Drivers for Rift Valley fever emergence in Mayotte: A Bayesian modelling approach

Rift Valley fever (RVF) is a major zoonotic and arboviral hemorrhagic fever. The conditions leading to RVF epidemics are still unclear, and the relative role of climatic and anthropogenic factors may vary between ecosystems. Here, we estimate the most likely scenario that led to RVF emergence on the island of Mayotte, following the 2006–2007 African epidemic. We developed the first mathematical model for RVF that accounts for climate, animal imports and livestock susceptibility, which is fitted to a 12-years dataset. RVF emergence was found to be triggered by the import of infectious animals, whilst transmissibility was approximated as a linear or exponential function of vegetation density. Model forecasts indicated a very low probability of virus endemicity in 2017, and therefore of re-emergence in a closed system (i.e. without import of infected animals). However, the very high proportion of naive animals reached in 2016 implies that the island remains vulnerable to the import of infectious animals. We recommend reinforcing surveillance in livestock, should RVF be reported is neighbouring territories. Our model should be tested elsewhere, with ecosystem-specific data

Disentangling the complexity of groundwater dependent social-ecological systems

Groundwater resources are part of larger social-ecological systems. In this chapter, we review the various dimensions of these complex systems in order to uncover the diversity of elements at stake in the evolution of an aquifer and the loci for possible actions to control its dynamics. Two case studies illustrate how the state of an aquifer is embedded in a web of biophysical and sociopolitical processes. We propose here a holistic view through an IGM-scape that describes the various possible pathways of evolution for a groundwater related social-ecological system. Then we describe the elements of this IGM-scape starting with physical entities and processes, including relations with surface water and quality issues. Interactions with society bring an additional layer of considerations, including decisions on groundwater abstraction, land use changes and even energy related choices. Finally we point out the policy levers for groundwater management and their possible consequences for an aquifer, taking into account the complexity of pathways opened by these levers

Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish

Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic region and transposable elements (TEs) may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be used to infer neutral and/or adaptive population genetic structure, whose study has been restricted to microsatellites, mtDNA, and AFLP markers in the past and more recently the use of SNPs. Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1538 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that six duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene sequence amplification. We also identified 175 CNVs associated with the divergence of three previously defined parapatric glacial lineages, of which 24% were located within protein-coding genes, making those loci potential candidates for reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, which was in stark contrast with that inferred based on SNPs in a previous study. Our findings underscore the complementarity of those two types of genomic variation in population genomics studies

Genome-wide DNA methylation predicts environmentally driven life history variation in a marine fish.

Epigenetic modifications are thought to be one of the molecular mechanisms involved in plastic adaptive responses to environmental variation. However, studies reporting associations between genome-wide epigenetic changes and habitat-specific variations in life history traits (e.g., lifespan, reproduction) are still scarce, likely due to the recent application of methylome resequencing methods to non-model species. In this study, we examined associations between whole genome DNA methylation and environmentally driven life history variation in 2 lineages of a marine fish, the capelin (Mallotus villosus), from North America and Europe. In both lineages, capelin harbor 2 contrasting life history tactics (demersal vs. beach-spawning). Performing whole genome and methylome sequencing, we showed that life history tactics are associated with epigenetic changes in both lineages, though the effect was stronger in European capelin. Genetic differentiation between the capelin harboring different life history tactics was negligible, but we found genome-wide methylation changes in both lineages. We identified 9,125 European and 199 North American differentially methylated regions (DMRs) due to life history. Gene ontology (GO) enrichment analysis for both lineages revealed an excess of terms related to neural function. Our results suggest that environmental variation causes important epigenetic changes that are associated with contrasting life history tactics in lineages with divergent genetic backgrounds, with variable importance of genetic variation in driving epigenetic variation. Our study emphasizes the potential role of genome-wide epigenetic variation in adaptation to environmental variation

Solute transport dynamics in small, shallow groundwater-dominated agricultural catchments: insights from a high-frequency, multisolute 10 yr-long monitoring study

International audienceHigh-frequency, long-term and multisolute measurements are required to assess the impact of human pressures on water quality due to (i) the high temporal and spatial variability of climate and human activity and (ii) the fact that chemical solutes combine short- and long-term dynamics. Such data series are scarce. This study, based on an original and unpublished time series from the Kervidy-Naizin headwater catchment (Brittany, France), aims to determine solute transfer processes and dynamics that characterise this strongly human-impacted catchment. The Kervidy-Naizin catchment is a temperate, intensive agricultural catchment, hydrologically controlled by shallow groundwater. Over 10 yr, five solutes (nitrate, sulphate, chloride, and dissolved organic and inorganic carbon) were monitored daily at the catchment outlet and roughly every four months in the shallow groundwater. The concentrations of all five solutes showed seasonal variations but the patterns of the variations differed from one solute to another. Nitrate and chloride exhibit rather smooth variations. In contrast, sulphate as well as organic and inorganic carbon is dominated by flood flushes. The observed nitrate and chloride patterns are typical of an intensive agricultural catchment hydrologically controlled by shallow groundwater. Nitrate and chloride originating mainly from organic fertilisers accumulated over several years in the shallow groundwater. They are seasonally exported when upland groundwater connects with the stream during the wet season. Conversely, sulphate as well as organic and inorganic carbon patterns are not specific to agricultural catchments. These solutes do not come from fertilisers and do not accumulate in soil or shallow groundwater; instead, they are biogeochemically produced in the catchment. The results allowed development of a generic classification system based on the specific temporal patterns and source locations of each solute. It also considers the stocking period and the dominant process that limits transport to the stream, i.e. the connectivity of the stocking compartment. This mechanistic classification can be applied to any chemical solute to help assess its origin, storage or production location and transfer mechanism in similar catchments