Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations

• Published in: Heredity
• Main Authors: Charbonnel, Emeline, Daguin-Thiébaut, Claire, Caradec, Lucille, Moittié, Eléonore, Gilg, Olivier, Gavrilo, Maria, V., Strøm, Hallvard, Mallory, Mark, L., Morrison, R. I. Guy, Gilchrist, H. Grant, Leblois, Raphaël, Roux, Camille, Yearsley, Jonathan, M., Yannic, Glenn, Broquet, Thomas
• Other Authors: Laboratoire d'Ecologie Alpine (LECA), Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Grenoble (Fédération OSUG)-Université Grenoble Alpes (UGA), Groupe de recherche en écologie arctique (GREA), Station biologique de Roscoff = Roscoff Marine Station (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff = Roscoff Marine Station (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences UMR 6282 (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Arctic and Antarctic Research Institute (AARI), Russian Federal Service for Hydrometeorology and Environmental Monitoring (Roshydromet), Norwegian Polar Institute, Acadia University, Department of Biology, Carleton University (Carleton University), Carleton University, National Wildlife Research Centre, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), School of Biology and Environmental Sciences (SBES), University College Dublin Dublin (UCD), This work was supported by grants from the foundation Ellis Elliot (Switzerland), Societe vaudoise des Sciences naturelles (Switzerland) and Nos Oiseaux (Switzerland) to GY, by a foundation Agassiz (Switzerland) grant to TB and by Nicolas Perrin's research group, Department of Ecology and Evolution at University of Lausanne, Switzerland. This work benefited from access to the Biogenouest genomic platform at Station Biologique de Roscoff and we are grateful to the Roscoff Bioinformatics platform ABiMS (http://abims.sb-roscoff.fr), the national INRA MIGALE (http://migale.jouy.inra.fr) and GENOTOUL (Toulouse Midi-Pyrenees) bioinformatics HPC platforms, as well as the CBGP and the local Montpellier Bioinformatics Biodiversity (MBB, supported by the LabEx CeMEB ANR-10-LABX-0004) HPC platform services for providing storage and computing resources. RL was supported by the Agence Nationale de la Recherche (projects GENOSPACE ANR-16-CE02-0008 and INTROSPEC ANR-19-CE02-0011). The sampling in Canada was funded by the Department of Environment and Climate Change Canada. The sampling in Greenland was supported by the Groupe de Recherche in Ecologie Arctique (GREA) and funded by the French Polar Institute-IPEV (Program 'Ivory 1210'). The sampling in Svalbard was funded by the Norwegian Polar Institute and the Norwegian seabird monitoring program SEAPOP (www.seapop.no, grant number 192141). The sampling in Russia was part of the work plan of the Joint Norwegian-Russian Commission on Environmental Protection and funded by the Norwegian Ministry of Environment, Arctic and Antarctic Research Institute and the Russian IPY 2007/08 program., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), ANR-19-CE02-0011,IntroSpec,Impact génomique et causes évolutives de l'introgression aux stades avancés de la spéciation(2019)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2022
• Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; Arctic; Canada; ivory gull; Pagophila eburnea; Sea ice
• Online Access: https://hal.science/hal-03658284; https://hal.science/hal-03658284v1/document; https://hal.science/hal-03658284v1/file/Charbonnel_Heredity_2022_FINAL.pdf; https://doi.org/10.1038/s41437-022-00515-3

DATA AVAILABILITY: Genotypic data are deposited in DRYAD: https://doi.org/10.5061/dryad.j0zpc86gk and the raw reads have been deposited in the SRA (Bioproject: PRJNA81085). International audience Genetic data are useful for detecting sudden population declines in species that are difficult to study in the field. Yet this indirect approach has its own drawbacks, including population structure, mutation patterns, and generation overlap. The ivory gull (Pagophila eburnea), a long-lived Arctic seabird, is currently suffering from rapid alteration of its primary habitat (i.e., sea ice), and dramatic climatic events affecting reproduction and recruitment. However, ivory gulls live in remote areas, and it is difficult to assess the population trend of the species across its distribution. Here we present complementary microsatellite- and SNP-based genetic analyses to test a recent bottleneck genetic signal in ivory gulls over a large portion of their distribution. With attention to the potential effects of population structure, mutation patterns, and sample size, we found no significant signatures of population decline worldwide. At a finer scale, we found a significant bottleneck signal at one location in Canada. These results were compared with predictions from simulations showing how generation time and generation overlap can delay and reduce the bottleneck microsatellite heterozygosity excess signal. The consistency of the results obtained with independent methods strongly indicates that the species shows no genetic evidence of an overall decline in population size. However, drawing conclusions related to the species' population trends will require a better understanding of the effect of age structure in long-lived species. In addition, estimates of the effective global population size of ivory gulls were surprisingly low (similar to 1000 ind.), suggesting that the evolutionary potential of the species is not assured.