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Early developmental carry-over effects on exploratory behaviour and DNA methylation in wild great tits (Parus major)

Adverse, postnatal conditions experienced during development are known to induce lingering effects on morphology, behaviour, reproduction and survival. Despite the importance of early developmental stress for shaping the adult phenotype, it is largely unknown which molecular mechanisms allow for the induction and maintenance of such phenotypic effects once the early environmental conditions are released. Here we aimed to investigate whether lasting early developmental phenotypic changes are associated with post-developmental DNA methylation changes. We used a cross-foster and brood size experiment in great tit (Parus major) nestlings, which induced post-fledging effects on biometric measures and exploratory behaviour, a validated personality trait. We investigated whether these post-fledging effects are associated with DNA methylation levels of CpG sites in erythrocyte DNA. Individuals raised in enlarged broods caught up on their developmental delay after reaching independence and became more explorative as days since fledging passed, while the exploratory scores of individuals that were raised in reduced broods remained stable. Although we previously found that brood enlargement hardly affected pre-fledging methylation levels, we found 420 CpG sites that were differentially methylated between fledged individuals that were raised in small versus large sized broods. A considerable number of the affected CpG sites were located in or near genes involved in metabolism, growth, behaviour and cognition. Since the biological functions of these genes line up with the observed post-fledging phenotypic effects of brood size, our results suggest that DNA methylation provides organisms the opportunity to modulate their condition once the environmental conditions allow it. In conclusion, this study shows that nutritional stress during early development associates with indirect, carry-over effects on DNA methylation. We propose that treatment-associated DNA methylation differences arise as a consequence of pre-fledging phenotypic changes, rather than that they cause early environmentally-induced effects.

Data from: The magnitude of Allee effects varies across Allee mechanisms, but not taxonomic groups

The Allee effect is a density-dependent phenomenon in which individual fitness increases as population density increases at low population densities. Over the past few decades, a growing number of studies have identified Allee effects in populations using experimental approaches and statistical modelling techniques. These studies have investigated multiple Allee mechanisms (e.g., mate-finding, predation, resource limitation), across a range of systems and taxa (e.g., plants, vertebrates, invertebrates). This meta-analysis aims to synthesize studies that experimentally manipulated population density and measured either per capita population growth or fitness components, with the goal of determining whether the "magnitude" of the Allee effect (defined here as the correlation between population density and population growth or fitness) varies with Allee mechanism across taxonomic groups. A total of 2305 studies were screened, and 62 of these studies met our meta-analysis inclusion criteria. Within these 62 studies, 155 effect sizes encompassing 9 different Allee mechanisms were identified across 5 broad taxa. When grouped by Allee mechanism and taxa, the magnitude of the Allee effect differed across mechanisms, whereas taxonomic group was less useful at explaining variation in the magnitude of Allee effects. Of the nine Allee mechanisms identified, interspecific competition was associated with the strongest Allee effects, followed by fear, pollen limitation and mate limitation. These findings suggest that Allee effects may be more dependent on mechanism than taxa and may function similarly within different taxonomic groups. However, as the majority of experimental Allee effect studies included in this meta-analysis focused on plants and invertebrates, more research is needed on Allee effects in other taxonomic groups to confirm this conclusion. This first quantitative synthesis of Allee effect research in ecology offers novel insight into how Allee mechanisms affect the manifestation of Allee effects in populations, providing important information for ecologists and conservation managers.

opencc-by-nc-4.0Dec 2023View details →

iGEMME Missense Mutational Effect Predictions for Entire Human Proteome

This dataset contains iGEMME single point mutation predictions of about ~19000 human proteins. In iGEMME predictions, only evolutionary data coming from multiple sequence alignment files is used.  <h2>Description of the data and file structure</h2> This dataset contains iGEMME predictions for all human proteins.  Data of each human protein is in a folder named after its uniprotID. Inside uniprotID folder, there is a subfolder called results that contain all input and output. An example results folder for uniprotID A0A0B4J245 will contain the following files: <ol> <li> Raw igemme predictions (output file): A0A0B4J245_normPred_evolCombi_igemme.txt </li> <li> Ranksorted (between 0-1) igemme predictions in csv format (output file): A0A0B4J245_normPred_evolCombiTransposedRanksorted_igemme.csv </li> <li> Colabfold MSA file (input file): aliA0A0B4J245.fasta </li> <li> JET2 file containing JET scores for each amino acid (output file) : A0A0B4J245_jet_igemme.res </li> <li> Configuration file containing default parameters (output file): default.conf </li> <li> Log file (output file): igemme.log </li> </ol>

opencc-by-4.0Feb 2025View details →

Effect of older age and/or ACL injury on the dose–response relationship between ambulatory load magnitude and immediate load-induced change in serum cartilage oligomeric matrix protein

The data presented here was used in the models in the pulication doi <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.jshs.2024.100993" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.jshs.2024.100993</a>. The purpose of this study was to assess the influence of age, anterior cruciate ligament (ACL) injury, and sex on resting sCOMP concentration, on the immediate load-induced sCOMP kinetics after a 30-minute treadmill walking stress, and on the dose-response relationship between ambulatory load magnitude and the load-induced sCOMP change. Overall, data of 85 participants in four groups (20–30 years healthy, HEA20–30, n=24; 20–30 years ACL-injured, ACL20–30, n=23; 40–60 years healthy, HEA40–60, n=23; 40–60 years ACL-injured, ACL40–60, n=15) were included in this dataset. ACL injured participants suffered from an ACL injury 2-10 years prior to inclusion. The dateaset includes, patient data and serum cartilage oligomeric matrix protein (sCOMP) concentration measured on three testdays (m1, m2, m3) immediately before (t0) and immediately after 30 minutes of treadmill walking (t1) where the ambulatory loads were 80% bodyweight (BW), 100% BW or 120% BW (block randomized order). This dateset represents a subset of data collected in the parent study. The detailed experimental protocol of the parent study has been described in Herger, S., Vach, W., Nüesch, C., Liphardt, A. M., Egloff, C., & Mündermann, A. (2022). Dose-response relationship of in vivo ambulatory load and mechanosensitive cartilage biomarkers—The role of age, tissue health and inflammation: A study protocol. PLoS One, 17(8), e0272694. <a href="https://doi.org/10.1371/journal.pone.0272694">https://doi.org/10.1371/journal.pone.0272694</a>

Weak effect of urbanisation on bdelloid rotifers living in lichens

Human activities have an overwhelming impact on the natural environment, leading to a deep biodiversity crisis whose effects range from genes to ecosystems. We here analysed the effect of such anthropogenic impacts on bdelloid rotifers (Rotifera: Bdelloidea), for whom these effects are poorly understood. We targeted bdelloid rotifers living in lichen patches across urbanisation gradients in Flanders and Brussels (Belgium). Urbanisation was measured as the percentage of built-up area across different spatial scales, at circles from 50 m to 3,200 m of radius around the lichen. Urbanisation effects on biodiversity were assessed on abundance, species richness, and community-weighted mean body size of bdelloid rotifers, as well as on genetic diversity of one of the most common and widespread bdelloid species, Adineta vaga. Overall, no negative effect of urbanisation was found at any diversity level and at any spatial scale. Counterintuitively, built-up area quantified at the largest spatial scale had a positive effect on abundance. These results leave open the question of whether negative effects of urbanisation are present for bdelloid rotifers, or if such effects are only visible at even larger spatial scales.

Data from: The effect of drainage on the fine root biomass, production, and turnover in hemiboreal old-growth forests on organic soils

Information on the capacity of organic soils to capture and store carbon in old-growth forests in the hemiboreal forest zone is scarce and fragmented. However, fine root data can provide valuable insights into soil carbon fluxes. Thus, the aim of the current study was to provide estimates of the fine root biomass (FRB), fine root production (FRP), and fine root turnover (FRT) rate by tree species and other functional groups in old-growth (stand age 131–179 years) forests on mesotrophic organic soils dominated by Scots pine (Pinus sylvestris L.), with (drained mesotrophic organic soil) and without (undrained mesotrophic organic soil) the effects of forest drainage. The sequential soil coring method was used to estimate the FRB and FRP. The total FRB (sum of the FRB of all functional groups) was significantly higher in the undrained sites (6.8±0.3 t ha 1) than in the drained sites (3.97±0.1 t ha 1). The FRB of Scots pine in the undrained forest was significantly higher (1.7±0.1 t ha 1) than in the drained forest (0.5±0.1 t ha 1), supporting an extensive foraging strategy. The significantly higher mean FRB of Norway spruce (Picea abies [L.] Karst.) (1.4±0.1 t ha 1) in the drained sites than the undrained sites (0.7±0.2 t ha-1) can be explained by there being a higher proportion of spruce in the stand compositions, thus a higher standing volume (cubic meters per hectare) of this species and an increased FRB. The FRB of dwarf shrubs (2.43±0.2 t ha-1) formed the largest part of the total FRB in the undrained sites and the second largest (1.16±0.1 t ha-1), following Norway spruce, in the drained sites. The total FRP was similar between the undrained (2.05±0.31 t ha-1 yr-1) and drained (1.82±0.26 t ha-1 yr-1) stands. However, considerable variability in the FRP was observed between different sites of the same forest site type. The FRT rate of Scots pine was twice as high in the drained sites than the undrained sites, suggesting faster nutrient and carbon input into the drained soil compared to the undrained soil. Estimates of FRB, FRP, and FRT rate for different functional groups can be used in carbon-cycle modeling and in further calculations to estimate the carbon budget (balance) in forests on organic soils.

Synergistic negative effects between a fungicide and high temperatures on homing behaviours in honey bees

Interactions between environmental stressors may contribute to ongoing pollinator declines, but have not been extensively studied. Here, we examined the interaction between the agricultural fungicide Pristine® (active ingredients: 25.2% boscalid, 12.8% pyraclostrobin) and high temperatures on critical honey bee behaviours. We have previously shown that consumption of field-realistic levels of this fungicide shortens worker lifespan in the field and impairs associative learning performance in a laboratory-based assay. We hypothesized that Pristine® would also impair homing and foraging behaviours in the field, and that an interaction with hot weather would exacerbate this effect. Both field-relevant Pristine® exposure and higher air temperatures reduced the probability of successful return on their own. Together, the two factors synergistically reduced the probability of return and increased the time required for bees to return to the hive. Pristine® did not affect the masses of pollen or volumes of nectar or water brought back to the hive by foragers, and it did not affect the ratio of forager types in a colony. However, Pristine®-fed bees brought more concentrated nectar back to the hive. As both agrochemical usage and heat waves increase, additive and synergistic negative effects may pose major threats to pollinators and sustainable agriculture.

Species richness: a pivotal factor mediating the effects of land use intensification and climate on grassland multifunctionality

Temperate semi-natural grasslands harbour unique biodiversity, support livestock farming through forage production, and deliver many essential ecosystem services (ESs) to human society; they are highly multifunctional. However, temperate grassland ecosystems are also among the most threatened ecosystems on earth due to land use and climate change. Understanding how biodiversity, climate, and land use intensification impact grassland multifunctionality through complex direct and indirect pathways is critical to better anticipate the future of these fragile ecosystems. Here, we evaluate how local plant species richness (SR) modulates the effect of land use intensification and climate on grassland multifunctionality (using six key ESs: biomass productivity and stability, forage quality, carbon storage, pollination, and local plant rarity) in the French Massif Central, the largest grassland in Western-Europe. We sampled 100 grassland fields with contrasted fertilisation rates, and SR over large elevational and latitudinal gradients related to variation in mean annual temperature (MAT), and drought severity (DS), two key climate change drivers that are predicted to increase in the future. Using a confirmatory path analysis, we found that SR was the main driver of multifunctionality. We also found significant SR × MAT and SR × fertilization interactions suggesting that warm climate and high fertilization rates may alter the biodiversity-ecosystem multifunctionality relationships. Furthermore, increasing temperature and fertilization indirectly influenced multifunctionality by decreasing SR and consequent multifunctionality in warm low-land and highly fertilized grasslands compared to colder montane grasslands or less fertilised ones. DS only impacted some ES individually (e.g. forage quality). Synthesis and applications: we identified SR as a pivotal factor mediating the effects of land use intensification and climate on multifunctionality through both direct and indirect pathways. Failing to account for changes in SR could thus bias any prediction of – or aggravate – the effects of land use intensification and climate change on ESs delivery in temperate grassland ecosystems. Considering that SR, MAT, and fertilization are major proxies of three main global change drivers (biodiversity loss, climate change, and land use intensification) our study may help to better anticipate the effect of multiple interacting global change drivers on grassland ecosystems.

Data from: field evaluation: the effect of two transgenic Bt maize events on predatory arthropods in the Huang-Huai-Hai summer maize-growing region of China

To illustrate the impact of genetically modified (GM) Bt maize on the natural enemy communities in the Huang-Huai-Hai summer maize-growing region in China, the abundance of seven common predator groups (Geocoris pallidipennis, Harmonia axyridis, lacewings, Orius sauteri, Propylea japonica, spiders, Staphylinidae) was quantitatively evaluated by planting Bt-Cry1Ab DBN9936 and Bt-Cry1Ab/Cry2Aj Ruifeng 125 events during the growing season from 2016 to 2019. A total of 11,172- 13,739 predators were observed in each varieties during four years, and the abundance of each groups on Bt maize varied between sample dates and among those enemy taxons. The shannon-Wiener diversity index from seven groups showed very similar temporal dynamics and there were not significant differences in Bt and non-Bt maize, showing that Bt maize did not disrupt the stability of predator enemy aggregation in the field. Spiders, H. axyridis, P. japonica, Lacewing, O. sauteri with positive taxon weights after using principal response curve (PRC) method, indicated that Bt maize had a positive effect on the abundances of individual taxa. All this indicating that the two Bt maize hybrids did not adversely affect predator community in the Huang-Huai-Hai summer maize-growing region of China.

opencc-by-4.0Nov 2023View details →

Supplementary data to "Radiative forcing and equivalent effective chlorine due to hydrochlorofluorocarbons peaked in 2021"

README for Supplementary data to “Radiative forcing and equivalent effective chlorine due to hydrochlorofluorocarbons peaked in 2021”   This repository contains 4 folders: 1) agage: contains the inputs to the 12-box model and the derived monthly and annual mole fractions (global and semi-hemispheric) using measurements from the AGAGE network. 2) noaa: contains the inputs to the 12-box model and the derived monthly and annual mole fractions (global and semi-hemispheric) using measurements from the NOAA network. 3) vollmer: contains the inputs to the 12-box model and the derived monthly and annual mole fractions (global and semi-hemispheric) using measurements from the measurements published in Vollmer et al. (2021). 4) Projections: contains a csv file with the merged mole fractions (i.e., mean) from the various networks and the projected quantities.   The 12-box model and the method used to quantify global mean mole fractions are available via GitHub (https://github.com/mrghg/py12box (last accessed 5 March 2024) and https://github.com/mrghg/py12box_invert (last accessed 5 March 2024)) and Zenodo (https://doi.org/10.5281/zenodo.6857447 and https://doi.org/10.5281/zenodo.6857794).   AGAGE data are also available at http://agage.mit.edu/data/agage-data (last accessed 5 March 2024) and https://data.ess-dive.lbl.gov/  (current dataset <a href="https://doi.org/10.15485/1998580">https://doi.org/10.15485/1998580</a>) and newer data can be made available upon request. The most recent NOAA atmospheric observations are available at https://gml.noaa.gov/aftp/data/hats/hcfcs/ (last accessed 5 March 2023).   References: Vollmer, M. K. et al. Unexpected nascent atmospheric emissions of three ozone-depleting hydrochlorofluorocarbons. Proc Natl Acad Sci USA 118, e2010914118 (2021).

Repeatedly experiencing the McGurk effect induces long-lasting changes in auditory speech perception

In the McGurk effect, presentation of incongruent auditory and visual speech evokes a fusion percept different than either component modality. We show that repeatedly experiencing the McGurk effect for 14 days induces a change in auditory-only speech perception: the auditory component of the McGurk stimulus begins to evoke the fusion percept, even when presented on its own without accompanying visual speech. This perceptual change, termed fusion-induced recalibration (FIR), was talker-specific and syllable-specific and persisted for a year or more in some participants without any additional McGurk exposure. Participants who did not experience the McGurk effect did not experience FIR, showing that recalibration was driven by multisensory prediction error. A causal inference model of speech perception incorporating multisensory cue conflict accurately predicted individual differences in FIR. Just as the McGurk effect demonstrates that visual speech can alter the perception of auditory speech, FIR shows that these alterations can persist for months or years. The ability to induce seemingly permanent changes in auditory speech perception will be useful for studying plasticity in brain networks for language and may provide new strategies for improving language learning.

opencc-zeroDec 2023View details →

Data for: Spillover effects of organic agriculture on pesticide use on nearby fields

The environmental impacts of organic agriculture are only partially understood and whether such practices have spillover effects on pests or pest control activity on nearby fields remains unknown. Using roughly 13,000 field observations per year from 2013-2019 in Kern County, CA , we estimate that organic crop producers benefit from surrounding organic fields, decreasing overall pesticide use and pesticides targeting insect pests. Conventional fields, in contrast, tend to increase pesticide use as the area of surrounding organic production increases.

Effect of Nd on high temperatures deformation and corrosion behavior of AZE Mg alloy

An extruded AZE Mg alloy (Mg-3Al-1Zn-0.6Nd) has been developed and prepared to examine the effect of the precipitated phase on corrosion and hot deformation behavior. High-temperature compression experiments show that dynamic recrystallization (DRX) occurs at various experimental parameters (473 to 673 K and 1×10-4 s-1 to 1×10-3 s-1). The deformation mechanism is dominated by dislocation slip and/or twinning. Al11Nd3 precipitates with two different sizes could impede nucleation and the growth of DRXed grains. Serrated flow occurred owing to the interactions between dislocations and precipitates. The corrosion current density decreases with the addition of Nd elements. Moreover, the continuous precipitation of the Al11Nd3 phase at grain boundaries reduces the corrosion rate in NaCl solution, thereby enhancing the corrosion resistance of AZE alloys.

Contrasting effects of host or local specialization: widespread haemosporidians are host generalist whereas local specialists are locally abundant

Aim: Despite the wide distribution of many parasites around the globe, the range of individual species varies significantly even among phylogenetically related taxa. Since parasites need suitable hosts to complete their development, parasite geographical and environmental ranges should be limited to communities where their hosts are found. Parasites may also suffer from a trade-off between being locally abundant or widely dispersed. We hypothesize that the geographical and environmental ranges of parasites are negatively associated to their host specificity and their local abundance. Location: Worldwide Time period: 2009 to 2021 Major taxa studied: Avian haemosporidian parasites Methods: We tested these hypotheses using a global database which comprises data on avian haemosporidian parasites from across the world. For each parasite lineage, we computed five metrics: phylogenetic host-range, environmental range, geographical range, and their mean local and total number of observations in the database. Phylogenetic generalized least squares models were ran to evaluate the influence of phylogenetic host-range and total and local abundances on geographical and environmental range. In addition, we analysed separately the two regions with the largest amount of available data: Europe and South America. Results: We evaluated 401 lineages from 757 localities and observed that generalism (i.e. phylogenetic host range) associates positively to both the parasites' geographical and environmental ranges at global and Europe scales. For South America, generalism only associates with geographical range. Finally, mean local abundance (mean local number of parasite occurrences) was negatively related to geographical and environmental range. This pattern was detected worldwide and in South America, but not in Europe. Main Conclusions: We demonstrate that parasite specificity is linked to both their geographical and environmental ranges. The fact that locally abundant parasites present restricted ranges, indicates a trade-off between these two traits. This trade-off, however, only becomes evident when sufficient heterogeneous host communities are considered.

Disentangling developmental effects of play aspects in rat rough-and-tumble play

Animal play encompasses a variety of aspects, with kinematic and social aspects being particularly prevalent in mammalian play behaviour. While the developmental effects of play have been increasingly documented in recent decades, understanding the specific contributions of different play aspects remains crucial to understand the function and evolutionary benefit of animal play. In our study, developing male rats were exposed to rough-and-tumble (RT) play selectively reduced in either the kinematic or the social aspect. We then assessed the developmental effects of reduced play on their appraisal of standardised human-rat play ('tickling') by examining their emission of 50-kHz ultrasonic vocalisations (USVs). Using a deep learning framework, we efficiently classified five subtypes of these USV across six behaviour states. Our results revealed that rats lacking the kinematic aspect in play emitted fewer USVs during tactile contacts by human and generally produced fewer USVs of positive valence compared to control rats. Rats lacking the social aspect did not differ from the control and the kinematically reduced group. These results indicate aspects of play have different developmental effects, underscoring the need for researchers to further disentangle how each aspect affects animals.

Figure 10 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)

Figure 10: PCA biplot of environmental parameters and abundance of microarthropods with month as grouping factor. sav ctrl: savanna; mb: maize bare; mbnpk: maize with chemical NPK fertilizer; mmdom: maize with dead organic matter.

Figure 9 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)

Figure 9. PCA biplot of environmental parameters and abundance of microarthropods with treatment as grouping factor. sav ctrl: savanna, mb: maize bare, mbnpk: maize with chemical NPK fertilizer, mmdom: maize with dead organic matter.

Figure 8 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)

Figure 8. Oribatida and Gamasina abundance (tsd. ind./m2) in plots (mb: maize bare, mmdom: maize with DOM). Abundances being significantly different from each other are marked by different letters for each microarthropod group (Wilcoxon signed rank test [p ˂ 0.05]). Error bars = standard error.

Figure 7 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)

Figure 7. Collembola, Oribatida and Gamasina abundance (tsd. ind./m2) in plots (mb: maize bare, mbnpk: maize with chemical NPK). Abundances being significantly different from each other are marked by different letters (Wilcoxon signed rank test [p ˂ 0.05]). Error bars = standard error.

Figure 6 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)

Figure 6. Effect of Maize cultivation on Collembola, Oribatida and Gamasina in control plots (sav ctrl: savanna, mb: maize bare). Abundances being significantly different from each other are marked by different letters for each microarthropod group (Wilcoxon signedrank test [p ˂ 0.05]). Error bars = standard error.