Papers by Bernard Cazelles
HAL (Le Centre pour la Communication Scientifique Directe), Mar 25, 2020
HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific r... more HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
BMC Infectious Diseases, Mar 19, 2007
Proceedings of The Royal Society B: Biological Sciences, May 7, 2005
Ecosystems and populations are known to be influenced not only by long-term climatic trends, but ... more Ecosystems and populations are known to be influenced not only by long-term climatic trends, but also by other short-term climatic modes, such as interannual and decadal-scale variabilities. Because interactions between climatic forcing, biotic and abiotic components of ecosystems are subtle and complex, analysis of long-term series of both biological and physical factors is essential to understanding these interactions. Here, we apply a wavelet analysis simultaneously to long-term datasets on the environment and on the populations and breeding success of three Antarctic seabirds (southern fulmar, snow petrel, emperor penguin) breeding in Terre Ade ´lie, to study the effects of climate fluctuations on Antarctic marine ecosystems. We show that over the past 40 years, populations and demographic parameters of the three species fluctuate with a periodicity of 3-5 years that was also detected in sea-ice extent and the Southern Oscillation Index. Although the major periodicity of these interannual fluctuations is not common to different species and environmental variables, their cyclic characteristics reveal a significant change since 1980. Moreover, sliding-correlation analysis highlighted the relationships between environmental variables and the demography of the three species, with important change of correlation occurring between the end of the 1970s and the beginning of the 1980s. These results suggest that a regime shift has probably occurred during this period, significantly affecting the Antarctic ecosystem, but with contrasted effects on the three species.
PLOS ONE, Oct 20, 2009
The recurrence of influenza A epidemics has originally been explained by a ''continuous antigenic... more The recurrence of influenza A epidemics has originally been explained by a ''continuous antigenic drift'' scenario. Recently, it has been shown that if genetic drift is gradual, the evolution of influenza A main antigen, the haemagglutinin, is punctuated. As a consequence, it has been suggested that influenza A dynamics at the population level should be approximated by a serial SIR model. Here, simple models are used to test whether a serial SIR model requires gradual antigenic drift within groups of strains with the same antigenic properties (antigenic clusters). We compare the effect of status based and history based frameworks and the influence of reduced susceptibility and infectivity assumptions on the transient dynamics of antigenic clusters. Our results reveal that the replacement of a resident antigenic cluster by a mutant cluster, as observed in data, is reproduced only by the status based model integrating the reduced infectivity assumption. This combination of assumptions is useful to overcome the otherwise extremely high model dimensionality of models incorporating many strains, but relies on a biological hypothesis not obviously satisfied. Our findings finally suggest the dynamical importance of gradual antigenic drift even in the presence of punctuated immune escape. A more regular renewal of susceptible pool than the one implemented in a serial SIR model should be part of a minimal theory for influenza at the population level.
Scientific Reports, Sep 13, 2016
Investigating the ontogeny of niche differentiation enables to determine at which life-stages sex... more Investigating the ontogeny of niche differentiation enables to determine at which life-stages sexual segregation arises, providing insights into the main factors driving resource partitioning. We investigated the ontogeny of foraging ecology in Antarctic fur seals (Arctocephalus gazella), a highly dimorphic species with contrasting breeding strategies between sexes. Sequential δ 13 C and δ 15 N values of whiskers provided a longitudinal proxy of the foraging niche throughout the whole life of seals, from weaning, when size dimorphism is minimal to the age of 5. Females exhibited an early-life ontogenetic shift, from a total segregation during their first year at-sea, to a similar isotopic niche as breeding females as early as age 2. In contrast, males showed a progressive change in isotopic niche throughout their development such that 5-year-old males did not share the same niche as territorial bulls. Interestingly, males and females segregated straight after weaning with males appearing to feed in more southerly habitats than females. This spatial segregation was of similar amplitude as observed in breeding adults and was maintained throughout development. Such early-life niche differentiation is an unusual pattern and indicates size dimorphism and breeding constraints do not directly drive sexual segregation contrary to what has been assumed in otariid seals.
HAL (Le Centre pour la Communication Scientifique Directe), May 31, 2012
HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific r... more HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
PLOS Computational Biology, Aug 15, 2018
The spread of disease through human populations is complex. The characteristics of disease propag... more The spread of disease through human populations is complex. The characteristics of disease propagation evolve with time, as a result of a multitude of environmental and anthropic factors, this non-stationarity is a key factor in this huge complexity. In the absence of appropriate external data sources, to correctly describe the disease propagation, we explore a flexible approach, based on stochastic models for the disease dynamics, and on diffusion processes for the parameter dynamics. Using such a diffusion process has the advantage of not requiring a specific mathematical function for the parameter dynamics. Coupled with particle MCMC, this approach allows us to reconstruct the time evolution of some key parameters (average transmission rate for instance). Thus, by capturing the time-varying nature of the different mechanisms involved in disease propagation, the epidemic can be described. Firstly we demonstrate the efficiency of this methodology on a toy model, where the parameters and the observation process are known. Applied then to real datasets, our methodology is able, based solely on simple stochastic models, to reconstruct complex epidemics, such as flu or dengue, over long time periods. Hence we demonstrate that timevarying parameters can improve the accuracy of model performances, and we suggest that our methodology can be used as a first step towards a better understanding of a complex epidemic, in situation where data is limited and/or uncertain.
American Journal of Epidemiology, Jun 15, 2005
Pertussis is a worldwide infectious disease which persists despite massive vaccination campaigns ... more Pertussis is a worldwide infectious disease which persists despite massive vaccination campaigns that have gone on for several decades. To obtain an overall view of pertussis dynamics and the impact of vaccination, the authors performed, using the wavelet method, a comparative analysis of pertussis time series in 12 countries to detect and quantify periodicity and synchrony between them. Results showed a clear 3-to 4-year cycle in all countries, but the main finding was that this periodicity was transient. No global pattern in the effect of vaccination on pertussis dynamics was observed, but some spatial synchrony between countries was detected. This largescale comparative analysis of pertussis dynamics sheds light on the complexity of the multiple interactions involved in global pertussis spatial dynamic patterns. It suggests a need to perform a global survey of human infectious diseases over the long term, which would permit better assessment of the risk of disease outbreaks in the future.
Proceedings of The Royal Society B: Biological Sciences, Dec 22, 2001
The e¡ects of migration in a network of patch populations, or metapopulation, are extremely impor... more The e¡ects of migration in a network of patch populations, or metapopulation, are extremely important for predicting the possibility of extinctions both at a local and a global scale. Migration between patches synchronizes local populations and bestows upon them identical dynamics (coherent or synchronous oscillations), a feature that is understood to enhance the risk of global extinctions. This is one of the central theoretical arguments in the literature associated with conservation ecology. Here, rather than restricting ourselves to the study of coherent oscillations, we examine other types of synchronization phenomena that we consider to be equally important. Intermittent and out-of-phase synchronization are but two examples that force us to reinterpret some classical results of the metapopulation theory. In addition, we discuss how asynchronous processes (for example, random timing of dispersal) can paradoxically generate metapopulation synchronization, another non-intuitive result that cannot easily be explained by the standard theory.
Nature Communications, Mar 22, 2019
Zika virus (ZIKV) is a mosquito-borne flavivirus that predominantly circulates between humans and... more Zika virus (ZIKV) is a mosquito-borne flavivirus that predominantly circulates between humans and Aedes mosquitoes. Clinical studies have shown that Zika viruria in patients persists for an extended period, and results in infectious virions being excreted. Here, we demonstrate that Aedes mosquitoes are permissive to ZIKV infection when breeding in urine or sewage containing low concentrations of ZIKV. Mosquito larvae and pupae, including from field Aedes aegypti can acquire ZIKV from contaminated aquatic systems, resulting in ZIKV infection of adult females. Adult mosquitoes can transmit infectious virions to susceptible type I/II interferon receptor-deficient (ifnagr-/-) C57BL/6 (AG6) mice. Furthermore, ZIKV viruria from infected AG6 mice can causes mosquito infection during the aquatic life stages. Our studies suggest that infectious urine could be a natural ZIKV source, which is potentially transmissible to mosquitoes when breeding in an aquatic environment.
Remote Sensing, Sep 7, 2019
Over the last century, climate change has impacted the physiology, distribution, and phenology of... more Over the last century, climate change has impacted the physiology, distribution, and phenology of marine and terrestrial primary producers worldwide. The study of these fluctuations has been hindered due to the complex response of plants to environmental forcing over large spatial and temporal scales. To bridge this gap, we investigated the synchrony in seasonal phenological activity between marine and terrestrial primary producers to environmental and climatic variability across northern Patagonia. We disentangled the effects on the biological activity of local processes using advanced time-frequency analysis and partial wavelet coherence on 15 years (2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014)(2015)(2016)(2017) of data from MODIS (Moderate Resolution Imaging Spectroradiometer) onboard the Terra and Aqua satellites and global climatic variability using large-scale climate indices. Our results show that periodic variations in both coastal ocean and land productivity are associated with sea surface temperature forcing over seasonal scales and with climatic forcing over multi-annual (2-4 years) modes. These complex relationships indicate that large-scale climatic processes primarily modulate the synchronous phenological seasonal activity across northern Patagonia, which makes these unique ecosystems highly exposed to future climatic change.
Canadian Journal of Fisheries and Aquatic Sciences, May 1, 2020
Long-term ecological surveys (LTES) often exhibit strong variability among sampling dates. The us... more Long-term ecological surveys (LTES) often exhibit strong variability among sampling dates. The use and interpretation of such interannual variability is challenging due to the combination of multiple processes involved and sampling uncertainty. Here, we analysed the interannual variability in ~30 years of 150 species-density (fish and invertebrate) and environmental-observation time series in four aquatic-systems (stream, river, estuary, and marine continental shelf) with different sampling efforts to identify the information provided by this variability. We tested, using two empirical methods, whether we could observe simultaneous fluctuation between detrended time series corresponding to widely acknowledged assumptions about aquatic population dynamics: spatial effects, cohort effects, and environmental effects. We found a low number of significant results (36, 9, 0% for spatial, cohort, and environmental effects), suggesting that sampling uncertainty overrode the effects of biological processes. Our study does not question the relevance of LTES for detecting important trends, but clearly indicated that the statistical power to interpret interannual variations in aquatic-species densities is low, especially in large systems where the degree of sampling effort is always limited.
Remote Sensing, Jun 15, 2018
Western Patagonia harbors unique and sparsely studied terrestrial ecosystems that are threatened ... more Western Patagonia harbors unique and sparsely studied terrestrial ecosystems that are threatened by land use changes and exposure to basin-scale climatic variability. We assessed the performance of two satellite vegetation indices derived from MODIS-Terra, EVI (Enhanced Vegetation Index) and NDVI (Normalized Difference Vegetation Index), over the northern and southern sectors of the Chiloé Island System (CIS) to advance our understanding of vegetation dynamics in the region. Then we examined their time-varying relationships with two climatic indices indicative of tropical and extratropical influence, the ENSO (El Niño-Southern Oscillation) and the Antarctic Oscillation (AAO) index, respectively. The 17-year time series showed that only EVI captured the seasonal pattern characteristic of temperate regions, with low (high) phenological activity during Autumn-Winter (Spring-Summer). NDVI saturated during the season of high productivity and failed to capture the seasonal cycle. Temporal patterns in productivity showed a weakened seasonal cycle during the past decade, particularly over the northern sector. We observed a non-stationary association between EVI and both climatic indices. Significant co-variation between EVI and the Niño-Southern Oscillation index in the annual band persisted from 2001 until 2008-2009; annual coherence with AAO prevailed from 2013 onwards and the 2009-2012 period was characterized by coherence between EVI and both climate indices over longer temporal scales. Our results suggest that the influence of large-scale climatic variability on local weather patterns drives phenological responses in the northern and southern regions of the CIS. The imprint of climatic variability on patterns of primary production across the CIS may be underpinned by spatial differences in the anthropogenic modification of this ecosystem, as the northern sector is strongly modified by forestry and agriculture. We highlight the need for field validation of satellite indices around areas of high biomass and high endemism, located in the southern sector of the island, in order to enhance the utility of satellite vegetation indices in the conservation and management of austral ecosystems.
Chaos Solitons & Fractals, 2001
Recently it has been shown that when there are chaotic attractors whose basins are such that ever... more Recently it has been shown that when there are chaotic attractors whose basins are such that every point in the basin has pieces of another attractors's basin arbitrarily nearby, the basins are said to be riddled. A key requirement for the occurrence of a riddled basin is the loss of transverse stability of an invariant subspace, of dimension less than
Physics Letters, 1995
We present an adaptive method that allows to control or synchronize chaotic systems to a goal beh... more We present an adaptive method that allows to control or synchronize chaotic systems to a goal behavior in presence of large additive noise. The method is based on a state-parameter estimator, the Kalman fillet, and requires the previous knowledge of the system dynamics. We show the robustness of the procedure in the presence of large noise both in discrete and continuous systems.
eLife, Nov 29, 2016
Before the outbreak that reached the Americas in 2015, Zika virus (ZIKV) circulated in Asia and t... more Before the outbreak that reached the Americas in 2015, Zika virus (ZIKV) circulated in Asia and the Pacific: these past epidemics can be highly informative on the key parameters driving virus transmission, such as the basic reproduction number (R 0 ). We compare two compartmental models with different mosquito representations, using surveillance and seroprevalence data for several ZIKV outbreaks in Pacific islands (Yap, Micronesia 2007, Tahiti and Moorea, French Polynesia 2013-2014, New Caledonia 2014). Models are estimated in a stochastic framework with recent Bayesian techniques. R 0 for the Pacific ZIKV epidemics is estimated between 1.5 and 4.1, the smallest islands displaying higher and more variable values. This relatively low range of R 0 suggests that intervention strategies developed for other flaviviruses should enable as, if not more effective control of ZIKV. Our study also highlights the importance of seroprevalence data for precise quantitative analysis of pathogen propagation, to design prevention and control strategies.
Stochastic Environmental Research and Risk Assessment, Mar 20, 2015
Dengue is the world's most important vector-borne viral disease. The dengue mosquito and virus ar... more Dengue is the world's most important vector-borne viral disease. The dengue mosquito and virus are sensitive to climate variability and change. Temperature, humidity and precipitation influence mosquito biology, abundance and habitat, and the virus replication speed. In this study, we develop a modelling procedure to quantify the added value of including climate information in a dengue model for the 76 provinces of Thailand, from 1982-2013. We first developed a seasonal-spatial model, to account for dependency structures from one month to the next and between provinces. We then tested precipitation and temperature variables at varying time lags, using linear and nonlinear functional forms, to determine an optimum combination of time lags to describe dengue relative risk. Model parameters were estimated using Integrated Nested Laplace Approximation (INLA). This approach provides a novel opportunity to perform model selection in a Bayesian framework, while accounting for underlying spatial and temporal dependency structures and linear or nonlinear functional forms. We quantified the additional variation explained by interannual climate variations, above that provided by the seasonal-spatial model. Overall, an additional 8% of the variance in dengue relative risk can be explained by accounting for interannual variations in precipitation and temperature in the previous month. The inclusion of nonlinear functions of climate in the model framework improved the model for 79% of the provinces. Therefore, climate forecast information could significantly contribute to a national dengue early warning system in Thailand.
The American Naturalist, Jun 1, 2001
Proceedings of The Royal Society B: Biological Sciences, Apr 27, 2011
Influenza usually spreads through the human population in multiple-wave outbreaks. Successive rei... more Influenza usually spreads through the human population in multiple-wave outbreaks. Successive reinfection of individuals over a short time interval has been explicitly reported during past pandemics. However, the causes of rapid reinfection and the role of reinfection in driving multiple-wave outbreaks remain poorly understood. To investigate these issues, we focus on a two-wave influenza A/H3N2 epidemic that occurred on the remote island of Tristan da Cunha in 1971. Over 59 days, 273 (96%) of 284 islanders experienced at least one attack and 92 (32%) experienced two attacks. We formulate six mathematical models invoking a variety of antigenic and immunological reinfection mechanisms. Using a maximum-likelihood analysis to confront model predictions with the reported incidence time series, we demonstrate that only two mechanisms can be retained: some hosts with either a delayed or deficient humoral immune response to the primary influenza infection were reinfected by the same strain, thus initiating the second epidemic wave. Both mechanisms are supported by previous empirical studies and may arise from a combination of genetic and ecological causes. We advocate that a better understanding and account of heterogeneity in the human immune response are essential to analysis of multiple-wave influenza outbreaks and pandemic planning.
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Papers by Bernard Cazelles