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1. Agricultural intensification alters marbled newt genetic diversity and gene flow through density and dispersal reduction

Author

Raphaël Leblois, Pierre Grillet, Olivier Lourdais, Alexandre Boissinot, Bertrand Gauffre, Vincent Quiquempois, Sophie Morin, Damien Picard, Cécile Ribout, School of Biological Sciences [Clayton], Monash University [Clayton], Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Réserve Naturelle Régionale du Bocage des Antonins [France], Office français de la biodiversité (OFB), Département de Biologie UFR Sciences - Université d'Angers [France], Université d'Angers (UA), and Centre d’Etudes Biologiques de Chizé (CEBC), UMR 7372 CNRS - La Rochelle Université, France, 79360, Villiers-en-Bois, France

Subjects
0106 biological sciences, Gene Flow, Triturus marmoratus, [SDV]Life Sciences [q-bio], Population, Biology, 010603 evolutionary biology, 01 natural sciences, microsatellites, 03 medical and health sciences, demographic inferences, Effective population size, Genetics, Animals, education, dispersal, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Ecosystem, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, Genetic diversity, Ecology, Genetic Variation, landscape genetics, genetic diversity, 15. Life on land, Salamandridae, Habitat destruction, Genetics, Population, Genetic distance, Genetic structure, [SDE]Environmental Sciences, Biological dispersal, Arable land, Microsatellite Repeats
Abstract

International audience; Recent agricultural intensification threatens global biodiversity with amphibians being one of the most impacted groups. Because of their biphasic life cycle, amphibians are particularly vulnerable to habitat loss and fragmentation that often result in small, isolated populations and loss of genetic diversity. Here, we studied how landscape heterogeneity affects genetic diversity, gene flow and demographic parameters in the marbled newt, Triturus marmoratus, over a hedgerow network landscape in Western France. While the northern part of the study area consists of preserved hedged farm-land, the southern part was more profoundly converted for intensive arable crops production after WWII. Based on 67 sampled ponds and 10 microsatellite loci, we characterized regional population genetic structure and evaluated the correlation between landscape variables and (i) local genetic diversity using mixed models and (ii) genetic distance using multiple regression methods and commonality analysis. We identified a single genetic population characterized by a spatially heterogeneous isolation- by- distance pattern. Pond density in the surrounding landscape positively affected local genetic diversity while arable crop land cover negatively affected gene flow and connectivity. We used demographic inferences to quantitatively assess dif-ferences in effective population density and dispersal between the contrasted land-scapes characterizing the northern and southern parts of the study area. Altogether, results suggest recent land conversion affected T. marmoratus through reduction in both effective population density and dispersal due to habitat loss and reduced connectivity.

Published
2021

2. Fine-scale genetic structure in a high dispersal capacity raptor, the Montagu’s harrier (Circus pygargus), revealed by a set of novel microsatellite loci

Author

Bertrand Gauffre, Damien Picard, Cécile Ribout, A Villers, Karine Monceau, S. Ruault, Vincent Bretagnolle, 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), LTSER «Zone Atelier Plaine & Val de Sevre» [France], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR), Département de Biologie UFR Sciences - Université d'Angers [France], Université d'Angers (UA), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), CEBC / INRA, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH)

Subjects
0106 biological sciences, 0301 basic medicine, Gene Flow, Male, Genetic Speciation, Population, Zoology, Plant Science, 010603 evolutionary biology, 01 natural sciences, Birds, 03 medical and health sciences, Circus pygargus, Circus cyaneus, Genetics, Animals, Raptor Spatial genetic structure, education, Microsatellites, ComputingMilieux_MISCELLANEOUS, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Polymorphism, Genetic, biology, Circus aeruginosus, Harrier, General Medicine, biology.organism_classification, 030104 developmental biology, Insect Science, Genetic structure, [SDE]Environmental Sciences, Microsatellite, Biological dispersal, Animal Science and Zoology, Philopatry, Female, Relatedness, Marsh harrier, Microsatellite Repeats
Abstract

International audience; The Montagu’s harrier (Circus pygargus) is a semi-colonial raptor species widely but patchily distributed across the Palearctic region with recorded cases of philopatry and presence of extra-pair copulation. In order to assess Montagu’s harrier spatial genetic structure and contemporary gene flow, we developed 16 new microsatellite markers using 454 pyrosequencing. Genotypes of 117 chicks sampled in a 200 × 300 km farmland area in Central Western France were analyzed to characterize genetic polymorphism at each locus and regional and fine-scale genetic structure. Fourteen markers were found polymorphic, with a number of alleles ranging from 3 to 11. The expected and observed heterozygosities ranged from 0.36 to 0.856 and from 0.35 to 0.868, respectively. A single genetic unit was found at the regional scale with higher genetic similarity observed at a small spatial scale (up to 10 km). Our results are consistent with overall large-scale juvenile and adult dispersal together with small-scale male philopatry. Cross-species amplification of this set of microsatellites makers has been successful in two closely related harrier species: the marsh harrier (Circus aeruginosus) and the Hen harrier (Circus cyaneus) for which 14 and 12 markers were polymorphic, respectively. These new microsatellite markers could be used to study the population genetic structure, contemporary gene flow and parentage analyses in these three species and to conduct microsatellite-based demographic inferences on the Montagu’s harrier.

Published
2019

3. Agricultural landscapes and the Loire River influence the genetic structure of the marbled newt in Western France

Author

Jean-Marc Costanzi, Quentin Le Petitcorps, Francis Isselin-Nondedeu, Pierre Grillet, Pascal Mège, Olivier Lourdais, Sophie Morin-Pinaud, Agathe Legrand, François Varenne, Audrey Trochet, Alexandre Boissinot, Damien Picard, Sandra Guérin, Faculty of Technology, Natural Sciences and Maritime Sciences [Norway], University of South-Eastern Norway (USN), Département de Biologie UFR Sciences - Université d'Angers [France], Université d'Angers (UA), 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), Cités, Territoires, Environnement et Sociétés (CITERES), Centre National de la Recherche Scientifique (CNRS)-Université de Tours (UT), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut de Recherche pour le Développement (IRD [France-Sud]), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), LPO Vendée, LPO, Pierre Grillet, Unité Avifaune migratrice, Direction de la Recherche et de l’Expertise (ONCFS France], Office National de la Chasse et de la Faune Sauvage (ONCFS), Région Pays de la Loire, Centre Beautour, Chinon SNB project (stratégie nationale pour la biodiversité 2011, French minister of ecology), Office National de la Chasse et de la Faune Sauvage (Pôle Bocage et Faune Sauvage) and Nouvelle-Aquitaine Region, ONF-Centre Val de Loire, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), ONCFS - Office National de la Chasse et de la Faune Sauvage, Centre National de la Recherche Scientifique (CNRS)-Université de Tours, Institut National de la Recherche Agronomique (INRA)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, Biodiversité et Ecologie, Science, Triturus marmoratus, Loire River, 010603 evolutionary biology, 01 natural sciences, Biodiversity and Ecology, 03 medical and health sciences, DAPC Results, Discriminant Analysis Of Principal Components (DAPC), Isolation by distance, Multidisciplinary, biology, Ecology, Marbled Newt, Fragmentation (computing), 15. Life on land, biology.organism_classification, Large Crop Fields, 030104 developmental biology, Geography, Genetic distance, Genetic structure, [SDE]Environmental Sciences, Medicine, Biological dispersal, Conservation biology, Arable land
Abstract

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Amphibians are particularly sensitive to landscape fragmentation. Potential barriers between breeding sites can negatively infuence the dispersal of individuals and increase genetic structure between populations. In this study, we genotyped 10 microsatellites for 334 marbled newts (Triturus marmoratus) at 11 diferent locations in Western France. Samples were collected in diferent regions with contrasting agricultural landscapes (low and high proportion of arable land in the north and south, respectively). We found a strong genetic structure between the northern and southern sampling sites. Isolation by distance was recorded after 62km, but within the northern region, little or no genetic structure was detected over large distances (up to 114km). Genetic structure at shorter distance (43km) was found between sites situated in landscapes with larger amounts of arable lands. A signifcant positive relationship was found between the pairwise genetic distance (Fst) between sites and the amount of arable land together with the distance between sites. Our results suggest that the Loire River might act as a corridor for the marbled newt, while arable land might act as a barrier. Finally, although a large city is located between sampling sites, no efect was detected on population structure.

Published
2018

4. Marking techniques in the Marbled Newt (Triturus marmoratus): PIT-Tag and tracking device implant protocols

Author

Le Chevalier, Hugo, Calvez, Olivier, Martinez-Silvestre, Albert, Picard, Damien, Guérin, Sandra, Isselin-Nondedeu, Francis, Riberon, Alexandre, Trochet, Audrey, Station d'écologie théorique et expérimentale (SETE), Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, University of Barcelona, Département de Biologie UFR Sciences - Université d'Angers [France], Université d'Angers (UA), Cités, Territoires, Environnement et Sociétés (CITERES), Centre National de la Recherche Scientifique (CNRS)-Université de Tours (UT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Études des Structures, des Processus d’Adaptation et des Changements de l’Espace (ESPACE), Université Côte d'Azur (UCA)-Avignon Université (AU)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Groupe ECologie et COnservation des vertébrés (GECCO), and Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, animal structures, 010604 marine biology & hydrobiology, Marbled Newt, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, implant protocols, body regions, lcsh:Zoology, embryonic structures, lcsh:QL1-991, Marking techniques, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Individual marking has become essential for studying population dynamics and ecological requirements. However, marking small-bodied species such as amphibians is becoming a challenge in the last decades. Amphibian surveys may require to mark manually individuals, using toe clipping, polymers and pigments, or passive integrated transponders (PIT-tags). Even if ethics committees have recently recommend avoiding toe clipping in amphibians, the use of PIT-tags led to controversial results because low tag retention reported in some studies. Here, we describe a protocol of potentially life-long PIT-tag marking in a protected species, the marbled newt Triturus marmoratus. In addition, we also detailed a second procedure of surgery for the implantation of transmitters needed in radio-tracking surveys. During both procedures, we found that the newt phase (either aquatic or terrestrial) strongly affected the anesthesia duration. Indeed, newts in aquatic phase were more quickly anesthetized than newts under terrestrial phase. We then recommend to pay attention of this physiological particularity when performing this kind of procedure. Improving our knowledge on ecological requirements and population dynamics of this species is crucial for management and conservation plans, and could be extended to other large newts., Acta Herpetologica, Vol 12 No 1 (2017)

Published
2017
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