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Caruso G, Alaimo Di Loro P, Mingione M, Tardella L, Pace DS, Jona Lasinio G. Finite mixtures in capture-recapture surveys for modeling residency patterns in marine wildlife populations. Biom J 2024; 66:e2200350. [PMID: 38285406 DOI: 10.1002/bimj.202200350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 09/13/2023] [Accepted: 09/25/2023] [Indexed: 01/30/2024]
Abstract
This work aims to show how prior knowledge about the structure of a heterogeneous animal population can be leveraged to improve the abundance estimation from capture-recapture survey data. We combine the Open Jolly-Seber model with finite mixtures and propose a parsimonious specification tailored to the residency patterns of the common bottlenose dolphin. We employ a Bayesian framework for our inference, discussing the appropriate choice of priors to mitigate label-switching and nonidentifiability issues, commonly associated with finite mixture models. We conduct a series of simulation experiments to illustrate the competitive advantage of our proposal over less specific alternatives. The proposed approach is applied to data collected on the common bottlenose dolphin population inhabiting the Tiber River estuary (Mediterranean Sea). Our results provide novel insights into this population's size and structure, shedding light on some of the ecological processes governing its dynamics.
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Affiliation(s)
- Gianmarco Caruso
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Department of Statistical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Marco Mingione
- Department of Political Sciences, University of Roma Tre, Rome, Italy
| | - Luca Tardella
- Department of Statistical Sciences, Sapienza University of Rome, Rome, Italy
| | - Daniela Silvia Pace
- Department of of Environmental Biology, Sapienza University of Rome, Rome, Italy
- Institute for the Study of Anthropogenic Impacts and Sustainability in the Marine Environment, CNR, Trapani, Italy
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2
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Sorel MH, Murdoch AR, Zabel RW, Jorgensen JC, Kamphaus CM, Converse SJ. Juvenile life history diversity is associated with lifetime individual heterogeneity in a migratory fish. Ecosphere 2023. [DOI: 10.1002/ecs2.4366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Mark H. Sorel
- Washington Cooperative Fish and Wildlife Research Unit, School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Andrew R. Murdoch
- Washington Department of Fish and Wildlife North Olympia Washington USA
| | - Richard W. Zabel
- National Marine Fisheries Service Northwest Fisheries Science Center Seattle Washington USA
| | - Jeffrey C. Jorgensen
- National Marine Fisheries Service Northwest Fisheries Science Center Seattle Washington USA
| | - Corey M. Kamphaus
- Yakama Nation Fisheries, Mid‐Columbia Field Station Peshastin Washington USA
| | - Sarah J. Converse
- US Geological Survey, Washington Cooperative Fish and Wildlife Research Unit, School of Environmental and Forest Sciences & School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
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3
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Cruz-Flores M, Pradel R, Bried J, Militão T, Neves VC, González-Solís J, Ramos R. Will climate change affect the survival of tropical and subtropical species? Predictions based on Bulwer's petrel populations in the NE Atlantic Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157352. [PMID: 35843319 DOI: 10.1016/j.scitotenv.2022.157352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/05/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
Climate change has repeatedly been shown to impact the demography and survival of marine top predators. However, most evidence comes from single populations of widely distributed species, limited mainly to polar and subpolar environments. Here, we aimed to evaluate the influence of environmental conditions on the survival of a tropical and migratory seabird over the course of its annual cycle. We used capture-mark-recapture data from three populations of Bulwer's petrel (Bulweria bulwerii) spread across the NE Atlantic Ocean, from the Azores, Canary, and Cabo Verde Islands (including temperate to tropical zones). We also inferred how the survival of this seabird might be affected under different climatic scenarios, defined by the Intergovernmental Panel on Climate Change. Among the environmental variables whose effect we evaluated (North Atlantic Oscillation index, Southern Oscillation Index, Sea Surface Temperature [SST] and wind speed), SST estimated for the breeding area and season was the variable with the greatest influence on adult survival. Negative effects of SST increase emerged across the three populations, most likely through indirect trophic web interactions. Unfortunately, our study also shows that the survival of Bulwer's petrel will be profoundly affected by the different scenarios of climate change, even with the most optimistic trajectory involving the lowest greenhouse gas emission. Furthermore, for the first time, our study predicts stronger impacts of climate change on tropical populations than on subtropical and temperate ones. This result highlights the devastating effect that climate change may also have on tropical areas, and the importance of considering multi-population approaches when evaluating its impacts which may differ across species distributions.
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Affiliation(s)
- Marta Cruz-Flores
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643, Barcelona 08028, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain; Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS-La Rochelle Université, 2 Rue Olympe de Gouges, FR-17000 La Rochelle, France.
| | - Roger Pradel
- CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, Montpellier, France
| | - Joël Bried
- Ocean Sciences Institute - Okeanos, University of the Azores, Horta, Portugal; 8 avenue de la reine Nathalie, 64200 Biarritz, France
| | - Teresa Militão
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643, Barcelona 08028, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Verónica C Neves
- Ocean Sciences Institute - Okeanos, University of the Azores, Horta, Portugal
| | - Jacob González-Solís
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643, Barcelona 08028, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Raül Ramos
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal 643, Barcelona 08028, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
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4
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Parkinson KJL, Hennin HL, Gilchrist HG, Hobson KA, Hussey NE, Love OP. Breeding stage and tissue isotopic consistency suggests colony-level flexibility in niche breadth of an Arctic marine bird. Oecologia 2022; 200:503-514. [PMID: 36229693 DOI: 10.1007/s00442-022-05267-9] [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: 10/05/2021] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
Organisms must overcome environmental limitations to optimize their investment in life history stages to maximize fitness. Human-induced climate change is generating increasingly variable environmental conditions, impacting the demography of prey items and, therefore, the ability of consumers to successfully access resources to fuel reproduction. While climate change effects are especially pronounced in the Arctic, it is unknown whether organisms can adjust foraging decisions to match such changes. We used a 9-year blood plasma δ13C and δ15N data set from over 700 pre-breeding Arctic common eiders (Somateria mollissima) to assess breeding-stage and inter-annual variation in isotopic niche, and whether inferred trophic flexibility was related to colony-level breeding parameters and environmental variation. Eider blood isotope values varied both across years and breeding stages, and combined with only weak relationships between isotopic metrics and environmental conditions suggests that pre-breeding eiders can make flexible foraging decisions to overcome constraints imposed by local abiotic conditions. From an investment perspective, an inshore, smaller isotopic niche predicted a greater probability to invest in reproduction, but was not related to laying phenology. Proximately, our results provide evidence that eiders breeding in the Arctic can alter their diet at the onset of reproductive investment to overcome increases in the energetic demand of egg production. Ultimately, Arctic pre-breeding common eiders may have the stage- and year-related foraging flexibility to respond to abiotic variation to reproduce successfully.
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Affiliation(s)
- Kyle J L Parkinson
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada. .,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1H 2W1, Canada.
| | - Holly L Hennin
- Environment and Climate Change Canada, National Wildlife Research Centre, Carleton University, Ottawa, ON, Canada
| | - H Grant Gilchrist
- Environment and Climate Change Canada, National Wildlife Research Centre, Carleton University, Ottawa, ON, Canada
| | - Keith A Hobson
- Department of Biology, University of Western Ontario, London, ON, Canada.,Environment and Climate Change Canada, Saskatoon, SK, Canada
| | - Nigel E Hussey
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada
| | - Oliver P Love
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada
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5
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Wan X, Holyoak M, Yan C, Le Maho Y, Dirzo R, Krebs CJ, Stenseth NC, Zhang Z. Broad-scale climate variation drives the dynamics of animal populations: a global multi-taxa analysis. Biol Rev Camb Philos Soc 2022; 97:2174-2194. [PMID: 35942895 DOI: 10.1111/brv.12888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 01/07/2023]
Abstract
Climate is a major extrinsic factor affecting the population dynamics of many organisms. The Broad-Scale Climate Hypothesis (BSCH) was proposed by Elton to explain the large-scale synchronous population cycles of animals, but the extent of support and whether it differs among taxa and geographical regions is unclear. We reviewed publications examining the relationship between the population dynamics of multiple taxa worldwide and the two most commonly used broad-scale climate indices, El Niño-Southern Oscillation (ENSO) and North Atlantic Oscillation (NAO). Our review and synthesis (based on 561 species from 221 papers) reveals that population changes of mammals, birds and insects are strongly affected by major oceanic shifts or irregular oceanic changes, particularly in ENSO- and NAO-influenced regions (Pacific and Atlantic, respectively), providing clear evidence supporting Elton's BSCH. Mammal and insect populations tended to increase during positive ENSO phases. Bird populations tended to increase in positive NAO phases. Some species showed dual associations with both positive and negative phases of the same climate index (ENSO or NAO). These findings indicate that some taxa or regions are more or less vulnerable to climate fluctuations and that some geographical areas show multiple weather effects related to ENSO or NAO phases. Beyond confirming that animal populations are influenced by broad-scale climate variation, we document extensive patterns of variation among taxa and observe that the direct biotic and abiotic mechanisms for these broad-scale climate factors affecting animal populations are very poorly understood. A practical implication of our research is that changes in ENSO or NAO can be used as early signals for pest management and wildlife conservation. We advocate integrative studies at both broad and local scales to unravel the omnipresent effects of climate on animal populations to help address the challenge of conserving biodiversity in this era of accelerated climate change.
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Affiliation(s)
- Xinru Wan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Marcel Holyoak
- Department of Environmental Science and Policy, University of California, California, Davis, 95616, USA
| | - Chuan Yan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yvon Le Maho
- Institut Pluridisciplinaire Hubert Curien (IPHC), Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, 67000, France.,Centre Scientifique de Monaco, Monaco, 98000, Monaco
| | - Rodolfo Dirzo
- Department of Biology and Woods Institute for the Environment, Stanford University, Stanford, California, 94305, USA
| | - Charles J Krebs
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, N-0316, Norway
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
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Tjørnløv RS, Ens BJ, Öst M, Jaatinen K, Karell P, Larsson R, Christensen TK, Frederiksen M. Drivers of Spatiotemporal Variation in Survival in a Flyway Population: A Multi-Colony Study. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.566154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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7
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Population trends of king and common eiders from spring migration counts at Point Barrow, Alaska between 1994 and 2016. Polar Biol 2019. [DOI: 10.1007/s00300-019-02581-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Oosthuizen WC, Postma M, Altwegg R, Nevoux M, Pradel R, Bester MN, Bruyn PJN. Individual heterogeneity in life‐history trade‐offs with age at first reproduction in capital breeding elephant seals. POPUL ECOL 2019. [DOI: 10.1002/1438-390x.12015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- W. Chris Oosthuizen
- Mammal Research Institute, Department of Zoology and Entomology University of Pretoria Hatfield South Africa
| | - Martin Postma
- Mammal Research Institute, Department of Zoology and Entomology University of Pretoria Hatfield South Africa
| | - Res Altwegg
- Centre for Statistics in Ecology Environment and Conservation, Department of Statistical Sciences University of Cape Town Rondebosch South Africa
- African Climate and Development Initiative, University of Cape Town Rondebosch South Africa
| | - Marie Nevoux
- Mammal Research Institute, Department of Zoology and Entomology University of Pretoria Hatfield South Africa
- UMRESE, Ecology and Ecosystem Health, Agrocampus Ouest, INRA Rennes France
| | - Roger Pradel
- Biostatistics and Population Biology Group, CEFE, CNRS, University of Montpellier Montpellier France
| | - Marthán N. Bester
- Mammal Research Institute, Department of Zoology and Entomology University of Pretoria Hatfield South Africa
| | - P. J. Nico Bruyn
- Mammal Research Institute, Department of Zoology and Entomology University of Pretoria Hatfield South Africa
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9
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Morganti M, Ambrosini R, Sarà M. Different trends of neighboring populations of Lesser Kestrel: Effects of climate and other environmental conditions. POPUL ECOL 2019. [DOI: 10.1002/1438-390x.1032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Roberto Ambrosini
- Department of Environmental Science and PolicyUniversity of Milan Milan Italy
| | - Maurizio Sarà
- Section of Animal BiologyDepartment STEBICEF, University of Palermo Palermo Italy
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10
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Guéry L, Rouan L, Descamps S, Bêty J, Fernández‐Chacón A, Gilchrist G, Pradel R. Covariate and multinomial: Accounting for distance in movement in capture-recapture analyses. Ecol Evol 2019; 9:818-824. [PMID: 30766671 PMCID: PMC6362441 DOI: 10.1002/ece3.4827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/13/2018] [Indexed: 11/11/2022] Open
Abstract
Many biological quantities cannot be measured directly but rather need to be estimated from models. Estimates from models are statistical objects with variance and, when derived simultaneously, covariance. It is well known that their variance-covariance (VC) matrix must be considered in subsequent analyses. Although it is always preferable to carry out the proposed analyses on the raw data themselves, a two-step approach cannot always be avoided. This situation arises when the parameters of a multinomial must be regressed against a covariate. The Delta method is an appropriate and frequently recommended way of deriving variance approximations of transformed and correlated variables. Implementing the Delta method is not trivial, and there is a lack of a detailed information on the procedure in the literature for complex situations such as those involved in constraining the parameters of a multinomial distribution. This paper proposes a how-to guide for calculating the correct VC matrices of dependant estimates involved in multinomial distributions and how to use them for testing the effects of covariates in post hoc analyses when the integration of these analyses directly into a model is not possible. For illustrative purpose, we focus on variables calculated in capture-recapture models, but the same procedure can be applied to all analyses dealing with correlated estimates with multinomial distribution and their variances and covariances.
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Affiliation(s)
- Loreleï Guéry
- Département de BiologieChimie et GéographieUniversité du Québec à Rimouski, Rimouski, Canada – Centre d'Etudes NordiquesLavalQuébecCanada
| | - Lauriane Rouan
- CIRAD – Biological Systems DepartmentUMR108 Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicalesMontpellierFrance
| | | | - Joël Bêty
- Département de BiologieChimie et GéographieUniversité du Québec à Rimouski, Rimouski, Canada – Centre d'Etudes NordiquesLavalQuébecCanada
| | | | - Grant Gilchrist
- National Wildlife Research Centre, Environment CanadaOttawaCanada
| | - Roger Pradel
- CEFEUMR 5175CNRS ‐ Université de Montpellier ‐ Université Paul‐Valéry Montpellier ‐EPHEMontpellierFrance
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11
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Bårdsen BJ, Hanssen SA, Bustnes JO. Multiple stressors: modeling the effect of pollution, climate, and predation on viability of a sub-arctic marine bird. Ecosphere 2018. [DOI: 10.1002/ecs2.2342] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Bård-Jørgen Bårdsen
- Arctic Ecology Department; Fram Centre; Norwegian Institute for Nature Research (NINA); N-9296 Tromsø Norway
| | - Sveinn Are Hanssen
- Arctic Ecology Department; Fram Centre; Norwegian Institute for Nature Research (NINA); N-9296 Tromsø Norway
| | - Jan Ove Bustnes
- Arctic Ecology Department; Fram Centre; Norwegian Institute for Nature Research (NINA); N-9296 Tromsø Norway
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12
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Gimenez O, Lebreton J, Choquet R, Pradel R. R2ucare: An
r
package to perform goodness‐of‐fit tests for capture–recapture models. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13014] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Olivier Gimenez
- CEFEUMR 5175CNRS ‐ Université de Montpellier ‐ Université Paul‐Valéry Montpellier ‐ EPHE Montpellier Cedex 5 France
| | - Jean‐Dominique Lebreton
- CEFEUMR 5175CNRS ‐ Université de Montpellier ‐ Université Paul‐Valéry Montpellier ‐ EPHE Montpellier Cedex 5 France
| | - Rémi Choquet
- CEFEUMR 5175CNRS ‐ Université de Montpellier ‐ Université Paul‐Valéry Montpellier ‐ EPHE Montpellier Cedex 5 France
| | - Roger Pradel
- CEFEUMR 5175CNRS ‐ Université de Montpellier ‐ Université Paul‐Valéry Montpellier ‐ EPHE Montpellier Cedex 5 France
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13
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Desprez M, Jenouvrier S, Barbraud C, Delord K, Weimerskirch H. Linking oceanographic conditions, migratory schedules and foraging behaviour during the non‐breeding season to reproductive performance in a long‐lived seabird. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13117] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Marine Desprez
- Biology Department MS‐50 Woods Hole Oceanographic Institution Woods Hole Massachusetts
| | - Stéphanie Jenouvrier
- Biology Department MS‐50 Woods Hole Oceanographic Institution Woods Hole Massachusetts
| | - Christophe Barbraud
- Centre d'Etudes Biologiques de Chizé UMR 7372 CNRS/Université La Rochelle Villiers en Bois France
| | - Karine Delord
- Centre d'Etudes Biologiques de Chizé UMR 7372 CNRS/Université La Rochelle Villiers en Bois France
| | - Henri Weimerskirch
- Centre d'Etudes Biologiques de Chizé UMR 7372 CNRS/Université La Rochelle Villiers en Bois France
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