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Introduction

Abstract Intra‐population heterogeneity in the behavioural response of predators to changes in prey availability caused by human activities can have major evolutionary implications. Among these activities, fisheries, while extracting resources, also provide new feeding opportunities for marine top predators. However, heterogeneity in the extent to which individuals have responded to these opportunities within populations is poorly understood. Here, we used 18 years of photo‐identification data paired with statistical models to assess variation in the way killer whale social units within a subantarctic population (Crozet Islands) interact with fisheries to feed on fish caught on fishing gear (i.e., depredation behaviour). Our results indicate large heterogeneity in both the spatial and temporal extents of depredation across social units. While some frequently depredated on fishery catches over large areas, others sporadically did so and in small areas consistently over the years. These findings suggest that killer whale social units are exposed to varying levels of impacts of depredation, both negative (potential retaliation from fishers) and positive (food provisioning), on their life history traits, and may explain the contrasted demographic patterns observed within the declining population at Crozet but also potentially within the many other killer whale populations documented depredating on fisheries catches worldwide.

Herbicides are the most applied pesticides in the world. Despite numerous laboratory studies demonstrating the toxic effect of herbicides on non-target organisms, the effect of herbicides on soil organisms in the field remains complex to understand and is still controversial. In order to understand how changes in agricultural practices aiming to reduce herbicide use could impact soil biodiversity, we studied the effect of the frequency of herbicide application on soil biodiversity in a tropical agroecosystem.Our study was conducted on banana farms in Martinique, an island with a humid tropical climate belonging to the Caribbean biodiversity hotspot. Thirteen banana plots from five different farms were selected, ranging from plots receiving no herbicides to plots receiving 4–5 applications per year. Soil macro-arthropods were sampled using pitfall traps resulting in the collection of over 6,200 individuals. Of the 100 taxa that were differentiated, 75 could be identified to species level which allowed to assign each taxon to a trophic group and when possible to classify them according to whether they were introduced or native.Macro-arthropod mean species richness was 21% lower in plots with the highest frequency of herbicide application. However, no conclusive effect of herbicides on macro-arthropod abundance was demonstrated. Mean species richness for different trophic groups also decreased with herbicide applications with decreases of 22% for predators, 17% for omnivores, 55% for herbivores, and 55% for decomposers in plots with 4–5 herbicide applications per year compared to plots with no herbicide use. Species composition of macro-arthropod communities varied significantly with herbicide applications. More specifically, we found that native species represented a higher proportion of individuals captured in plots where no herbicides were used; suggesting that agroecological practices implemented at the field level to reduce the frequency of herbicide use potentially play a relevant role in soil biodiversity conservation.

Genotype-by-environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype-by-environment interactions in a maize multiparent advanced generation intercross population grown across 5 environments. We found that genotype-by-environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. To understand how genetic correlations between traits change across environments, we estimated the genetic variance-covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype-by-environment variance. We also performed a genome-wide association study to identify markers associated with genotype-by-environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype-by-environment interactions in this population.

The search for quantitative trait loci that explain complex traits such as yield and drought tolerance has been ongoing in all crops. Methods such as biparental quantitative trait loci mapping and genome-wide association studies each have their own advantages and limitations. Multiparent advanced generation intercross populations contain more recombination events and genetic diversity than biparental mapping populations and are better able to estimate effect sizes of rare alleles than association mapping populations. Here, we discuss the results of using a multiparent advanced generation intercross population of doubled haploid maize lines created from 16 diverse founders to perform quantitative trait loci mapping. We compare 3 models that assume bi-allelic, founder, and ancestral haplotype allelic states for quantitative trait loci. The 3 methods have differing power to detect quantitative trait loci for a variety of agronomic traits. Although the founder approach finds the most quantitative trait loci, all methods are able to find unique quantitative trait loci, suggesting that each model has advantages for traits with different genetic architectures. A closer look at a well-characterized flowering time quantitative trait loci, qDTA8, which contains vgt1, highlights the strengths and weaknesses of each method and suggests a potential epistatic interaction. Overall, our results reinforce the importance of considering different approaches to analyzing genotypic datasets, and shows the limitations of binary SNP data for identifying multiallelic quantitative trait loci.

The highly variable ’leafscapes’ of plants across the world represent billions of square metres of mite habitat. The phytoseiid mites (Acari: Phytoseiidae), an extremely species-rich group of mostly generalist predators, are providers of ecosystem services for humanity worth many hundreds of millions of dollars annually by helping suppress phytophagous mites and insects in forests, agro-ecosystems, shade-houses and home gardens. In this study, the phytoseiid mite assemblages on the leaves of four species of common tree species, namely oak (Quercus cerris var. cerris), poplar (Populus deltoides, P. nigra) and walnut (Juglans regia), were compared. The three data sets used were generated in three independent seasonal studies in Samsun Province, Türkiye, between 2018 and 2022. In total, mite species in 18 families, including 15 families on walnut, were recorded. Nineteen phytoseiid species in 13 genera, Amblydromalus, Amblyseius, Euseius, Kampimodromus, Neoseiulella, Neoseiulus, Paraseiulus, Phytoseius, Transeius, Typhlodromina, Typhlodromips, Typhlodromus and Typhloseiulus, were collected. Only Eusieus amissibilis was collected from all three tree genera, whereas 14 species were collected from only one tree genus. Shannon diversity and Jaccard similarity indexes were calculated for mite families and phytoseiid genera and species. Potential reasons for the observed differences in the phytoseiid assemblages on the different host trees are explored in depth. In the ‘big picture’, global biodiversity, likely including many undescribed phytoseiid species, is threatened by widespread habitat degradation and destruction, especially in the tropics, and accelerating climate change, and rapidly stopping them is imperative.

Abstract Background Genomic tests are a useful tool for adjuvant chemotherapy decision‐making in the case of hormone receptor‐positive (HR+), and human epidermal growth factor receptor 2‐negative (HER2−) breast cancer with intermediate prognostic factors. Real‐life data on the use of tests can help identify the target population for testing. Methods French multicentric study (8 centers) including patients, all candidates for adjuvant chemotherapy for HR‐positive, HER2‐negative early breast cancer. We describe the percentage of tests performed outside recommendations, according to the year of testing. We calculated a ratio defined as the number of tests required to avoid chemotherapy for one patient, and according to patient and cancer characteristics. We then performed a cost‐saving analysis using medical cost data over a period of 1 year from diagnosis, calculated from a previous study. Finally, we calculated the threshold of the ratio (number of tests required to avoid chemotherapy for one patient) below which the use of genomic tests was cost‐saving. Results A total of 2331 patients underwent a Prosigna test. The ratio (performed test/avoided chemotherapy) was 2.8 [95% CI: 2.7–2.9] in the whole population. In the group following recommendations for test indication, the ratio was 2.3 [95% CI: 2.2–2.4]. In the case of non‐abidance by recommendations, the ratio was 3 [95% CI: 2.8–3.2]. Chemotherapy was avoided in 841 patients (36%) following the results of the Prosigna test. The direct medical costs saved over 1 year of care were 3,878,798€ and 1,718,472€ in the group of patients following test recommendations. We calculated that the ratio (performed test/avoided chemotherapy) needed to be under 6.9 for testing to prove cost‐saving. Conclusion The use of genomic testing proved cost‐saving in this large multicentric real‐life analysis, even in certain cases when the test was performed outside recommendations.

Abstract Background Genetic diversity is a necessary condition for populations to evolve under natural adaptation, artificial selection, or both. However, genetic diversity is often threatened, in particular in domestic animal populations where artificial selection, genetic drift and inbreeding are strong. In this context, cryopreserved genetic resources are a promising option to reintroduce lost variants and to limit inbreeding. However, while the use of ancient genetic resources is more common in plant breeding, it is less documented in animals due to a longer generation interval, making it difficult to fill the gap in performance due to continuous selection. This study investigates one of the only concrete cases available in animals, for which cryopreserved semen from a bull born in 1977 in a lost lineage was introduced into the breeding scheme of a French local dairy cattle breed, the Abondance breed, more than 20 years later. Results We found that this re-introduced bull was genetically distinct with respect to the current population and thus allowed part of the genetic diversity lost over time to be restored. The expected negative gap in milk production due to continuous selection was absorbed in a few years by preferential mating with elite cows. Moreover, the re-use of this bull more than two decades later did not increase the level of inbreeding, and even tended to reduce it by avoiding mating with relatives. Finally, the reintroduction of a bull from a lost lineage in the breeding scheme allowed for improved performance for reproductive abilities, a trait that was less subject to selection in the past. Conclusions The use of cryopreserved material is an efficient way to manage the genetic diversity of an animal population, by mitigating the effects of both inbreeding and strong selection. However, attention should be paid to mating of animals to limit the disadvantages associated with incorporating original genetic material, notably a discrepancy in the breeding values for selected traits or an increase in inbreeding. Therefore, careful characterization of the genetic resources available in cryobanks could help to ensure the sustainable management of populations, in particular local or small populations. These results could also be transferred to the conservation of wild threatened populations.

In order to generate an atlas of the functional elements driving genome expression in domestic animals, the Functional Annotation of Animal Genome (FAANG) strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This article presents the collection of tissue samples for four species produced by two pilot projects, at INRAE (National Research Institute for Agriculture, Food and Environment) and the University of California, Davis. There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata characterizing these reference sets (1) for animals with origin and selection history, physiological status, and environmental conditions; (2) for samples with collection site and tissue/cell processing; (3) for quality control; and (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues for which collection can be standardized and for which representative aliquots can be easily distributed (liver, spleen, lung, heart, fat depot, skin, muscle, and peripheral blood mononuclear cells); set 2 comprises tissues requiring special protocols because of their cellular heterogeneity (brain, digestive tract, secretory organs, gonads and gametes, reproductive tract, immune tissues, cartilage); set 3 comprises specific cell preparations (immune cells, tracheal epithelial cells). Dedicated sampling protocols were established and uploaded in https://data.faang.org/protocol/samples. Specificities between mammals and chicken are described when relevant. A total of 73 different tissues or tissue sections were collected, and 21 are common to the four species. Having a common set of tissues will facilitate the transfer of knowledge within and between species and will contribute to decrease animal experimentation. Combining data on the same samples will facilitate data integration. Quality control was performed on some tissues with RNA extraction and RNA quality control. More than 5,000 samples have been stored with unique identifiers, and more than 4,000 were uploaded onto the Biosamples database, provided that standard ontologies were available to describe the sample. Many tissues have already been used to implement FAANG assays, with published results. All samples are available without restriction for further assays. The requesting procedure is described. Members of FAANG are encouraged to apply a range of molecular assays to characterize the functional status of collected samples and share their results, in line with the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

Depredation (wild predators feeding on fish caught by man) is a global concern in the fishing industry. Solutions to this type of conflict necessarily involve setting up an observation program to understand and quantify the phenomenon. This study takes the example of the toothfish (Dissostichus eleginoides) fishery around the Kerguelen and Crozet archipelagos in the southern Indian Ocean. Collaboration between the various stakeholders involved like the management authority (TAF or Terres australes françaises), the scientists (MNHN, CNRS, IRD) and the fishermen was the key to the rapid implementation of data collection from the late 90s onwards. The fishery observers employed by TAF cover 100% of the fishing effort on board the eight authorized vessels. The experience gained has been presented and benefited to other observer programs.

Despite non-structural carbohydrate (NSC) importance for tree productivity and resilience, little is known about their seasonal regulations and trade-off with growth and reproduction. We characterize the seasonal dynamics of NSC in relation to the aboveground phenology and temporal growth patterns of three deciduous Mediterranean species: almond (Prunus dulcis (Mill.) D. A. Webb), walnut (Juglans regia L.) and pistachio (Pistacia vera L.). Seasonal dynamics of NSC were synchronous between wood tissues from trunk, branches and twigs. Almond had almost identical levels and patterns of NSC variation in twigs, branches and trunks whereas pistachio and walnut exhibited clear concentration differences among plant parts whereby twigs had the highest and most variable NSC concentration, followed by branches and then trunk. While phenology had a significant influence on NSC seasonal trends, there was no clear trade-off between NSC storage and growth suggesting that both were similarly strong sinks for NSC. A temporal trade-off observed at the seasonal scale was influenced by the phenology of the species. We propose that late senescing species experience C allocation trade-off at the end of the growing season because of C-limiting thermal conditions and priority allocation to storage in order to survive winter.

Implemented for decades as part of the ‘best management practices (BMPs)’ for controlling urban runoff impacts on receiving waters, stormwater management ponds (SMPs) have been increasingly viewed as potential habitats for urban wildlife. However, since SMPs are subject to a lot of environmental constraints, research toward assessing their ecological quality and their actual benefits as habitats for biota is needed. In this study, the sediment toxicity of eight SMPs located in Southern Ontario, Canada was assessed using the sediment quality triad (SQT) approach. Sediment samples were collected for chemical, ecotoxicological and biological analyses. An oligochaete-based index approach (Oligochaete Index of Lake Bioindication and percentage of pollution-sensitive species) was used as the biological endpoint and integrated into a weight-of-evidence approach to assessing the general sediment quality of the ponds. Our results showed that (i) heavy metals in the sediment and (ii) chloride concentrations in the sediment interstitial water caused detrimental effects on the ecological quality of the sediments in the ponds studied. The oligochaete indices applied in this study showed value as biological endpoints to be integrated into the SQT and used for setting up sediment ecological quality goals. HIGHLIGHTS An oligochaete-based index approach was used as a line of evidence in the SQT to assess the ecological quality of eight stormwater ponds in Southern Ontario.; High concentrations of chloride in pore water and of heavy metals in the sediment matrix were linked to detrimental effects.; The oligochaete-based index approach was used to set up ecological quality goals for stormwater pond sediment.;

BackgroundStereotactic arrhythmia radioablation (STAR) is a potential new therapy for patients with refractory ventricular tachycardia (VT). The arrhythmogenic substrate (target) is synthesized from clinical and electro-anatomical information. This study was designed to evaluate the baseline interobserver variability in target delineation for STAR.MethodsDelineation software designed for research purposes was used. The study was split into three phases. Firstly, electrophysiologists delineated a well-defined structure in three patients (spinal canal). Secondly, observers delineated the VT-target in three patients based on case descriptions. To evaluate baseline performance, a basic workflow approach was used, no advanced techniques were allowed. Thirdly, observers delineated three predefined segments from the 17-segment model. Interobserver variability was evaluated by assessing volumes, variation in distance to the median volume expressed by the root-mean-square of the standard deviation (RMS-SD) over the target volume, and the Dice-coefficient.ResultsTen electrophysiologists completed the study. For the first phase interobserver variability was low as indicated by low variation in distance to the median volume (RMS-SD range: 0.02–0.02 cm) and high Dice-coefficients (mean: 0.97 ± 0.01). In the second phase distance to the median volume was large (RMS-SD range: 0.52–1.02 cm) and the Dice-coefficients low (mean: 0.40 ± 0.15). In the third phase, similar results were observed (RMS-SD range: 0.51–1.55 cm, Dice-coefficient mean: 0.31 ± 0.21).ConclusionsInterobserver variability is high for manual delineation of the VT-target and ventricular segments. This evaluation of the baseline observer variation shows that there is a need for methods and tools to improve variability and allows for future comparison of interventions aiming to reduce observer variation, for STAR but possibly also for catheter ablation.

Coffee silverskin is a byproduct of the coffee industry, appearing in large quantities during the roasting step. In this work, a sober and simple water process is proposed, using extractions cycles, to produce valuable products including (a) an extract rich in caffeine, (b) possibly pure caffeine, and (c) insoluble fibers. The hypothetical number of necessary cycles was calculated and compared to the number of cycles used experimentally. Two types of cycles, with and without water compensation, were compared for their water consumption and the amount of caffeine extracted. The use of cycles, with the resulting product from a previous extraction as a solvent for fresh biomass, drove a significant rise in the content of caffeine determined by a UV–visible detector with a spectrophotometer and ultra-performance liquid chromatography (UPLC). After 11 extraction cycles with water compensation, we obtained an extract 4.5 times more concentrated in caffeine (4.25 mg/mL) than after a single extraction (1.03 mg/mL).

Trees in seasonal climates gauge winter progression to assure vital and productive blooming. However, how dormant plants asses environmental conditions remains obscure. We postulated that it involves the energetic reserves required for bloom, and therefore studied winter carbohydrate metabolism in deciduous trees. We quantified non-structural carbohydrates throughout winter in almond, peach, and pistachio trees in California and Israel and characterized winter metabolism. We constructed a carbohydrate-temperature (C–T) model that projects changes in starch and soluble carbohydrate concentrations by temperature mediated kinetics. Then, we tested the C–T model projections of bloom times by 20 years of temperature and phenology records from California. The C–T model attributes winter carbohydrate regulation in dormant trees to continuous updates of metabolic pathways. The model projects a surge in starch synthesis at the end of winter, and critically low concentrations of soluble carbohydrates, that trigger bloom. This is supported by field measurements of starch accumulation at the end of winter (˜50 mg g−1 DW in almonds) that preceded bloom by ˜10 days. The C–T model provides a physiological framework for bloom forecasts in deciduous orchards. It integrates contrasting notions of chill and heat and elucidates why abnormal winter temperatures may compromise bloom in deciduous orchards.

Trees in seasonal climates gauge winter progression to assure vital and productive blooming. However, how dormant plants asses environmental conditions remains obscure. We postulated that it involves the energetic reserves required for bloom, and therefore studied winter carbohydrate metabolism in deciduous trees. We quantified non-structural carbohydrates throughout winter in almond, peach, and pistachio trees in California and Israel and characterized winter metabolism. We constructed a carbohydrate-temperature (C–T) model that projects changes in starch and soluble carbohydrate concentrations by temperature mediated kinetics. Then, we tested the C–T model projections of bloom times by 20 years of temperature and phenology records from California. The C–T model attributes winter carbohydrate regulation in dormant trees to continuous updates of metabolic pathways. The model projects a surge in starch synthesis at the end of winter, and critically low concentrations of soluble carbohydrates, that trigger bloom. This is supported by field measurements of starch accumulation at the end of winter (˜50 mg g−1 DW in almonds) that preceded bloom by ˜10 days. The C–T model provides a physiological framework for bloom forecasts in deciduous orchards. It integrates contrasting notions of chill and heat and elucidates why abnormal winter temperatures may compromise bloom in deciduous orchards.