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opencc-by-4.0Apr 2022View details →

Pre-Analysis Bioinformatics Files for The Microbiome and Volatile Organic Compounds Reflect the State of Decomposition in an Indoor Environment

Data statistics before and after trimming, FastQC reports before and after trimming, MultiQC reports before and after trimming, commands for the Kraken2-Bracken analysis, and classification reports. Read the read.me file for file names and descriptions.

opencc-zeroApr 2022View details →

Linking agri-environment scheme habitat area, predation and the abundance of chick invertebrate prey to the nesting success of a declining farmland bird

Across Europe, farmland bird populations have continued to decline since the 1970s owing to the intensification of farming practices. Studies of such declines have tended to focus specifically on either the impacts of habitats (nesting and foraging), nest predators or prey availability on bird demographics. The study presented here provides new insights into the relative effects of each of these factors on Yellowhammer nest survival. The Yellowhammer was selected for this study as it is a UK red-listed bird species whose population is in decline across much of Europe. We use a long-term dataset of 147 nests, monitored between 1995 and 2007, to provide an insight into how Yellowhammer nest survival is influenced by nesting habitat (nest concealment and nest height), foraging habitats (habitat coverage within 100 m of nests), the removal of nest predators (Magpie Pica pica abundance as an inverse measure of avian predator removal through gamekeeping) and food availability (measured with a D-vac invertebrate suction sampler). Our results indicated that Yellowhammer hatching success was negatively related to the coverage of spring agri-environment scheme habitats, a group which represents invertebrate-rich agri-environment habitats, but hatching success increased with nest height. Fledging success was positively related to the coverage of the seed-rich habitat Wild Bird Seed mixture. The farm-level abundance of Yellowhammer chick-food invertebrates declined over the study period. Our results highlight the importance of simultaneously considering multiple agents that shape avian breeding success, i.e. their ability to produce offspring, to inform conservation management. Our key finding for land managers relates to the positive relationship between the proportion seed rich foraging habitat within the Yellowhammer's average foraging range and Yellowhammer fledging success, which shows that a habitat intended primarily to provide winter food resources is also important to breeding birds. Chick food abundance in this habitat was, however, similar to broadleaf and cereal crops. We recommend that this habitat should be provided near to potential Yellowhammer nesting sites and adjacent to invertebrate-rich agri-environment scheme habitats such as beetle banks and conservation headlands to further boost invertebrate resources for a declining farmland bird.

Unraveling the roles of genotype and environment in the expression of plant defense phenotypes

1. Phenotypic variability results from interactions between genotype and environment and is a major driver of ecological and evolutionary interactions. Measuring the relative contributions of genetic variation, the environment, and their interaction to phenotypic variation remains a fundamental goal of evolutionary ecology. 2. In this study, we assess the question: How do genetic variation and local environmental conditions interact to influence phenotype within a single population? We explored this question using seed from a single population of common milkweed, Asclepias syriaca, in northern Michigan. We first measured resistance and resistance traits of 14 maternal lines in two common garden experiments (field and greenhouse) to detect genetic variation within the population. We carried out a reciprocal transplant experiment with three of these maternal lines to assess effects of local environment on phenotype. Finally, we compared the phenotypic traits measured in our experiments with the phenotypic traits of the naturally-growing maternal genets to be able to compare relative effect of genetic and environmental variation on naturally-occurring phenotypic variation. We measured defoliation levels, arthropod abundances, foliar cardenolide concentrations, foliar latex exudation, foliar carbon and nitrogen concentrations, and plant growth. 3. We found a striking lack of correlation in trait expression of the maternal lines between the common gardens, or between the common gardens and the naturally-growing maternal genets, suggesting that environment plays a larger role in phenotypic trait variation of this population. We found evidence of significant genotype-by-environment interactions for all traits except foliar concentrations of nitrogen and cardenolide. Milkweed resistance to chewing herbivores was associated more strongly with the growing environment. We observed no variation in foliar cardenolide concentrations among maternal lines but did observe variation among maternal lines in foliar latex exudation. 4. Overall, our data reveal powerful genotype-by-environment interactions on the expression of most resistance traits in milkweed.

Data from: A role for the local environment in driving species-specific parasitism in a multi-host parasite system

The extent and magnitude of parasitism often vary among closely related host species and across populations within species. Determining the ecological basis for this species and population-level variation in parasitism is critical for understanding infection dynamics in multi-host-parasite systems. To investigate such ecological underpinnings of variation in parasitism, we studied Enallagma damselflies host species and their water mite (Arrenurus spp.) ectoparasites in lakes. We first evaluated how host identity and density could shape parasitism. To test the effects of con- and heterospecific host density on parasitism, we used a field experiment with E. basidens and E. signatum. We found that parasitism did not vary with con- or heterospecific density and was determined by host identity alone, with no spillover effects. We also evaluated the potential role of local adaptation and resource availability in shaping parasitism. To do so, we used E. signatum in a reciprocal transplant experiment crossed with a prey resource level manipulation. This experiment revealed that parasitism declined sharply for one host population in its non-local lake, but not the other source population, with no effects of prey levels. This asymmetry implies that damselflies express enhanced defenses against parasitism that are not population specific nor dependent on resource abundance, or that mites developed heightened local host specificity. The results of multivariate modeling from an observational study generally supported these experimental findings: neither host density nor resource abundance strongly explained among population variation in parasitism. Instead, local abiotic conditions (pH) had the strongest relationship with parasitism, with minimal associations with predator density, temperature, and a measure of immune function. Collectively, our findings suggest a crucial role for the local environment in shaping host-parasite interactions within multi-host-parasite systems. More generally, these results show that research at the intersection of community ecology and disease ecology is critical for understanding host-parasite dynamics within natural communities.

Extreme environments filter functionally rich communities of Atlantic Forest treefrogs along altitudinal and latitudinal gradients

Understanding how environmental filtering and biotic interactions structure communities across elevational and latitudinal gradients is still a matter of debate. To provide insight into their relative importance, we explore the mismatch between three dimensions of biodiversity (taxonomic, functional, and phylogenetic), and compare their patterns to null models of random community assembly. We focus on a highly diverse tropical group: the tree frogs (hylids) of the Atlantic Forest of Brazil. For that, we combined geographic distribution data with phylogenetic and trait information for 158 species to produce maps of the three dimensions of diversity. We show that communities of tree frogs of the Hylidae family tend to have high functional richness along the Atlantic Forest, potentially driven by niche partitioning. However, environmental filtering gains importance in extreme environments, both at high elevations and higher latitudes. In these areas of the forest, clustering of both functional and phylogenetic diversity is observed. Trait overdispersion is found in areas of contact between vegetation types, or of adjacent biomes, reflecting the encounter of amphibian species adapted to distinct environmental conditions and landscape configurations. Considering all three dimensions of diversity along with multiple axes of environmental variation allows for a more comprehensive understanding of the processes shaping amphibian community assembly in this biodiversity hotspot.

Light environment interacts with visual displays in a species-specific manner in multimodal signaling wolf spiders

Light availability is highly variable, yet predictable, over various timescales and the light environment is expected to play an important role in the evolution of visual signals. Courtship displays within the wolf spider genus Schizocosa always involve the use of substrate borne vibrations, however, there is substantial variation between species in the use of visual displays. We assessed the impact of light intensity on the courtship of four species of Schizocosa that vary in their use of visual signals during courtship. To examine the effects of the light environment on mating success and courtship effort in each species, we ran behavioral trials at three light intensities (bright, dim and dark). We also examined each species' circadian activity patterns. We found multiple effects of the light environment and these varied between species. Circadian activity patterns also differed between species and sexes. Our results suggest that dim-light might favor more conspicuous visual displays, while less conspicuous displays might be favored in bright light conditions. Additionally, we found evidence for light-dependent changes in selection on male traits, illustrating that short-term changes in light intensity have the potential for strong effects on the dynamics of sexual selection.

Use of cenotes and the cave environment by mammals on the Yucatán Peninsula, Mexico

Mammals are important sources of nutrients to cave ecosystems, and in some circumstances, caves may be an essential resource for mammals. Few studies, however, have focused on the use of caves by terrestrial mammals. We used camera traps at 17 cenotes on the Yucatán Peninsula to determine patterns of use by mammals. Eighteen non-volant mammal taxa were identified using cenotes, the most commonly occurring being lowland paca (Agouti paca), opossums (Didelphis spp.), white-nosed coati (Nasua narica), gray fox (Urocyon cinereoargenteus), tayra, (Eira barbara) and gray four-eyed opossum (Philander opossum); collectively these taxa accounted for 76% of all mammal records. We also recorded several felids using cenotes, including jaguar (Panthera onca) and puma (Puma concolor). Activity patterns at cenotes usually matched normal activity schedules but some species were nocturnal in the forest but diurnal at cenotes. Mammals mostly accessed cenotes to drink, but a range of activities were recorded including foraging, nesting, mating, resting and bathing.

Strong selective environments determine evolutionary outcome in time-dependent fitness seascapes

The impact of fitness landscape features on evolutionary outcomes has attracted considerable interest in recent decades. However, evolution often occurs under time-dependent selection in so-called fitness seascapes where the landscape is under flux. Fitness seascapes are an inherent feature of natural environments, where the landscape changes owing both to the intrinsic fitness consequences of previous adaptations and extrinsic changes in selected traits caused by new environments. The complexity of such seascapes may curb the predictability of evolution. However, empirical efforts to test this question utilising a comprehensive set of regimes are lacking. Here we employed an in vitro microbial model system to investigate differences in evolutionary outcomes between time-invariant and -dependent environments, including all possible temporal permutations, with three subinhibitory antimicrobials and a viral parasite (phage) as selective agents. Expectedly, time-invariant environments caused stronger directional selection for resistances compared to time-dependent environments. Intriguingly, however, multidrug resistance outcomes in both cases were largely driven by two strong selective agents (rifampicin and phage) out of four agents in total. These agents either caused cross-resistance or obscured the phenotypic effect of other resistance mutations, modulating the evolutionary outcome overall in time-invariant environments and as a function of exposure epoch in time-dependent environments. This suggests that identifying strong selective agents and their pleiotropic effects is critical for predicting evolution in fitness seascapes, with ramifications for evolutionarily informed strategies to mitigate drug resistance evolution.

opencc-zeroDec 2021View details →

Data from: A trait‒environment relationship approach to participatory plant breeding for organic agriculture

The extent of intraspecific variation in trait‒environment relationships is an open question with limited empirical support in crops. In organic agriculture, with high environmental heterogeneity, this knowledge could guide breeding programs to optimize crop attributes. We propose a three-dimensional framework involving crop performance, crop traits, and environmental axes to uncover the multidimensionality of trait‒environment relationships within a crop. We modeled instantaneous photosynthesis (Asat) and water-use efficiency (WUE) as functions of four phenotypic traits, three soil variables, five carrot (D. carota) varieties, and their interactions in a national participatory plant breeding program involving a suite of farms across Canada. We used these interactions to describe the resulting 12 trait‒environment relationships across varieties. We found one significant trait‒environment relationship for Asat (taproot tissue density‒soil phosphorus), which was consistent across varieties. For WUE, we found that three relationships (petiole diameter‒soil nitrogen, petiole diameter‒soil phosphorus, and leaf area‒soil phosphorus) varied significantly across varieties. As a result, WUE was maximized by different combinations of trait values and soil conditions depending on the variety. Our three-dimensional framework supports the identification of functional traits behind the differential responses of crop varieties to environmental variation and thus guides breeding programs to optimize crop attributes from an eco-evolutionary perspective.

opencc-by-4.0May 2022View details →

Research data supporting "Ephemeral Ice-Like Local Environments in Classical Rigid Models of Liquid Water"

This repository contains the set of data shown in the paper "Ephemeral Ice-Like Local Environments in Classical Rigid Models of Liquid Water", published on the Journal of Chemical Physics (DOI:10.1063/5.0088599).

opencc-by-4.0May 2022View details →

Data and Analysis Script for Cluster2022 Submission pap254: "Painless Transposition of Reproducible Distributed Environments with NixOS Compose"

Data and Analysis Script for Cluster2022 Submission pap254: "Painless Transposition of Reproducible Distributed Environments with NixOS Compose" The experiments repository is available at: <a href="https://gitlab.inria.fr/nixos-compose/articles/cluster2022">https://gitlab.inria.fr/nixos-compose/articles/cluster2022</a>

A gas-only bioreactor system maintains stable culture environments and reveals that moderate pH deviations trigger transcriptome-wide responses in human cells cultured in physioxia and physiological buffers

Although pH instability is emerging as a potential driver of changes in cell physiology, pH is still poorly controlled during cell culture and in vitro experiments. Standard procedures include the use of chemicals usually not present in the primary physiological buffering system (CO2/HCO3-), such as acids and bases, to manipulate pH levels. This, however, leads to artifacts that potentially affect scientists' findings. Here, we propose a novel method for controlling pH levels by relying only on the physiological buffering system. pH was manipulated in a repurposed commercial bioreactor set-up, using a two-sided control loop of CO2 and N2 gas in NaHCO3--buffered medium. This method produces optimal and stable dO2 profiles and tightly maintains pH levels. With this procedure, we analyzed the effects of different pH levels (6.8, 7.0, 7.2, and 7.4) on the performance and transcriptome of the human GM12878 cell line over a 72-hours experiment. Our results showed that inflammation and negative cellular proliferation are among the signatures activated at low pH. This further highlights the importance of a thorough pH control during cell culture.

Extensive polyploid clonality was a successful strategy for seagrass to expand into a newly submerged environment

Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon's ribbon weed, Posidonia australis. This seagrass is at the northern extent of its natural geographic range and experiences extreme temperatures and salinities. Our genomic and cytogenetic assessments of ten meadows identified geographically restricted, diploid clones (2n = 20) in a single location, and widespread, high heterozygosity, polyploid clones (2n = 40) in all other locations. A single polyploid clone spanned at least 180 km, making it the largest known example of a clone in any environment on earth. Whole genome duplication through polyploidy, combined with clonality, may have provided the mechanism for P. australis to expand into new habitats and adapt to new environments that became increasingly stressful for its diploid progenitor(s). The new polyploid clones likely formed in the shallow waters after inundation of Shark Bay < 8,500 years ago and subsequently expanded via vegetative growth into newly submerged habitats.

Sexual dimorphism of the gut microbiota in the Chinese alligator and its convergence in the wild environment

The gut microbiota forms a complex microecosystem in vertebrates and is affected by various factors. As a key intrinsic factor, sex has a persistent impact on the formation and development of gut microbiota. Few studies have analysed sexual dimorphism of gut microbiota, particularly in wild animals. We used 16S rRNA sequencing to analyse the gut microbiota of juvenile and adult Chinese alligators, and untargeted metabolomics to study serum metabolomes of adult alligators. We observed significant sex-biased differences in the community diversity in juvenile, but not adult, alligators. In terms of taxonomic composition, the phylum Fusobacteriota and genus Cetobacterium were highly abundant in adult alligators, similar to that in carnivorous fishes, whereas the gut microbiota composition in juvenile alligators resembled that in terrestrial reptiles, indicating that adults are affected by their wild aquatic environment and lack sex dimorphism in gut microbiota. The correlation analysis revealed that the gut microbiota of adults was also affected by cyanobacteria in the external environment, and this effect was sex-biased and mediated by sex hormones. Overall, this study reveals sexual differences in the gut microbiota of crocodilians and their convergence in the external environment. It also provides insights into host-microbiota interactions in the wild.

Energetic constraints on body-size niches in a resource-limited marine environment

Body size of life on Earth spans many orders of magnitude, and with it scales the energetic requirements of organisms. Thus, changes in environmental energy should impact community body-size distributions in predictable ways by reshaping ecological and niche dynamics. We examine how carbon, oxygen, and temperature, three energetic drivers, impact community size-based assembly in deep-sea bivalves. We demonstrate that body-size distributions are influenced by multiple energetic constraints. Relaxation in these constraints leads to an expansion of body-size niche space through the addition of novel large size classes, increasing the standard deviation and mean of the body-size distribution. With continued Anthropogenic increases in temperature and reductions in carbon availability and oxygen in most ocean basins, our results point to possible radical shifts in invertebrate body size with the potential to impact ecosystem function.

NiMARE: Neuroimaging Meta-Analysis Research Environment

Dataset provided for NeuroLibre preprint. Author repo: https://github.com/NBCLab/nimare-paper NeuroLibre fork:https://github.com/roboneurolibre/nimare-paper For details, please visit the corresponding <a href="https://github.com/neurolibre/neurolibre-reviews/issues/7">NeuroLibre technical screening.</a> <a href="https://neurolibre.org">https://neurolibre.org</a>

opencc-by-4.0Jun 2022View details →

CM1 files for JGR-Atmospheres Paper Sensitivities of Cross-Tropopause Transport in Midlatitude Overshooting Convection to the Lower Stratosphere Environment

Initial conditions to run the CM1 model simulations used in the JGR-Atmospheres Paper Sensitivities of Cross-Tropopause Transport in Midlatitude Overshooting Convection to the Lower Stratosphere Environment. The namelist.input file contains the initial conditions used to run the simulations, and the input sounding files (input_sounding_st_plume, input_sounding_st_noplume, input_sounding_dt_plume, input_sounding_dt_noplume) are the initial soundings used to run the CM1 model for each of the four different stratospheric environments.

Environment and mate attractiveness in a wild insect

Abstract The role of female choice in sexual selection is well established, including the recognition that females choose their mates based on multiple cues. These cues may include intrinsic aspects of a male's phenotype as well as aspects of the environment associated with the male. The role of the spatial location of a potential mate has been well studied in territorial vertebrates. However, despite their role as laboratory models for studies of sexual selection, the potential for insects to choose their mates on the basis of location has scarcely been studied. We studied a natural population of individually tagged crickets (Gryllus campestris) in a meadow in Northern Spain. Adults typically move between burrows every few days, allowing us to examine how pairing success of males can be predicted by the burrow they occupy, independent of their own characteristics. We observed the entirety of ten independent breeding seasons to provide replication and to determine whether the relative importance of these factors is stable across years. We find that both male ID and the ID his burrow affect the likelihood that he is paired with a female, but the burrow has a consistently greater influence. Furthermore, the two factors interact: the relative attractiveness of an individual male depends on which burrow he occupies. Our finding demonstrates a close interaction between naturally and sexually selected traits. It also demonstrates that mate choice studies may benefit from considering not only obvious secondary sexual traits, but also more cryptic traits such as microhabitat choice.

opencc-by-4.0Jun 2022View details →

eDoer - A Human-AI based Learning Environment - Ethics and Privacy related issues

The eDoer platform was presented on the first Ethical, Legal, and Societal Aspects (ELSA) workshop of the German NFDI FAIR Data Spaces community.   eDoer platform: <a href="http://edoer.eu/%C2%A0">http://edoer.eu/ </a>

Ancestral environment determines the current reaction to ultraviolet radiation in Daphnia magna

An individual's phenotype can be altered by direct contact with its present environment but also by environmental features experienced by previous generations, i.e. parental or grandparental effects. However, the strength and direction of these transgenerational effects may be highly variable according to the ecological conditions experienced by ancestral generations. Here we performed a reciprocal split-brood experiment to compare transgenerational responses to the threat of ultraviolet radiation (UVR) in the zooplankter Daphnia magna, which had, or had not, been exposed to UVR for more than 150 generations, respectively. We found that the environment at which parents and grandparents were reared significantly influenced both behavior and life-history traits of their descendants. However, such transgenerational responses differed between D. magna individuals with contrasting ancestral stress history, that is, when exposed to UVR previously unexposed individuals rapidly changed their behavior and life-history traits, whereas individuals previously exposed to UVR showed less pronounced response when the UVR threat level relaxed. Hence, we here demonstrate an asymmetric transgenerational plasticity in response to UVR threat. The findings advance our understanding on the evolutionary ecology of such transgenerational effects and their potential role in response to changes in the local environment.