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21. Reproductive behaviours in male parasitoids: From mating system to pairing pattern.

Author

Charrat, Blandine, Amat, Isabelle, Allainé, Dominique, and Desouhant, Emmanuel

Subjects
ANIMAL sexual behavior, HUMAN sexuality, ASSORTATIVE mating, SEXUAL selection, BIOLOGICAL fitness, LONGEVITY, ONTOGENY
Abstract

It is now acknowledged that mating system is a dynamic characteristic within species or populations. Indeed, behavioural characteristics shaping the mating system can vary at the inter‐individual level, providing raw material for sexual and natural selections, and at the intra‐individual level, because of phenotypic plasticity and ontogeny of individual behaviours. Social environment is an additional source of variation in sexual behaviours. By focusing on males of the parasitoid wasp Venturia canescens, we assessed how sexual behaviours (courtship and mating) vary between and within individuals, considering males' size as inter‐individual source of variation, and age and mating experience as intra‐individual sources of variation. Consequences of the variations in sexual behaviours at the individual level are appraised by quantifying the costs in longevity and offspring production incurred by (repeatedly) mated males. At the population level, we tested the "agility hypothesis" predicting that smaller males win the male–male competition to access females, resulting in a non‐random assortative mating by size and a negative sexual selection on body size. We showed that V. canescens males are polygynous and that mating incurred longevity cost. Old males had a higher probability to court females, but no mating advantage. Smaller males tended to have a higher mating probability, but size was not under sexual selection and there was a random mating pattern according to individual size. Male–male competition intensity did not influence pairing pattern but tended to influence mating dynamic. Overall, our results suggest that sexual behaviours tended to vary at the inter‐ and intra‐individual levels and the effect of social environment remains to be more precisely described. These variations may impact individuals' reproductive success with potential ecological and evolutionary consequences that are discussed. [ABSTRACT FROM AUTHOR]

Published
2023
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25. Revisiting giraffe photo-identification using deep learning and network analysis

Author

Miele, Vincent, Dussert, Gaspard, Spataro, Bruno, Chamaillé-Jammes, Simon, Allainé, Dominique, Bonenfant, Christophe, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-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), 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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and 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)

Subjects
SIFT, deep metric learning, opensource, [SDE]Environmental Sciences, image similarity networks, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, animal identification
Abstract

An increasing number of research programs rely on photographic capture-recapture (vs. direct marking) of individuals to study distribution and demography within animal populations. Photo-identification of individuals living in the wild is sometimes feasible using idiosyncratic coat or skin patterns, like for giraffes. When performed manually, the task is tedious and becomes almost impossible as populations grow in size. Computer vision techniques are an appealing and unavoidable help to tackle this apparently simple task in the big-data era. In this context, we propose to revisit giraffe re-identification using convolutional neural networks (CNNs).We first developed an end-to-end pipeline to retrieve a comprehensive set of re-identified giraffes from about 4, 000 raw photographs. To do so, we combined CNN-based object detection, SIFT pattern matching, and image similarity networks. We then quantified the performance of deep metric learning to retrieve the identity of known and unknown individuals. The re-identification performance of CNNs reached a top 5 accuracy of about 90%. Fully based on open-source software packages, our work paves the way for further attempts to build CNN-based pipelines for re-identification of individual animals, in giraffes but also in other species.

Published
2020

30. Efficient spatial multi‐state capture–recapture model to study natal dispersal: An application to the Alpine marmot.

Author

Dupont, Pierre, Allainé, Dominique, Ferrandiz‐Rovira, Mariona, and Pradel, Roger

Subjects
*LIFE history theory, *YOUNG adults, *DISPERSAL (Ecology), *PHILOPATRY
Abstract

Studying natal dispersal in natural populations using capture–recapture data is challenging as an unknown proportion of individuals leaves the study area when dispersing and are never recaptured. Most dispersal (and survival) estimates from capture–recapture studies are thus biased and only reflect what happens within the study area, not the population.Here, we elaborate on recent methodological advances to build a spatially explicit multi‐state capture–recapture model to study natal dispersal in a territorial mammal while accounting for imperfect detection and movement in and out of the study area.We validate our model using a simulation study where we compare it to a non‐spatial multi‐state capture–recapture model. We then apply it to a long‐term individual‐based dataset on Alpine marmot Marmota marmota.Our model was able to accurately estimate natal dispersal and survival probabilities, as well as mean dispersal distance for a large range of dispersal patterns. By contrast, the non‐spatial multi‐state estimates underestimated both survival and natal dispersal even for short dispersal distances relative to the study area size. We discuss the application of our approach to other species and monitoring setups.We estimated higher inheritance probabilities of female Alpine marmots, which suggests higher levels of philopatry, although the probability to become dominant after dispersal did not differ between sexes. Nonetheless, the lower survival of young adult males suggests higher costs of dispersal for males. We further discuss the implications of our findings in light of the life history of the species. [ABSTRACT FROM AUTHOR]

Published
2022
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42. Sex-specific determinants of fitness in a social mammal

Author

Lardy, S., Allainé, Dominique, Bonenfant, C., Cohas, A., Evolution, adaptation et comportement, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio]
Published
2015

43. Mate choice for neutral and MHC genetic characteristics in Alpine marmots : different targets in different contexts?

Author

Ferrandiz‐Rovira, Mariona, Allainé, Dominique, Callait‐Cardinal, Marie‐Pierre, Cohas, Aurélie, Ferrandiz‐Rovira, Mariona, Allainé, Dominique, Callait‐Cardinal, Marie‐Pierre, and Cohas, Aurélie

Abstract

We warmly thank all students and Earthwatch volunteers involved in catching the marmots and the authorities of the Vanoise National Park for granting us permission to work in the Grande Sassière Nature Reserve. We thank M. Harrington for English editing and Dr. E. Rajon for helpful discussions on the manuscript. This work was supported by the "Agence Nationale de la Recherche" (ANR, project ANR‐08‐BLAN‐0214‐03, ANR‐13‐JSV7‐0005), the "Centre National de la Recherche Scientifique" (CNRS), the "FR41 BioEnvironnement et Santé de l'Université de Lyon" and the "Earthwatch Institute", the scholarship for postgraduate studies "Obra Social Fundació La Caixa" and Vetagro‐Sup., Sexual selection through female mate choice for genetic characteristics has been suggested to be an important evolutionary force maintaining genetic variation in animal populations. However, the genetic targets of female mate choice are not clearly identified and whether female mate choice is based on neutral genetic characteristics or on particular functional loci remains an open question. Here, we investigated the genetic targets of female mate choice in Alpine marmots (Marmota marmota), a socially monogamous mammal where extra‐pair paternity (EPP) occurs. We used 16 microsatellites to describe neutral genetic characteristics and two MHC loci belonging to MHC class I and II as functional genetic characteristics. Our results reveal that (1) neutral and MHC genetic characteristics convey different information in this species, (2) social pairs show a higher MHC class II dissimilarity than expected under random mate choice, and (3) the occurrence of EPP increases when social pairs present a high neutral genetic similarity or dissimilarity but also when they present low MHC class II dissimilarity. Thus, female mate choice is based on both neutral and MHC genetic characteristics, and the genetic characteristics targeted seem to be context dependent (i.e., the genes involved in social mate choice and genetic mate choice differ). We emphasize the need for empirical studies of mate choice in the wild using both neutral and MHC genetic characteristics because whether neutral and functional genetic characteristics convey similar information is not universal.

Published
2016

46. Testing determinants of the annual individual fitness: An overall mean mixture model for de‐lifing data.

Author

Dupont, Pierre, Allainé, Dominique, Cohas, Aurélie, and Pradel, Roger

Subjects
BIOLOGICAL fitness, BIOLOGICAL evolution, ECOLOGY, LINEAR statistical models, MIXTURE distributions (Probability theory), MATHEMATICAL models
Abstract

Abstract: The de‐lifing method (Coulson et al., 2006, Proceedings of the Royal Society of London B: Biological Sciences, 273, 547), though very promising for studying ecological and evolutionary changes, has been scarcely used to identify factors influential on fitness. Through simulations representative of a variety of iteroparous species, we establish that a two‐component normal mixture usually provides a much better representation of de‐lifing data than the single normal distribution assumed in classical linear models. To test determinants of the annual individual fitness, we propose the overall mean mixture model (O3M), a mixture model parameterised in terms of the overall mean of the mixture distribution. We examine the gain in performance and accuracy when using the O3M over classical linear models and bootstrap methods on simulated finite normal mixture distributions for different regression shapes and variance structure, and apply it to a real dataset to study how the annual individual fitness varies with age in alpine marmots. The O3M improves considerably the precision of the estimates and hence the power of the analysis. We discuss the adaptation of the O3M model to more complex distributions and advise on its use. [ABSTRACT FROM AUTHOR]

Published
2018
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47. Contrasting patterns of selection acting on MHC class I and class II DRB genes inthe Alpine marmot (Marmota marmota)

Author

Kuduk, K., Johanet, Aurélie, Allainé, Dominique, Cohas, Aurélie, Radwan, J., Evolution, adaptation et comportement, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
bottleneck, duplication, positive selection, [SDV]Life Sciences [q-bio], rodent, Sciuridae, parasites, polymorphism
Published
2012
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48. La sélection sexuelle

Author

Cézilly , Frank, Allainé , Dominique, Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Evolution, adaptation et comportement, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), F. Thomas, T. Lefèvre, M. Raymond, Laffont, Rémi, Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), F. Thomas, T. Lefèvre & M. Raymond, Biogéosciences [UMR 6282] [Dijon] (BGS), and Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Subjects
[ SDV.BID.EVO ] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]
Abstract

36 pages

Published
2010

49. Evolution et typologie des régimes d'appariement

Author

Allainé, Dominique, Cézilly, Frank, Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), F. Thomas, T. Lefèvre & M. Raymond, Evolution, adaptation et comportement, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and Laffont, Rémi

Subjects
[ SDV.BID.EVO ] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]
Abstract

30 pages

Published
2010

50. Unexpected male choosiness for mates in a spider

Author

Bel-Venner, Marie-Claude, Dray, S., Allainé, Dominique, Menu, F., Venner, Samuel, Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Evolution, adaptation et comportement

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT]
Published
2008

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