Uncovering latent structure in valued graphs: A variational approach

As more and more network-structured data sets are available, the statistical analysis of valued graphs has become common place. Looking for a latent structure is one of the many strategies used to better understand the behavior of a network. Several methods already exist for the binary case. We present a model-based strategy to uncover groups of nodes in valued graphs. This framework can be used for a wide span of parametric random graphs models and allows to include covariates. Variational tools allow us to achieve approximate maximum likelihood estimation of the parameters of these models. We provide a simulation study showing that our estimation method performs well over a broad range of situations. We apply this method to analyze host--parasite interaction networks in forest ecosystems.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS361 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Avoid, attack or do both? Behavioral and physiological adaptations in natural enemies faced with novel hosts

BACKGROUND: Confronted with well-defended, novel hosts, should an enemy invest in avoidance of these hosts (behavioral adaptation), neutralization of the defensive innovation (physiological adaptation) or both? Although simultaneous investment in both adaptations may first appear to be redundant, several empirical studies have suggested a reinforcement of physiological resistance to host defenses with additional avoidance behaviors. To explain this paradox, we develop a mathematical model describing the joint evolution of behavioral and physiological adaptations on the part of natural enemies to their host defenses. Our specific goals are (i) to derive the conditions that may favor the simultaneous investment in avoidance and physiological resistance and (ii) to study the factors that govern the relative investment in each adaptation mode. RESULTS: Our results show that (i) a simultaneous investment may be optimal if the fitness costs of the adaptive traits are accelerating and the probability of encountering defended hosts is low. When (i) holds, we find that (ii) the more that defended hosts are rare and/or spatially aggregated, the more behavioral adaptation is favored. CONCLUSION: Despite their interference, physiological resistance to host defensive innovations and avoidance of these same defenses are two strategies in which it may be optimal for an enemy to invest in simultaneously. The relative allocation to each strategy greatly depends on host spatial structure. We discuss the implications of our findings for the management of invasive plant species and the management of pest resistance to new crop protectants or varieties

Dizziness and Convergence Insufficiency in Children: Screening and Management

International audienceObjective: In children screened for dizziness with vergence disorders, we tested short and long term efficacy of orthoptic vergence training (OVT) and instructions to reduce screen usage.Methods: Prospective study: Of the 179 children referred for vertigo or dizziness (over 3 years) with ophthalmological disorder as the only problem after complete oto-neuro-vestibular testing, 69 presented vergence insufficiency, and 49 accepted to participate in this study. 109 healthy children served as controls. All subjects had classic orthoptic evaluation and video binocular movement recordings during various oculomotor tasks. Patients were evaluated before OVT (M0), 3 months after the end of OVT (M3) and 9 months after the end of OVT (M9). Statistics compared orthoptic and oculomotor parameters between patients and controls over time with one-way ANCOVA, and mixed models, controlling for age and gender.Results: Patients reported vertigo that was usually rotatory, lasting <15 min, associated with or alternating with headache (50%). Their exposure to small video screens and TV was intensive (∼3.6 h per day). At M0, all orthoptic and oculomotor parameters were statistically different in patients relative to controls (p < 0.0001) except for divergence. At M3, vertigo symptoms had disappeared in all of the patients, and all eye movement parameters improved significantly (p < 0.0001). At M9, this improvement remained stable or continued.Conclusion: Vergence disorders (assessed by abnormal orthoptic and oculomotor parameters) can generate symptoms of dizziness in children. Orthoptic treatment and instruction to reduce screen usage has a significant and long term effect on vertigo symptoms as well as oculomotor performances. Dizzy children should be screened for vergence disorders

Maternal effects shape the seed mycobiome in Quercus petraea

The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.Peer reviewe

Next-Generation Global Biomonitoring: Large-scale, Automated Reconstruction of Ecological Networks

We foresee a new global-scale, ecological approach to biomonitoring emerging within the next decade that can detect ecosystem change accurately, cheaply, and generically. Next-generation sequencing of DNA sampled from the Earth's environments would provide data for the relative abundance of operational taxonomic units or ecological functions. Machine-learning methods would then be used to reconstruct the ecological networks of interactions implicit in the raw NGS data. Ultimately, we envision the development of autonomous samplers that would sample nucleic acids and upload NGS sequence data to the cloud for network reconstruction. Large numbers of these samplers, in a global array, would allow sensitive automated biomonitoring of the Earth's major ecosystems at high spatial and temporal resolution, revolutionising our understanding of ecosystem change

Architecture of an Antagonistic Tree/Fungus Network: The Asymmetric Influence of Past Evolutionary History

Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions.Based on a long-term (1972-2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns.Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependent on recent ecological processes

The phyllosphere: microbial jungle at the plant–climate interface

The phyllosphere: microbial jungle at the plant–climate interface. Eawag Spring Serie

Network science in ecology

Network science in ecology. Séminaires de l'UMR Mathématiques et Informatique Appliquées, AgroParisTec

Investigating microbial networks in the phyllosphere using high-throughput sequencing

Investigating microbial networks in the phyllosphere using high-throughput sequencing. Formation "Traitement des données issues des nouvelles techniques de séquençage

La phyllosphère des arbres forestiers: un habitat peu exploré mais très peuplé!

La phyllosphère des arbres forestiers: un habitat peu exploré mais très peuplé!. Séminaires de l'UMR Biogec