Using the multivariate Hawkes process to study interactions between multiple species from camera trap data.

Interspecific interactions can influence species' activity and movement patterns. In particular, species may avoid or attract each other through reactive responses in space and/or time. However, data and methods to study such reactive interactions have remained scarce and were generally limited to two interacting species.

PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets.

In phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, can decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phylogenomic analyses precludes manual error detection and removal. However, a simple and efficient way to automate the identification of outliers from a collection of gene trees is still missing.

Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity.

Objectives: Mycobacterium tuberculosis (Mtb) infections result in a wide spectrum of clinical presentations but without proven Mtb genetic determinants. Herein, we hypothesized that the genetic features of Mtb clinical isolates, such as specific polymorphisms or microdiversity, may be linked to tuberculosis (TB) severity.

Methods: A total of 234 patients with pulmonary TB (including 193 drug-susceptible and 14 monoresistant cases diagnosed between 2017 and 2020 and 27 multidrug-resistant cases diagnosed between 2010 and 2020) were stratified according to TB disease severity, and Mtb genetic features were explored using whole genome sequencing, including heterologous single-nucleotide polymorphism (SNP), calling to explore microdiversity.

Are human natal sex ratio differences across the world adaptive? A test of Fisher's principle.

Fisher's principle states that natural selection favours an equal number of male and female births at the population level, unless there are sex differences in rearing costs or sex differences in mortality before the end of the period of parental investment. Sex differences in rearing costs should be more pronounced in low- than in high-resource settings. We, therefore, examined whether human development index and sex differences in child mortality contribute to the natural variation in human sex ratio at birth across the globe.

Can an herbivore affect where a top predator kills its prey by modifying woody vegetation structure?

In large mammal communities, little is known about modification of interspecific interactions through habitat structure changes. We assessed the effects of African elephants (Loxodonta africana) on features of woody habitat structure that can affect predator-prey interactions. We then explored how this can influence where African lions (Panthera leo) kill their prey.

Investigating microbial associations from sequencing survey data with co-correspondence analysis.

Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next-generation sequencing (NGS) techniques with refined statistical analysis (e.

Flower phenology as a disruptor of the fruiting dynamics in temperate oak species.

Many perennial plants display masting, that is, fruiting with strong interannual variations, irregular and synchronized between trees within the population. Here, we tested the hypothesis that the early flower phenology in temperate oak species promotes stochasticity into their fruiting dynamics, which could play a major role in tree reproductive success. From a large field monitoring network, we compared the pollen phenology between temperate and Mediterranean oak species.

Phenotypic plasticity in the invasive pest : activity rhythms and gene expression in response to temperature.

Phenotypic plasticity may contribute to the invasive success of an alien species in a new environment. A highly plastic species may survive and reproduce in more diverse environments, thereby supporting establishment and colonization. We focused on plasticity in the circadian rhythm of activity, which can favour species coexistence in invasion, for the invasive species , which is expected to be a weaker direct competitor than other species of the resident community.

Diversity indices for ecological networks: a unifying framework using Hill numbers.

Describing how ecological interactions change over space and time and how they are shaped by environmental conditions is crucial to understand and predict ecosystem trajectories. However, it requires having an appropriate framework to measure network diversity locally, regionally and between samples (α-, γ- and β-diversity). Here, we propose a unifying framework that builds on Hill numbers and accounts both for the probabilistic nature of biotic interactions and the abundances of species or groups.

Integrating spatial and phylogenetic information in the fourth-corner analysis to test trait-environment relationships.

The fourth-corner analysis aims to quantify and test for relationships between species traits and site-specific environmental variables, mediated by site-specific species abundances. Since there is no common unit of observation, the significance of the relationships is tested using a double permutation procedure (site based and species based). This method implies that all species and sites are independent of each other.

Optimizing the choice of a spatial weighting matrix in eigenvector-based methods.

Eigenvector-mapping methods such as Moran's eigenvector maps (MEM) are derived from a spatial weighting matrix (SWM) that describes the relations among a set of sampled sites. The specification of the SWM is a crucial step, but the SWM is generally chosen arbitrarily, regardless of the sampling design characteristics. Here, we compare the statistical performances of different types of SWMs (distance-based or graph-based) in contrasted realistic simulation scenarios.

Factors shaping community assemblages and species co-occurrence of different trophic levels.

Species assemblages are the results of various processes, including dispersion and habitat filtering. Disentangling the effects of these different processes is challenging for statistical analysis, especially when biotic interactions should be considered. In this study, we used plants (producers) and leafhoppers (phytophagous) as model organisms, and we investigated the relative importance of abiotic versus biotic factors that shape community assemblages, and we infer on their biotic interactions by applying three-step statistical analysis.

A critical issue in model-based inference for studying trait-based community assembly and a solution.

Statistical testing of trait-environment association from data is a challenge as there is no common unit of observation: the trait is observed on species, the environment on sites and the mediating abundance on species-site combinations. A number of correlation-based methods, such as the community weighted trait means method (CWM), the fourth-corner correlation method and the multivariate method RLQ, have been proposed to estimate such trait-environment associations. In these methods, valid statistical testing proceeds by performing two separate resampling tests, one site-based and the other species-based and by assessing significance by the largest of the two -values (the test).

Interspecific interference competition at the resource patch scale: do large herbivores spatially avoid elephants while accessing water?

Animals may anticipate and try to avoid, at some costs, physical encounters with other competitors. This may ultimately impact their foraging distribution and intake rates. Such cryptic interference competition is difficult to measure in the field, and extremely little is known at the interspecific level.

Spatial Distribution of a Large Herbivore Community at Waterholes: An Assessment of Its Stability over Years in Hwange National Park, Zimbabwe.

The spatial structuring of populations or communities is an important driver of their functioning and their influence on ecosystems. Identifying the (in)stability of the spatial structure of populations is a first step towards understanding the underlying causes of these structures. Here we studied the relative importance of spatial vs.

Addressing ecological effects of radiation on populations and ecosystems to improve protection of the environment against radiation: Agreed statements from a Consensus Symposium.

This paper reports the output of a consensus symposium organized by the International Union of Radioecology in November 2015. The symposium gathered an academically diverse group of 30 scientists to consider the still debated ecological impact of radiation on populations and ecosystems. Stimulated by the Chernobyl and Fukushima disasters' accidental contamination of the environment, there is increasing interest in developing environmental radiation protection frameworks.

The global spectrum of plant form and function.

Earth is home to a remarkable diversity of plant forms and life histories, yet comparatively few essential trait combinations have proved evolutionarily viable in today's terrestrial biosphere. By analysing worldwide variation in six major traits critical to growth, survival and reproduction within the largest sample of vascular plant species ever compiled, we found that occupancy of six-dimensional trait space is strongly concentrated, indicating coordination and trade-offs. Three-quarters of trait variation is captured in a two-dimensional global spectrum of plant form and function.

Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification.

The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily.

Statistical ecology comes of age.

The desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1-4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology.

Functional analysis of normalized difference vegetation index curves reveals overwinter mule deer survival is driven by both spring and autumn phenology.

Large herbivore populations respond strongly to remotely sensed measures of primary productivity. Whereas most studies in seasonal environments have focused on the effects of spring plant phenology on juvenile survival, recent studies demonstrated that autumn nutrition also plays a crucial role. We tested for both direct and indirect (through body mass) effects of spring and autumn phenology on winter survival of 2315 mule deer fawns across a wide range of environmental conditions in Idaho, USA.

Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation.

Assessing trait responses to environmental gradients requires the simultaneous analysis of the information contained in three tables: L (species distribution across samples), R (environmental characteristics of samples), and Q (species traits). Among the available methods, the so-called fourth-corner and RLQ methods are two appealing alternatives that provide a direct way to test and estimate trait-nvironment relationships. Both methods are based on the analysis of the fourth-corner matrix, which crosses traits and environmental variables weighted by species abundances.