiser, Adeel, Karapetis, Chris, Kaubisch, Andreas, Ko, Yon-Dschun, Kröning, Hendrik, Lammert, Frank, Liauw, Winston, Limentani, Steven, Louafi, Samy, de Man, Marc, Margolis, Jeffrey, Martin, Robert, Martoni, Andrea, Marx, Gavin, Matos, Marco, Monsaert, Els, Moons, Veerle, Nott, Louise, Nusch, Arnd, O'Donnell, Anne, Ozer, Howard, Padia, Siddarth, Pavlakis, Nick, Peeters, Marc, Perez, David, Pluntke, Stefan, Polus, Marc, Powell, Alex, Pracht, Marc, Price, Timothy, Ransom, David, Rebischung, Christine, Ricke, Jens, Ridwelski, Karsten, Riera-Knorrenschild, Jorge, Riess, Hanno, Rilling, William, Robinson, Bridget, Rodríguez, Javier, Sanchez, Federico, Sauerbruch, Tilmann, Savin, Michael, Scheidhauer, Klemens, Schneiderman, Elyse, Seeger, Grant, Segelov, Eva, Schmueli, Einat Shaham, Shani, Adi, Shannon, Jenny, Sharma, Navesh, Shibata, Stephen, Singhal, Nimit, Smith, Denis, Smith, Randall, Stemmer, Salomon, Stötzer, Oliver, Strickland, Andrew, Taieb, Julien, Tatsch, Klaus, Terrebonne, Eric, Tichler, Thomas, Vehling-Kaiser, Ursula, Vera-Garcia, Ruth, Vogl, Thomas, Walpole, Euan, Wang, Eric, Whiting, Samuel, Wolf, Ido, Ades, Steven, Aghmesheh, Morteza, Auber, Miklos, Ayala, Hubert, Boland, Patrick, Bouche, Eveline, Bowers, Charles, Bremer, Christoph, Burge, Mathew, Casado, Ana Ruiz, Cooray, Prasad, Crain, Martin, De Wit, Maike, Dowling, Kyran, Durand, Aurelie, Faivre, Sandrine, Feeney, Kynan, Ferguson, Tom, Ferru, Aurelie, Fragoso, Maria, Granetto, Cristina, Hammel, Pascal, Issacs, Richard, Iyer, Renuka, Kim, Yeul Hong, Liang, Jin Tung, Lim, Lionel, Liu, Jin Hwang, Masi, Gianluca, Mosconi, Stefania, Numico, Gianmauro, Ratner, Lynn, Sae-Won, Han, Singh, Madhu, Stoltzfus, Patricia, Tan, Iain, Trogu, Antonio, Underhill, Craig, Westcott, Mark, Wasan, Harpreet S, Sharma, Navesh K, Francis, Anne, Moschandreas, Joanna, Virdee, Pradeep S, Dutton, Peter, Love, Sharon, Gebski, Val, and Gray, Alastair

Published
2017
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29. The political biogeography of migratory marine predators

Author

Harrison, Autumn-Lynn, Costa, Daniel P., Winship, Arliss J., Benson, Scott R., Bograd, Steven J., Antolos, Michelle, Carlisle, Aaron B., Dewar, Heidi, Dutton, Peter H., Jorgensen, Salvador J., Kohin, Suzanne, Mate, Bruce R., Robinson, Patrick W., Schaefer, Kurt M., Shaffer, Scott A., Shillinger, George L., Simmons, Samantha E., Weng, Kevin C., Gjerde, Kristina M., and Block, Barbara A.

Published
2018
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31. Somatic POLE proofreading domain mutation, immune response, and prognosis in colorectal cancer: a retrospective, pooled biomarker study

Author

Domingo, Enric, Freeman-Mills, Luke, Rayner, Emily, Glaire, Mark, Briggs, Sarah, Vermeulen, Louis, Fessler, Evelyn, Medema, Jan Paul, Boot, Arnoud, Morreau, Hans, van Wezel, Tom, Liefers, Gerrit-Jan, Lothe, Ragnhild A, Danielsen, Stine A, Sveen, Anita, Nesbakken, Arild, Zlobec, Inti, Lugli, Alessandro, Koelzer, Viktor H, Berger, Martin D, Castellví-Bel, Sergi, Muñoz, Jenifer, de Bruyn, Marco, Nijman, Hans W, Novelli, Marco, Lawson, Kay, Oukrif, Dahmane, Frangou, Eleni, Dutton, Peter, Tejpar, Sabine, Delorenzi, Mauro, Kerr, Rachel, Kerr, David, Tomlinson, Ian, and Church, David N

Published
2016
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34. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.

Abstract

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

Published
2023
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35. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

University of Massachusetts, National Marine Fisheries Service (US), National Science Foundation (US), National Research Council of Canada, Rockefeller University, Howard Hughes Medical Institute, Wellcome Sanger Institute, Max Planck Society, Agencia Nacional de Investigación y Desarrollo (Chile), Fundação de Amparo à Pesquisa do Estado de São Paulo, Federal Ministry of Education and Research (Germany), National Library of Medicine (US), Generalitat de Catalunya, Fundación la Caixa, Vienna Science and Technology Fund, Welsh Government, European Commission, Sea Turtle Conservancy (US), Kuhlwilm, Martin [0000-0002-0115-1797], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Bentley, Blair P., Carrasco-Valenzuela, Tomás, Ramos, Elisa K. S., Pawar, Harvinder, Souza Arantes, Larissa, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, Todd, Erica V., Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Françoise, Nery, Mariana F., Marqués-Bonet, Tomàs, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., University of Massachusetts, National Marine Fisheries Service (US), National Science Foundation (US), National Research Council of Canada, Rockefeller University, Howard Hughes Medical Institute, Wellcome Sanger Institute, Max Planck Society, Agencia Nacional de Investigación y Desarrollo (Chile), Fundação de Amparo à Pesquisa do Estado de São Paulo, Federal Ministry of Education and Research (Germany), National Library of Medicine (US), Generalitat de Catalunya, Fundación la Caixa, Vienna Science and Technology Fund, Welsh Government, European Commission, Sea Turtle Conservancy (US), Kuhlwilm, Martin [0000-0002-0115-1797], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Bentley, Blair P., Carrasco-Valenzuela, Tomás, Ramos, Elisa K. S., Pawar, Harvinder, Souza Arantes, Larissa, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, Todd, Erica V., Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Françoise, Nery, Mariana F., Marqués-Bonet, Tomàs, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.

Abstract

[Significance] Sea turtle populations have undergone recent global declines. We analyzed de novo assembled genomes for both extant sea turtle families through the Vertebrate Genomes Project to inform their conservation and evolutionary biology. These highly conserved genomes were differentiated by localized gene-rich regions of divergence, particularly within microchromosomes, suggesting that these genomic elements play key functional roles in the evolution of sea turtles and possibly other vertebrates. We further demonstrate that dissimilar evolutionary histories impact standing genomic diversity and genetic load, and are critical to consider when using these metrics to assess adaptive potential and extinction risk. Our results also demonstrate how reference genome quality impacts inferences of comparative and conservation genomics analyses that need to be considered in their application., [Abstract] Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

Published
2023

40. Histograms of genotyping mismatches between sequencing replicates;Tables showing yields of genotype calls from the different genotyping softwares used;Additional nesting data from Non-random mating within an Island rookery of Hawaiian hawksbill turtles: demographic discontinuity at a small coastline scale

Author

Horne, John B., Frey, Amy, Gaos, Alexander R., Martin, Summer, and Dutton, Peter H.

Abstract

Supplementary figure 1: Histogram distributions of mismatches among genotype calls. Top row: mismatching single-locus genotype pairs across 137 replicate samples. Bottom row: mismatching single-locus genotypes across all variants called by two calling algorithms. Variants with mismatches exceeding the blue-line thresholds (7% top, 5.5% bottom) were removed from the data sets.;Supplementary table 1a: Data filtering: Raw genotyping results for 229 Hawksbill PCR amplicons from 1,032 Hawaiian Hawksbill turtles, plus 137 replicates.Supplementary table 1b: Data filtering: Variants with genotyping error rates of less than 7% (not including missing data). Error rates were calculated from mismatch tallies across 137 replicate sample pairs. Supplementary table 1c: Data filtering: Low-error genotype variants from each caller that were also called by at least one other caller. Also, variants with less than 5.5% mismatched allele calls between callers across 137 replicate sample pairs. Supplementary table 1d: Data filtering: Variants remaining after filtering for > 30% missing data and a minor allele frequency < 0.01. Supplementary table 1e: Data filtering: Microhaplotype calls before and after filtering. The filtration requirements were: a minimum sequence depth of 12, minimum heterozygote allelic ratio of 0.25, maximum homozygote allelic ratio of 0.09, and callable microhaplotypes in at least 70% of individuals.;Available nest data for 2017 Hawksbill nests from Hawaii Island, including dates and hatch success rate.

Published
2023
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41. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

Bentley, Blair P., primary, Carrasco-Valenzuela, Tomás, additional, Ramos, Elisa K. S., additional, Pawar, Harvinder, additional, Souza Arantes, Larissa, additional, Alexander, Alana, additional, Banerjee, Shreya M., additional, Masterson, Patrick, additional, Kuhlwilm, Martin, additional, Pippel, Martin, additional, Mountcastle, Jacquelyn, additional, Haase, Bettina, additional, Uliano-Silva, Marcela, additional, Formenti, Giulio, additional, Howe, Kerstin, additional, Chow, William, additional, Tracey, Alan, additional, Sims, Ying, additional, Pelan, Sarah, additional, Wood, Jonathan, additional, Yetsko, Kelsey, additional, Perrault, Justin R., additional, Stewart, Kelly, additional, Benson, Scott R., additional, Levy, Yaniv, additional, Todd, Erica V., additional, Shaffer, H. Bradley, additional, Scott, Peter, additional, Henen, Brian T., additional, Murphy, Robert W., additional, Mohr, David W., additional, Scott, Alan F., additional, Duffy, David J., additional, Gemmell, Neil J., additional, Suh, Alexander, additional, Winkler, Sylke, additional, Thibaud-Nissen, Françoise, additional, Nery, Mariana F., additional, Marques-Bonet, Tomas, additional, Antunes, Agostinho, additional, Tikochinski, Yaron, additional, Dutton, Peter H., additional, Fedrigo, Olivier, additional, Myers, Eugene W., additional, Jarvis, Erich D., additional, Mazzoni, Camila J., additional, and Komoroske, Lisa M., additional

Published
2023
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47. Chapter 16. Sea Turtle–Fisheries Interactions in Coastal Fisheries

Author

Yeo, Bee Hong, primary, Squires, Dale, additional, Ibrahim, Kamarruddin, additional, Gjertsen, Heidi, additional, Kamil, Syarifah Khadiejah Syed Mohd., additional, Zulkifli, Rahayu, additional, Groves, Theodore, additional, Dutton, Peter H., additional, Hong, Meen Chee, additional, and Tan, Chun Hong, additional

Published
2017
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