West Nile virus spread in Europe: Phylogeographic pattern analysis and key drivers.

Background: West Nile virus (WNV) outbreaks in birds, humans, and livestock have occurred in multiple areas in Europe and have had a significant impact on animal and human health. The patterns of emergence and spread of WNV in Europe are very different from those in the US and understanding these are important for guiding preparedness activities.

Methods: We mapped the evolution and spread history of WNV in Europe by incorporating viral genome sequences and epidemiological data into phylodynamic models.

From biomarkers to community composition: Negative effects of UV/chlorine-treated reclaimed urban wastewater on freshwater biota.

The use of urban wastewater reclaimed water has recently increased across the globe to restore stream environmental flows and mitigate the effects of water scarcity. Reclaimed water is disinfected using different treatments, but their effects into the receiving rivers are little studied. Physiological bioassays and biomarkers can detect sub-lethal effects on target species, but do not provide information on changes in community structure.

A fast and inexpensive genotyping system for the simultaneous analysis of human and Aedes albopictus short tandem repeats.

Background: Determination of the interactions between hematophagous mosquitoes and their human hosts is of great importance for better understanding the transmission dynamics of mosquito-borne arboviruses and developing effective strategies to mitigate risk. Genetic analysis of human and mosquito DNA can play a key role in this, but commercial kits for human short tandem repeat (STR) genotyping are expensive and do not allow for the simultaneous STR analysis of host and vector DNA. Here, we present an inexpensive and straightforward STR-loci multiplex system capable of simultaneously amplifying Aedes albopictus and human STRs from blood-fed mosquitoes.

Benthic sediment as stores and sources of bacteria and viruses in streams: A comparison of baseflow vs. stormflow longitudinal transport and residence times.

The presence of bacteria and viruses in freshwater represents a global health risk. The substantial spatial and temporal variability of microbes leads to difficulties in quantifying the risks associated with their presence in freshwater. Fine particles, including bacteria and viruses are transported and accumulated into shallow streambed (i.

Global methane emissions from rivers and streams.

Methane (CH) is a potent greenhouse gas and its concentrations have tripled in the atmosphere since the industrial revolution. There is evidence that global warming has increased CH emissions from freshwater ecosystems, providing positive feedback to the global climate. Yet for rivers and streams, the controls and the magnitude of CH emissions remain highly uncertain.

Joint estimation of survival and dispersal effectively corrects the permanent emigration bias in mark-recapture analyses.

Robust and reliable estimates of demographic parameters are essential to understand population dynamics. Natal dispersal is a common process in monitored populations and can cause underestimations of survival and dispersal due to permanent emigration. Here, we present a multistate Bayesian capture-mark-recapture approach based on a joint estimation of natal dispersal kernel and detection probabilities to address biases in survival, dispersal, and related demographic parameters when dispersal information is limited.

New insights on patterns of genetic admixture and phylogeographic history in Iberian high mountain populations of midwife toads.

Multiple Quaternary glacial refugia in the Iberian Peninsula, commonly known as "refugia within refugia", allowed diverging populations to come into contact and admix, potentially boosting substantial mito-nuclear discordances. In this study, we employ a comprehensive set of mitochondrial and nuclear markers to shed light onto the drivers of geographical differentiation in Iberian high mountain populations of the midwife toads Alytes obstetricans and A. almogavarii from the Pyrenees, Picos de Europa and Guadarrama Mountains.

Microbes from Mum: symbiont transmission in the tropical reef sponge Ianthella basta.

Most marine sponge species harbour distinct communities of microorganisms which contribute to various aspects of their host's health and physiology. In addition to their key roles in nutrient transformations and chemical defence, these symbiotic microbes can shape sponge phenotype by mediating important developmental stages and influencing the environmental tolerance of the host. However, the characterisation of each microbial taxon throughout a sponge's life cycle remains challenging, with several sponge species hosting up to 3000 distinct microbial species.

Stream Hydrology Controls the Longitudinal Bioreactive Footprint of Urban-Sourced Fine Particles.

The relevance of wastewater treatment plant (WWTP) effluents in fluvial networks is increasing as urbanization grows in catchments. Urban-sourced fine particles from WWTP effluents deposit and accumulate in the streambed sediment of receiving streams over time and can fuel respiration rates, which can thus potentially increase rates of biogeochemical reactions and CO emissions to the atmosphere. We aimed to provide a quantitative assessment of the influence of WWTP-sourced fine particles deposited in the streambed sediment on stream metabolic activity for 1 year in an intermittent Mediterranean stream.

DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets.

DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors.

To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography.

Background: The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies.

Trophic Ecology of Endangered Gold-Spotted Pond Frog in Ecological Wetland Park and Rice Paddy Habitats.

The gold-spotted pond frog () is an endangered amphibian species in South Korea. In order to obtain ecological information regarding the gold-spotted pond frog's habitat environment and biological interactions, we applied stable isotope analysis to quantify the ecological niche space (ENS) of frogs including black-spotted pond frogs () and bullfrogs () within the food web of two different habitats-an ecological wetland park and a rice paddy. The gold-spotted pond frog population exhibited a broader ENS in the ecological wetland park than in the rice paddy.

Author Correction: Removal of deep-sea sponges by bottom trawling in the Flemish Cap area: conservation, ecology and economic assessment.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Modelling the seasonal impacts of a wastewater treatment plant on water quality in a Mediterranean stream using microbial indicators.

Faecal pollution modelling is a valuable tool to evaluate and improve water management strategies, especially in a context of water scarcity. The reduction dynamics of five faecal indicator organisms (E. coli, spores of sulphite-reducing clostridia, somatic coliphages, GA17 bacteriophages and a human-specific Bifidobacterium molecular marker) were assessed in an intermittent Mediterranean stream affected by a wastewater treatment plant (WWTP).

Removal of deep-sea sponges by bottom trawling in the Flemish Cap area: conservation, ecology and economic assessment.

Deep-sea sponge grounds are vulnerable marine ecosystems, which through their benthic-pelagic coupling of nutrients, are of functional relevance to the deep-sea realm. The impact of fishing bycatch is here evaluated for the first time at a bathyal, sponge-dominated ecosystem in the high seas managed by the Northwest Atlantic Fisheries Organization. Sponge biomass surfaces created from research survey data using both random forest modeling and a gridded surface revealed 231,140 t of sponges in the area.

A Randomized Trait Community Clustering approach to unveil consistent environmental thresholds in community assembly.

Similarities and differences of phenotypes within local co-occurring species hold the key to inferring the contribution of stochastic or deterministic processes in community assembly. Developing both phylogenetic-based and trait-based quantitative methods to unravel these processes is a major aim in community ecology. We developed a trait-based approach that: (i) assesses if a community trait clustering pattern is related to increasing environmental constraints along a gradient; and (ii) determines quantitative thresholds for an environmental variable along a gradient to interpret changes in prevailing community assembly drivers.

Cryptosporidium oocyst persistence in agricultural streams -a mobile-immobile model framework assessment.

Rivers are a means of rapid and long-distance transmission of pathogenic microorganisms from upstream terrestrial sources. Pathogens enter streams and rivers via overland flow, shallow groundwater discharge, and direct inputs. Of concern is the protozoal parasite, Cryptosporidium, which can remain infective for weeks to months under cool and moist conditions, with the infectious stage (oocysts) largely resistant to chlorination.

Historical shifts in oxygenation regime as recorded in the laminated sediments of lake Montcortès (Central Pyrenees) support hypoxia as a continental-scale phenomenon.

Recent expansion of anoxia has become a global issue and there is potential for worsening under global warming. At the same time, obtaining proper long-term instrumental oxygen records is difficult, thus reducing the possibility of recording long-term changes in oxygen shifts that can be related with climate or human influence. Varved lake sediments provide the better time frame to study this phenomenon at high resolution.

Early-life foraging: Behavioral responses of newly fledged albatrosses to environmental conditions.

In order to survive and later recruit into a population, juvenile animals need to acquire resources through the use of innate and/or learnt behaviors in an environment new to them. For far-ranging marine species, such as the wandering albatross , this is particularly challenging as individuals need to be able to rapidly adapt and optimize their movement strategies in response to the highly dynamic and heterogeneous nature of their open-ocean pelagic habitats. Critical to this is the development and flexibility of dispersal and exploratory behaviors.

Regional and local environmental conditions do not shape the response to warming of a marine habitat-forming species.

The differential response of marine populations to climate change remains poorly understood. Here, we combine common garden thermotolerance experiments in aquaria and population genetics to disentangle the factors driving the population response to thermal stress in a temperate habitat-forming species: the octocoral Paramuricea clavata. Using eight populations separated from tens of meters to hundreds of kilometers, which were differentially impacted by recent mortality events, we identify 25 °C as a critical thermal threshold.

Redescription and establishment of a holotype and three paratypes for the species sp. nov.

Background: In a recent paper, we described a new sponge species named Uriz, Garate & Agell, 2017. However, we failed to designate a holotype and a type locality, as required by the International Commission on Zoological Nomenclature (ICZN). Although the validity of the previous conclusions remains unchanged, the species name cannot be considered available according to ICZN regulations until a holotype is designated.

Molecular phylogenies confirm the presence of two cryptic species in the Mediterranean and reveal the polyphyly of the genera and (Demospongiae: Poecilosclerida).

Background: Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of suggested larger genetic differences than those expected between sponge populations.

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA.

We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons.