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International audience; This is an introduction to the issue: Special feature: improving biodiversity monitoring using satellite remote sensing. The preservation of biodiversity has become a major challenge for sustainable development at national, European (Natura 2000 and Habitats Directive) and international levels (Convention on Biological Diversity, 2011-2020). To address the current conservation needs, there is a need to operationalise methods to assess the distribution of natural resources while integrating information on habitat condition; inform conservation planning and support the assessment of ecosystem services. Increased access to satellite imagery and new developments in data analyses can support progress towards biodiversity conservation targets by stepping up monitoring processes at various spatial and temporal scales. Satellite remote sensing is however no panacea, and little can be achieved without a robust understanding of the socio‐ecological system considered. We aim to demonstrate how the coupling of satellite remote sensing data with ground observations and adequate modelling can provide tangible operational solutions towards a better understanding and management of natural systems.

International audience; 1. Biodiversity includes multiscalar and multitemporal structures and processes, with different levels of functional organization, from genetic to ecosystemic levels. One of the mostly used methods to infer biodiversity is based on taxonomic approaches and community ecology theories. However, gathering extensive data in the field is difficult due to logistic problems, especially when aiming at modelling biodiversity changes in space and time, which assumes statistically sound sampling schemes. In this context, airborne or satellite remote sensing allows information to be gathered over wide areas in a reasonable time. 2. Most of the biodiversity maps obtained from remote sensing have been based on the inference of species richness by regression analysis. On the contrary, estimating compositional turnover (beta‐diversity) might add crucial information related to relative abundance of different species instead of just richness. Presently, few studies have addressed the measurement of species compositional turnover from space. 3. Extending on previous work, in this manuscript, we propose novel techniques to measure beta‐diversity from airborne or satellite remote sensing, mainly based on: (1) multivariate statistical analysis, (2) the spectral species concept, (3) self‐organizing feature maps, (4) multidimensional distance matrices, and the (5) Rao's Q diversity. Each of these measures addresses one or several issues related to turnover measurement. This manuscript is the first methodological example encompassing (and enhancing) most of the available methods for estimating beta‐diversity from remotely sensed imagery and potentially relating them to species diversity in the field.

International audience; The preservation of biodiversity has become a major challenge for sustainable development at national, European (Natura 2000 and Habitats Directive) and international levels (Convention on Biological Diversity, 2011-2020). To address the current conservation needs, there is a need to operationalise methods to assess the distribution of natural resources while integrating information on habitat condition; inform conservation planning and support the assessment of ecosystem services. Increased access to satellite imagery and new developments in data analyses can support progress towards biodiversity conservation targets by stepping up monitoring processes at various spatial and temporal scales. Satellite remote sensing is however no panacea, and little can be achieved without a robust understanding of the socio‐ecological system considered. We aim to demonstrate how the coupling of satellite remote sensing data with ground observations and adequate modelling can provide tangible operational solutions towards a better understanding and management of natural systems.

International audience; Amphibian chytridiomycosis, an emerging infectious disease caused by the fungus Batrachochytrium dendrobatidis (Bd), has been a significant driver of amphibian declines. While globally widespread, Bd had not yet been reported from within Madagascar. We document surveys conducted across the country between 2005 and 2014, showing Bd's first record in 2010. Subsequently, Bd was detected in multiple areas, with prevalence reaching up to 100%. Detection of Bd appears to be associated with mid to high elevation sites and to have a seasonal pattern, with greater detectability during the dry season. Lineage-based PCR was performed on a subset of samples. While some did not amplify with any lineage probe, when a positive signal was observed, samples were most similar to the Global Panzootic Lineage (BdGPL). These results may suggest that Bd arrived recently, but do not exclude the existence of a previously undetected endemic Bd genotype. Representatives of all native anuran families have tested Bd-positive and exposure trials confirm infection by Bd is possible. Bd's presence could pose significant threats to Madagascar's unique “megadiverse” amphibians.

This project aimed at evaluating the impact of the hurricanes of December 1999 on the dynamics of roe deer populations, in the short and the medium term, at understanding the ecological processes involved, at coupling models of the dynamics of the plants and the herbivores for long term prediction, and at improving the methods of monitoring the forestherbivore equilibria. Based on a long term (>25 years) study of populations of roe deer in two lowland deciduous forests heavily hit by the hurricanes, we show that the storms had no negative effect on survival or reproduction of the roe deer. The main effect, through the creation of openings, was an improvement of the quality of the roe deer habitat, which led to a decline on the size of the home ranges. The plant dynamics have led to marked changes in visibility which has affected the use of the ecological indicators. The implications of these results for the future management of roe deer populations are discussed. In populations close to the carrying capacity, the hurricanes will have increased the availability of the animals' resources, and so should increase the populations' rates of increase. Where resources were already abundant, the hurricanes will have had little or no effect. Adaptation of management actions post-hurricane therefore requires knowledge of the state of the equilibrium between the animals and their resources. This is available in populations where the integrated monitoring methods proposed by the French National Hunting Office (Office National de la Chasse et de la Faune Sauvage) for several years are applied., Ce projet avait pour objectif d'évaluer l'impact des tempêtes de décembre 1999 sur la dynamique des populations de chevreuils à court et à moyen terme, de comprendre les processus écologiques qui régissent ces populations, de coupler des modèles de dynamique des plantes et de dynamique des grands herbivores pour la prévision à long terme, et d'affiner les méthodes de suivi des équilibres forêt-grands herbivores. A partir du suivi à long terme (>25 ans) de deux populations de chevreuils dans des forêts de plaine caducifoliées fortement touchées par les tempêtes, nous avons montré que ces tempêtes n'avaient eu aucune influence négative sur la survie ou la reproduction des animaux. Au contraire, les tempêtes, en créant des ouvertures, ont entraîné une amélioration de la qualité de l'habitat pour le chevreuil qui s'est accompagnée d'une diminution de la taille des domaines vitaux. Ce projet a permis de quantifier les effets des tempêtes et de les intégrer dans des bases de données spatialisées sur les animaux et les deux forêts qui serviront aux gestionnaires comme aux chercheurs à l'avenir. La base de données à Chizé sert aussi pour l'enseignement universitaire et la formation, universitaire et permanente. - 4 - Les implications de cette perturbation pour la gestion future des populations de chevreuils dépendent de l'état d'équilibre entre les animaux et leurs ressources. Dans les populations qui montraient avant tempête une limitation de performance due à une forte densité par rapport aux ressources, la tempête est attendue avoir eu des effets très positifs sur la performance de ces populations. Ce processus « coup de fouet » aura cependant été de courte durée (3 ans environ) dans les forêts productives. Dans le contexte où les populations de chevreuils ne montraient avant tempête aucune réponse densité-dépendante (ressources abondantes), le passage des tempêtes n'aura eu que peu ou pas d'effets sur la dynamique des populations de chevreuils, puisque les performances étaient déjà proches du maximum possible. Ce constat devrait permettre aux gestionnaires d'ajuster les plans de chasse selon le contexte, dans des conditions analogues, afin de ne pas s'éloigner de leur objectif de gestion. Les tempêtes ont entraîné des changements marqués de visibilité qui ont perturbé l'utilisation de l'indicateur d'abondance, l'IKA, ce qui, en cas de changement de visibilité de ce type, devra être pris en compte dans les procédures de décision sur la gestion. A un niveau plus général, ce projet a permis de * publier des recommandations claires pour la gestion des chevreuils dans des peuplements en régénération après tempête ou après coupe, et * de développer la diffusion des méthodes de suivi par indicateurs de changements écologiques et des résultats de la recherche vers les gestionnaires.

A recent paper by Kolby et al. [1], surveying for Batrachochytrium dendrobatidis (Bd) and ranavirus in Madagascar, presents results for 508 amphibian specimens and 68 water bodies sampled during a 2-month period of the 2013–14 wet season. Kolby et al. [1] did not detect Bd in any of the samples, presenting evidence that add to our understanding of Bd dynamics in Madagascar. Earlier in 2015, we published “Widespread presence of the pathogenic fungus Batrachochytrium dendrobatidis in wild amphibian communities in Madagascar” in the journal Scientific Reports [2]. We presented rigorous spatial and temporal surveillance data for 4,155 amphibians sampled across a 10-year period, and used two independent molecular diagnostics to demonstrate the occurrence of a molecular signature of Bd infection at multiple locations across the island. We focus here on solely the Bd results, which directly relate to our published study. While the conclusions of Bd’s occurrence and prevalence in Madagascar may appear to conflict between these papers, upon closer investigation the data sets actually complement each other. Our evidence for Bd’s presence and its widespread incidence is based on multi-year monitoring data carried out through the National Monitoring Program [3] and allied survey efforts, occurring in both the wet and dry season. Our data collected during the same time as Kolby et al.’s sampling (2013–14 wet season), is consistent with their recently published results [1,2] (summarized in Table 1). Therefore, Kolby et al.’s conclusion that our data “highly contradict” those reported in their study is inaccurate. In the 2013–14 wet season, we sampled 569 frogs from 8 locations, of which only 3 samples showed a positive signal for Bd. The positive samples were collected from one individual at each of three sites: Antoetra, Ranomafana, and Ankaratra. While both datasets (the sampling reported in Kolby et al. 2015 and the wet season 2013–2014 sampling reported in Bletz et al. 2015) surveyed numerous individuals and locations across the island, there are some differences in sampling locations. More specifically, one of our positive occurrences came from Antoetra, which was not surveyed by Kolby et al [1]. Two of our positives do come from locations surveyed by both groups: Ranomafana and Ankaratra; if we combine the sub-sites within these locations, the prevalence is 0.0043 and 0.0062 respectively, which falls within the prevalence confidence intervals presented in Kolby et al. [1] (Table 1). This same logic is used by Kolby et al. [1] to show the complementarity of their field survey data and Kolby’s previous work showing Bd’s presence in amphibians imported into the US from Madagascar [4]. Both datasets are consistent with the conclusion that Bd had a very low prevalence during the 2013–2014 wet season. Table 1 Summary of published Bd survey data for the 2013–2014 wet season. The low prevalence detected in the wet season may likely be explained by seasonality of Bd. Both papers discuss the possibility of seasonal patterns, where Bd prevalence decreases in the warmer, wetter season and increases in the cooler, dryer season due to climatic or so-far un-described environmental factors. This phenomenon is not unusual and several studies have noted a high degree of seasonal variation in the prevalence of Bd (e.g. [5, 6, 7, 8]). In our published study [2] we present preliminary evidence of a seasonal pattern of Bd, showing that prevalence and/or detection was greater in the dryer, cooler season (May-Oct) than the wetter, warmer season (Nov-April) [2]. This seasonal pattern we documented likely explains the lack of detection by Kolby et al. since they sampled only in the wet (and warmer) season. Kolby et al. [1] supplement their individual sampling with the analysis of filtered water from natural habitats. In this case, the lack of Bd detection might be associated with increased water flow due to increased rainfall during the wet season, which could lower the concentration of Bd zoospores to undetectable levels. Additionally, water-filters of natural water bodies have also been found to be less sensitive than direct sampling of amphibians [9,10]. To better understand seasonal variation as well as other factors such as geographic distribution and host species variation, additional sampling across wet and dry season in a uniform and standardize manner will be important. The major difference between these papers is that we draw from data collected in multiple years and seasons and from a much larger sample of amphibians with further validation using chytrid lineage-based PCR amplification, making our study more comprehensive in nature. Kolby et al. [1] surveyed for a 2-month period, which makes it difficult to make general assumptions about pathogen occurrence from such a small snap shot in time. Our data set thus allows for the conclusion of the “widespread presence of Bd” as we document repeated detections of Bd at geographically distant locations in Madagascar albeit with varying degree of prevalence among sites and seasons. We also have secondary confirmation and validation of Bd’s presence from an independent non-nuclear lineage specific qPCR designed to the Bd mtDNA locus, which is unique to our study. Kolby et al. [1] suggest that Bd in Madagascar cannot yet be described with certainty in part due to the variability of sampling and detection methods. We acknowledge ourselves that our use of various methods may confound some of our findings, such as the seasonal pattern of Bd; however, and importantly, this does not negate or question the evidence for Bd-positive samples collected from Madagascar. While the data presented by both studies indicate a low prevalence of Bd in Madagascar in 2014, we argue that the additional multi-year data we have collected strongly supports the occurrence of one or more Bd lineage(s) in the samples collected from wild Madagascar amphibians. A similar conclusion was also made by Kolby et al. [4] based on their observations of Bd in wild-caught frogs from Madagascar that were imported into the USA. Definitive and final confirmation of Bd in Madagascar awaits histopathology, isolation of a Bd culture, and/or genome sequencing. These additional analyses can clarify whether Madagascar is facing the panzootic, hypervirulent Bd-GPL or a different (possibly endemic) Bd-lineage. More importantly, our results may have serious conservation implications. We presented strong evidence that at least one lineage of Bd exists in Madagascar, with increased prevalence at some locations during the dry season. It remains to be understood if this genotype is virulent with respect to the resident anuran fauna and capable of causing population declines. Using the ‘precautionary principle’ in reacting to suspected introductions of novel emerging infectious diseases infecting wildlife [11] it is essential to initiate conservation actions. Continuing ongoing population monitoring of Madagascar's amphibians and pathogen surveillance through the NMP are therefore essential and are a priority of the national amphibian conservation strategy for the country known as ‘A Conservation Strategy for the Amphibians of Madagascar (ACSAM) [12,13]. If it is relatively hypovirulent, it gives conservationists time to engage in mitigation strategies and to plan for the possible (and likely inevitable) arrival of a virulent genotype, which could threaten the diverse, endemic frog communities.