Reciprocal modulation of internal and external factors determines individual movements

Summary 1. Movement is fundamental to individual and population dynamics, as it allows individuals to meet their basic requirements. Although movement patterns reflect interactions between internal and external factors, only few studies have examined the effects of these factors on movement simultaneously, and they generally focused on particular biological contexts (e.g. dispersal, foraging). 2. However, the relative importance of these factors in driving individual routine movements might reflect a species' potential flexibility to cope with landscape changes and therefore buffer their potential impact on fitness. 3. We used data from GPS collars on Scandinavian brown bears to investigate the relative role of these factors, as well as an additional factor (period of the year) on routine movements at two spatial scales (hourly and daily relocations). 4. As expected, internal factors played a major role in driving movement, compared to external factors at both scales, but its relative importance was greater at a finer scale. In particular, the interaction between reproductive status and period of the year was one of the most influential variables, females being constrained by the movement capacity of their cubs in the first periods of the year. The effect of human disturbance on movement was also greater for females with cubs than for lone females. 5. This study showed how reciprocal modulation of internal and external factors is shaping space use of brown bears. We stress that these factors should be studied simultaneously to avoid the risk of obtaining context-dependent inferences. Moreover, the study of their relative contribution is also highly relevant in the context of multiple-use landscapes, as human activities generally affect the landscape more than they affect the internal states of an individual. Species or individuals with important internal constraints should be less responsive to changes in their environment as they have less freedom from internal constraints and should thus be more sensitive to human alteration of the landscape, as shown for females with cubs in this study

Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.

Some species responded successfully to prehistoric changes in climate [1, 2], while others failed to adapt and became extinct [3]. The factors that determine successful climate adaptation remain poorly understood. We constructed a reference genome and studied physiological adaptations in the Alpine marmot (Marmota marmota), a large ground-dwelling squirrel exquisitely adapted to the "ice-age" climate of the Pleistocene steppe [4, 5]. Since the disappearance of this habitat, the rodent persists in large numbers in the high-altitude Alpine meadow [6, 7]. Genome and metabolome showed evidence of adaptation consistent with cold climate, affecting white adipose tissue. Conversely, however, we found that the Alpine marmot has levels of genetic variation that are among the lowest for mammals, such that deleterious mutations are less effectively purged. Our data rule out typical explanations for low diversity, such as high levels of consanguineous mating, or a very recent bottleneck. Instead, ancient demographic reconstruction revealed that genetic diversity was lost during the climate shifts of the Pleistocene and has not recovered, despite the current high population size. We attribute this slow recovery to the marmot's adaptive life history. The case of the Alpine marmot reveals a complicated relationship between climatic changes, genetic diversity, and conservation status. It shows that species of extremely low genetic diversity can be very successful and persist over thousands of years, but also that climate-adapted life history can trap a species in a persistent state of low genetic diversity.This work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001134), the UK Medical Research Council (FC001134), and the Wellcome Trust (FC001134). CB and AC are supported by the Agence Nationale de la Recherche (project ANR-13-JSV7-0005) and the Centre National de la Recherche Scientifique (CNRS), CB is supported by the Rhône-Alpes region (Grant 15.005146.01). LD is supported by Agence Nationale de la Recherche (project ANR-12-ADAP-0009). TIG is supported by a Leverhulme Early Career Fellowship (Grant ECF-2015-453) and a NERC grant (NE/N013832/1). JMG is supported by a Hertha Finberg Fellowship (FWF T703). LDR is supported by the Diabetes UK RD Lawrence Fellowship (16/0005382)

Importance des échelles spatio-temporelles dans la variabilité et l'évolution de la dispersion chez les mamifères (les multiples visages du chat domestique (Felis catus L.))

Ce travail a abordé la variabilité du processus de dispersion chez les mammifères sous deux angles différents mais néanmoins complémentaires. Dans une 1ère partie, l'analyse comparative interspécifique a montré, au niveau empirique, l'existence de relation de covariation entre l'intensité de la dispersion et deux traits d'histoire de vie (les degrés de précocité à la naissance et de socialité) importants dans les stratégies bio-démographiques des mammifères. Dans une 2ème partie, la variabilité démographique (patrons de dispersion et de survie) des populations de chats domestiques errants (Felis catus L.) vivant dans des environnements contrastés a été appréhendée. Les analyses démographiques et génétiques ont confirmé l'extrême plasticité phénotypique comportementale chez cette espèce. L'ensemble du travail met en évidence la pertinence d'une approche à échelles multiples spatiales et temporelles, dans la compréhension de l'évolution et de la variabilité des patrons de dispersionLYON1-BU.Sciences (692662101) / SudocSudocFranceF

Impact de la diversité génétique dans la détermination de la valeur sélective individuelle au sein de populations de mammifères sauvages

Ce travail a abordé la question de l'influence du génome dans la détermination de composantes de la valeur sélective individuelle. Pour ce, trois populations de mammifères (marmotte Marmota marmota, chevreuil Capreolus capreolus, et mouflon du Canada Ovis canadensis) ont été considérées en conditions naturelles. Il s'est agi d'étudier l'existence d'une corrélation entre hétérozygotie et survie juvénile (pour la marmotte et le chevreuil) et succès reproducteur annuel des mâles (pour le mouflon). La diversité génétique a été estimée à partir de microsatellites " aléatoirement " répartis dans le génome mais aussi avec des microsatellites situés dans des gènes potentiellement sélectionnés (chez le chevreuil et le mouflon). Les résultats laissent apparaître une relation positive entre la diversité génétique et la survie juvénile chez la marmotte et le chevreuil, alors que chez le mouflon le déterminisme génétique du succès reproducteur n'a pas pu clairement être mis en évidence. Les travaux réalisés suggèrent un poids non négligeable du génome dans la détermination de la valeur sélectiveLYON1-BU.Sciences (692662101) / SudocSudocFranceF

Revisiting animal photo-identification using deep metric learning and network analysis

An increasing number of ecological monitoring programmes rely on photographic capture–recapture of individuals to study distribution, demography and abundance of species. Photo-identification of individuals can sometimes be done using idiosyncratic coat or skin patterns, instead of using tags or loggers. However, when performed manually, the task of going through photographs is tedious and rapidly becomes too time-consuming as the number of pictures grows. 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 animal re-identification using image similarity networks and metric learning with convolutional neural networks (CNNs), taking the giraffe as a working example. 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 individuals, and to detect unknown individuals never seen in the previous years of monitoring. After a data augmentation procedure, the re-identification performance of the CNN reached a Top-1 accuracy of about 90%, despite the very small number of images per individual in the training dataset. While the complete pipeline succeeded in re-identifying known individuals, it slightly under-performed with unknown individuals. Fully based on open-source software packages, our work paves the way for further attempts to build automatic pipelines for re-identification of individual animals, not only in giraffes but also in other species.DATA AVAILABILITY STATEMENT: The curated dataset of re-identified giraffe individuals is freely available at ftp://pbil.univ-lyon1.fr/pub/datasets/miele2021. The code to reproduce the analysis is available at https://plmlab.math.cnrs.fr/vmiele/animal-reid/ with explanations and test cases.French National Center for Scientific Research (CNRS) and Statistical Ecology Research Group (EcoStat).https://besjournals.onlinelibrary.wiley.com/journal/2041210x2022-03-17hj2021Mammal Research InstituteZoology and Entomolog

Brown bear habitat suitability in the Pyrenees: transferability across sites and linking scales to make the most of scarce data

1. Identification of suitable habitats for small, endangered populations is important to preserve key areas for potential augmentation. However, replicated spatial data from a sufficient number of indi- viduals are often unavailable for such populations, leading to unreliable habitat models. This is the case for the endangered Pyrenean brown bear Ursus arctos population, with only about 20 individu- als surviving in two isolated groups. 2. We conducted habitat suitability analyses at two spatial scales (coarse and local). Given the lim- ited available data, we used information from the nearby Cantabrian brown bear population in Spain to develop a two-dimensional model (human and natural variables) at a coarse scale, based on logistic regression, which we applied in the Pyrenees. At a local scale, we used bear presence in the Pyrenees to describe the population’s ecological niche and develop a habitat suitability model using presence-only methods. We combined these models to obtain a more integrative understand- ing of bear requirements. 3. The coarse-scale model showed a good transferability to the Pyrenees, identifying preference for areas with high forest connectivity, masting trees, rugged terrain and shrubs and avoidance of areas with anthropogenic structures. The local-scale model was consistent with the coarse-scale model. Bears showed a trade-off between food resources (scarcer at high elevations) and human presence (higher at low elevations). 4. Our models illustrated that there is unoccupied good habitat for bears in the Pyrenees that could host new individuals. Combining two scales allowed us to identify areas that should be prioritized for management actions and also those that should be easier to manage for bears. 5. Synthesis and applications. Our study illustrates how a nested-scale approach, combining coarse data from a different population and fine-scale local data, can aid in the management of small popu- lations with limited data. This was applied to remnant brown bear populations to identify priorities for conservation management.Peer reviewe

Variation in growth form and precocity at birth in eutherian mammals

International audienceUsing the flexible Chapman-Richards model for describing the growth curves from birth to adulthood of 69 species of eutherian mammals, we demonstrate that growth form differs among eutherian mammals. Thereby the commonly used Gompertz model can no longer be considered as the general model for describing mammalian growth. Precocial mammals have their peak growth rate earlier in the growth process than altricial mammals. However, the position on the altricial-precocial continuum accounts for most growth-form differences only between mammalian lineages. Within mammalian genera differences in growth form are not related to precocity at birth. This indicates that growth form may have been associated with precocity at birth early in mammalian evolution, when broad patterns of body development radiated. We discuss four non-exclusive interpretations to account for the role of precocity at birth on the observed variation in growth form among mammals. Precocial and altricial mammals could differ according to (i) the distribution of energy output by the mother, (ii) the ability of the young to assimilate the milk yield, (ii) the allocation of energy by the young between competing functions and (iv) the position of birth between conception and attainment of physical maturity

Recherche de l'impact des mouettes rieuses sur une population de poissons dans une region d'etangs: rapport final

SIGLECNRS RP 185 (1984) / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc