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1. Convergence of marine megafauna movement patterns in coastal and open oceans.

Author

Sequeira, AMM, Rodríguez, JP, Eguíluz, VM, Harcourt, R, Hindell, M, Sims, DW, Duarte, CM, Costa, DP, Fernández-Gracia, J, Ferreira, LC, Hays, GC, Heupel, MR, Meekan, MG, Aven, A, Bailleul, F, Baylis, AMM, Berumen, ML, Braun, CD, Burns, J, Caley, MJ, Campbell, R, Carmichael, RH, Clua, E, Einoder, LD, Friedlaender, Ari, Goebel, ME, Goldsworthy, SD, Guinet, C, Gunn, J, Hamer, D, Hammerschlag, N, Hammill, M, Hückstädt, LA, Humphries, NE, Lea, M-A, Lowther, A, Mackay, A, McHuron, E, McKenzie, J, McLeay, L, McMahon, CR, Mengersen, K, Muelbert, MMC, Pagano, AM, Page, B, Queiroz, N, Robinson, PW, Shaffer, SA, Shivji, M, Skomal, GB, Thorrold, SR, Villegas-Amtmann, S, Weise, M, Wells, R, Wetherbee, B, Wiebkin, A, Wienecke, B, and Thums, M

Subjects
Animals, Vertebrates, Animal Migration, Ecosystem, Databases, Factual, Oceans and Seas, displacements, global satellite tracking, probability density function, root-mean-square, turning angles, Life Below Water
Abstract

The extent of increasing anthropogenic impacts on large marine vertebrates partly depends on the animals' movement patterns. Effective conservation requires identification of the key drivers of movement including intrinsic properties and extrinsic constraints associated with the dynamic nature of the environments the animals inhabit. However, the relative importance of intrinsic versus extrinsic factors remains elusive. We analyze a global dataset of ∼2.8 million locations from >2,600 tracked individuals across 50 marine vertebrates evolutionarily separated by millions of years and using different locomotion modes (fly, swim, walk/paddle). Strikingly, movement patterns show a remarkable convergence, being strongly conserved across species and independent of body length and mass, despite these traits ranging over 10 orders of magnitude among the species studied. This represents a fundamental difference between marine and terrestrial vertebrates not previously identified, likely linked to the reduced costs of locomotion in water. Movement patterns were primarily explained by the interaction between species-specific traits and the habitat(s) they move through, resulting in complex movement patterns when moving close to coasts compared with more predictable patterns when moving in open oceans. This distinct difference may be associated with greater complexity within coastal microhabitats, highlighting a critical role of preferred habitat in shaping marine vertebrate global movements. Efforts to develop understanding of the characteristics of vertebrate movement should consider the habitat(s) through which they move to identify how movement patterns will alter with forecasted severe ocean changes, such as reduced Arctic sea ice cover, sea level rise, and declining oxygen content.

Published
2018

23. Runs of homozygosity in killer whale genomes provide a global record of demographic histories.

Author

Foote, AD, Hooper, R, Alexander, A, Baird, RW, Baker, CS, Ballance, L, Barlow, J, Brownlow, A, Collins, T, Constantine, R, Dalla Rosa, L, Davison, NJ, Durban, JW, Esteban, R, Excoffier, L, Martin, SLF, Forney, KA, Gerrodette, T, Gilbert, MTP, Guinet, C, Hanson, MB, Li, S, Martin, MD, Robertson, KM, Samarra, FIP, de Stephanis, R, Tavares, SB, Tixier, P, Totterdell, JA, Wade, P, Wolf, JBW, Fan, G, Zhang, Y, Morin, PA, Foote, AD, Hooper, R, Alexander, A, Baird, RW, Baker, CS, Ballance, L, Barlow, J, Brownlow, A, Collins, T, Constantine, R, Dalla Rosa, L, Davison, NJ, Durban, JW, Esteban, R, Excoffier, L, Martin, SLF, Forney, KA, Gerrodette, T, Gilbert, MTP, Guinet, C, Hanson, MB, Li, S, Martin, MD, Robertson, KM, Samarra, FIP, de Stephanis, R, Tavares, SB, Tixier, P, Totterdell, JA, Wade, P, Wolf, JBW, Fan, G, Zhang, Y, and Morin, PA

Abstract

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.

Published
2021

41. A global cline in a colour polymorphism suggests a limited contribution of gene flow towards the recovery of a heavily exploited marine mammal

Author

Hoffman, J. I., Bauer, E., Paijmans, A. J., Humble, E., Beckmann, L. M., Kubetschek, C., Christaller, F., Kröcker, N., Fuchs, B., Moreras, A., Shihlomule, Y. D., Bester, M. N., Cleary, A. C., De Bruyn, P. J. N., Forcada, J., Goebel, M. E., Goldsworthy, S. D., Guinet, C., Hoelzel, A. R., Lydersen, C., Kovacs, K. M., Lowther, A., Department of Animal Behaviour, Universität Bielefeld, Department of Zoology and Entomology [Pretoria], University of Pretoria [South Africa], Norwegian Polar Institute, British Antarctic Survey NERC [UK], Antarctic Ecosystem Research Division, National Oceanic and Atmospheric Administration (NOAA)-National Marine Fisheries Service, South Australian Research and Development Institute [Australia], Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Durham University, Department of Zoology and Entomology University of Pretoria, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR), Department of Biosciences - Durham University [UK], and Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)

Subjects
fur seal, Biology (Whole Organism), population structure, melanocortin 1 receptor, colour polymorphism, [SDE]Environmental Sciences, melanocortin 1 receptor gene, lcsh:Q, lcsh:Science, Research Article, pinniped
Abstract

International audience; Evaluating how populations are connected by migration is important for understanding species resilience because gene flow can facilitate recovery from demographic declines. We therefore investigated the extent to which migration may have contributed to the global recovery of the Antarctic fur seal (Arctocephalus gazella), a circumpolar distributed marine mammal that was brought to the brink of extinction by the sealing industry in the eighteenth and nineteenth centuries. It is widely believed that animals emigrating from South Georgia, where a relict population escaped sealing, contributed to the re-establishment of formerly occupied breeding colonies across the geographical range of the species. To investigate this, we interrogated a genetic polymorphism (S291F) in the melanocortin 1 receptor gene, which is responsible for a cream-coloured phenotype that is relatively abundant at South Georgia and which appears to have recently spread to localities as far afield as Marion Island in the sub-Antarctic Indian Ocean. By sequencing a short region of this gene in 1492 pups from eight breeding colonies, we showed that S291F frequency rapidly declines with increasing geographical distance from South Georgia, consistent with locally restricted gene flow from South Georgia mainly to the South Shetland Islands and Bouvetøya. The S291F allele was not detected farther afield, suggesting that although emigrants from South Georgia may have been locally important, they are unlikely to have played a major role in the recovery of geographically more distant populations.

Published
2018
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44. Male pelvis

Author

Arrive, L., Malbec, L., Buy, J. N., Guinet, C., Vadrot, D., Meary, E., Bigot, J. M., Ecoiffier, J., Vanel, Daniel, editor, Mc Namara, Michael T., editor, Arcangioli, O., editor, Arrive, L., editor, Aubert, B., editor, Bénacerraf, R., editor, Bigot, J.-M., editor, Bittoun, J., editor, Blangy, S., editor, Bonnin, A., editor, Broussin, J., editor, Buthiau, D., editor, Buy, J.-N., editor, Cabée, A.-E., editor, Caille, J.-M., editor, Chagnon, S., editor, Chateil, J.-F., editor, Chevrot, A., editor, Coffre, C., editor, Couanet, D., editor, Desprès, E., editor, De Tœuf, J., editor, Ecoiffier, J., editor, Engelholm, L., editor, Frija, G., editor, Gires, F., editor, Grenier, N., editor, Grenier, P., editor, Guinet, C., editor, Héran, F., editor, Idy-Peretti, I., editor, Jean-Mart, J., editor, Kien, P., editor, Kressel, H., editor, Lavayssière, R., editor, Leclère, J., editor, Leroy-Willig, A., editor, Malbec, L., editor, Marichez, M., editor, Masselot, J., editor, Meary, E., editor, Menu, Y., editor, Pallardy, G., editor, Parienty, R.-A., editor, Piekarski, J.-D., editor, Roucayrol, J.-C., editor, Schouman-Claeys, E., editor, Segebarth, C., editor, Sibert, A., editor, Somveille, E., editor, Taieb, A., editor, Tavière, V., editor, Vadrot, D., editor, Vallée, C., editor, Vanel, D., editor, Zalcman, M., editor, and Wybier, M., editor

Published
1989
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45. Transferability of PCR-based diagnostic protocols: An international collaborative case study assessing protocols targeting the quarantine pine pathogen Fusarium circinatum

Author

Universitat Politècnica de València. Instituto Agroforestal Mediterráneo - Institut Agroforestal Mediterrani, Estonian Science Foundation, Forestry Commission, Reino Unido, Slovenian Research Agency, European Cooperation in Science and Technology, Ministry for Primary Industries, Nueva Zelanda, Fundação para a Ciência e a Tecnologia, Portugal, Ministry of Agriculture, Forestry and Food, Eslovenia, Instituto Nacional de Investigação Agrária e Veterinária, Portugal, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Francia, Ioos, R., Aloi, F., Piskur, B., Guinet, C., Mullett, M., Berbegal Martinez, Monica, Bragança, H., Cacciola, S.O., Oskay, F., Cornejo, C., Adamson, K., Kacergius, A., Martínez-Álvarez, P., Nowakowska, J.A., Luchi, N., Universitat Politècnica de València. Instituto Agroforestal Mediterráneo - Institut Agroforestal Mediterrani, Estonian Science Foundation, Forestry Commission, Reino Unido, Slovenian Research Agency, European Cooperation in Science and Technology, Ministry for Primary Industries, Nueva Zelanda, Fundação para a Ciência e a Tecnologia, Portugal, Ministry of Agriculture, Forestry and Food, Eslovenia, Instituto Nacional de Investigação Agrária e Veterinária, Portugal, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Francia, Ioos, R., Aloi, F., Piskur, B., Guinet, C., Mullett, M., Berbegal Martinez, Monica, Bragança, H., Cacciola, S.O., Oskay, F., Cornejo, C., Adamson, K., Kacergius, A., Martínez-Álvarez, P., Nowakowska, J.A., and Luchi, N.

Abstract

[EN] Fusarium circinatum is a harmful pathogenic fungus mostly attacking Pinus species and also Pseudotsuga menziesii, causing cankers in trees of all ages, damping-off in seedlings, and mortality in cuttings and mother plants for clonal production. This fungus is listed as a quarantine pest in several parts of the world and the trade of potentially contaminated pine material such as cuttings, seedlings or seeds is restricted in order to prevent its spread to disease-free areas. Inspection of plant material often relies on DNA testing and several conventional or real-time PCR based tests targeting F. circinatum are available in the literature. In this work, an international collaborative study joined 23 partners to assess the transferability and the performance of nine molecular protocols, using a wide panel of DNA from 71 representative strains of F. circinatum and related Fusarium species. Diagnostic sensitivity, specificity and accuracy of the nine protocols all reached values >80%, and the diagnostic specificity was the only parameter differing significantly between protocols. The rates of false positives and of false negatives were computed and only the false positive rates differed significantly, ranging from 3.0% to 17.3%. The difference between protocols for some of the performance values were mainly due to cross-reactions with DNA from non-target species, which were either not tested or documented in the original articles. Considering that participating laboratories were free to use their own reagents and equipment, this study demonstrated that the diagnostic protocols for F. circinatum were not easily transferable to end-users. More generally, our results suggest that the use of protocols using conventional or real-time PCR outside their initial development and validation conditions should require careful characterization of the performance data prior to use under modified conditions (i.e. reagents and equipment). Suggestions to improve the transfer are pr

Published
2019

46. Animal-borne telemetry: An integral component of the ocean observing toolkit

Author

Harcourt, R. (Rob), Sequeira, A.M.M. (Ana M.M.), Zhang, X. (Xuelei), Roquet, F. (Fabien), Komatsu, K. (Kosei), Heupel, M. (Michelle), McMahon, C. (Clive), Whoriskey, F. (Fred), Meekan, M. (Mark), Carroll, G. (Gemma), Brodie, S. (Stephanie), Simpfendorfer, C. (Colin), Hindell, M. (Mark), Jonsen, I. (Ian), Costa, D.P. (Daniel P.), Block, B. (Barbara), Muelbert, M. (Mônica), Woodward, B. (Bill), Weise, M. (Mike), Aarestrup, K. (Kim), Biuw, M. (Martin), Boehme, L. (Lars), Bograd, S.J. (Steven J.), Cazau, D. (Dorian), Charrassin, J.-B. (Jean-Benoit), Cooke, S.J. (Steven), Cowley, P. (Paul), de Bruyn, P.J.N. (P.J. Nico), Jeanniard du Dot, T. (Tiphaine), Duarte, C. (Carlos), Eguíluz, V.M. (Víctor M.), Ferreira, L.C. (Luciana C.), Fernández-Gracia, J. (Juan), Goetz, K. (Kimberly), Goto, Y. (Yusuke), Guinet, C. (Christophe), Hammill, M. (Mike), Hays, G.C. (Graeme C.), Hazen, E.L. (Elliott L.), Hückstädt, L.A. (Luis A.), Huveneers, C. (Charlie), Iverson, S. (Sara), Jaaman, S.A. (Saifullah Arifin), Kittiwattanawong, K. (Kongkiat), Kovacs, K.M. (Kit M.), Lydersen, C. (Christian), Moltmann, T. (Tim), Naruoka, M. (Masaru), Phillips, L. (Lachlan), Picard, B. (Baptiste), Queiroz, N. (Nuno), Reverdin, G. (Gilles), Sato, K. (Katsufumi), Sims, D.W. (David W.), Thorstad, E.B. (Eva B.), Thums, M. (Michele), Treasure, A.M. (Anne M.), Trites, A.W. (Andrew W.), Williams, G.D. (Guy D.), Yonehara, Y. (Yoshinari), Fedak, M.A. (Mike A.), Harcourt, R. (Rob), Sequeira, A.M.M. (Ana M.M.), Zhang, X. (Xuelei), Roquet, F. (Fabien), Komatsu, K. (Kosei), Heupel, M. (Michelle), McMahon, C. (Clive), Whoriskey, F. (Fred), Meekan, M. (Mark), Carroll, G. (Gemma), Brodie, S. (Stephanie), Simpfendorfer, C. (Colin), Hindell, M. (Mark), Jonsen, I. (Ian), Costa, D.P. (Daniel P.), Block, B. (Barbara), Muelbert, M. (Mônica), Woodward, B. (Bill), Weise, M. (Mike), Aarestrup, K. (Kim), Biuw, M. (Martin), Boehme, L. (Lars), Bograd, S.J. (Steven J.), Cazau, D. (Dorian), Charrassin, J.-B. (Jean-Benoit), Cooke, S.J. (Steven), Cowley, P. (Paul), de Bruyn, P.J.N. (P.J. Nico), Jeanniard du Dot, T. (Tiphaine), Duarte, C. (Carlos), Eguíluz, V.M. (Víctor M.), Ferreira, L.C. (Luciana C.), Fernández-Gracia, J. (Juan), Goetz, K. (Kimberly), Goto, Y. (Yusuke), Guinet, C. (Christophe), Hammill, M. (Mike), Hays, G.C. (Graeme C.), Hazen, E.L. (Elliott L.), Hückstädt, L.A. (Luis A.), Huveneers, C. (Charlie), Iverson, S. (Sara), Jaaman, S.A. (Saifullah Arifin), Kittiwattanawong, K. (Kongkiat), Kovacs, K.M. (Kit M.), Lydersen, C. (Christian), Moltmann, T. (Tim), Naruoka, M. (Masaru), Phillips, L. (Lachlan), Picard, B. (Baptiste), Queiroz, N. (Nuno), Reverdin, G. (Gilles), Sato, K. (Katsufumi), Sims, D.W. (David W.), Thorstad, E.B. (Eva B.), Thums, M. (Michele), Treasure, A.M. (Anne M.), Trites, A.W. (Andrew W.), Williams, G.D. (Guy D.), Yonehara, Y. (Yoshinari), and Fedak, M.A. (Mike A.)

Abstract

Animal telemetry is a powerful tool for observing marine animals and the physical environments that they inhabit, from coastal and continental shelf ecosystems to polar seas and open oceans. Satellite-linked biologgers and networks of acoustic receivers allow animals to be reliably monitored over scales of tens of meters to thousands of kilometers, giving insight into their habitat use, home range size, the phenology of migratory patterns and the biotic and abiotic factors that drive their distributions. Furthermore, physical environmental variables can be collected using animals as autonomous sampling platforms, increasing spatial and temporal coverage of global oceanographic observation systems. The use of animal telemetry, therefore, has the capacity to provide measures from a suite of essential ocean variables (EOVs) for improved monitoring of Earth's oceans. Here we outline the design features of animal telemetry systems, describe current applications and their benefits and challenges, and discuss future directions. We describe new analytical techniques that improve our ability to not only quantify animal movements but to also provide a powerful framework for comparative studies across taxa. We discuss the application of animal telemetry and its capacity to collect biotic and abiotic data, how the data collected can be incorporated into ocean observing systems, and the role these data can play in improved ocean management.

Published
2019
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47. De là-haut on voit mieux ! Télé-observation dans la Zone Atelier Antarctique et Subantarctique

Author

Lebouvier, M., Barbraud, C., Chapuis, J.-L., Delord, K., Fourcy, Damien, Guinet, C., Ropert‐Coudert, Yan, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS), CNFRA, Troccaz, Olivier, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), and Briand, Valerie

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

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