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Data from: Stimulus dependent emergence of understanding analogical relations in budgerigars

The ability for analogical reasoning, such as understanding that the relationship between two items is similar to the relationship between two other items, has long been considered to be unique to humans. Whether and to what extent non-human animals can recognize such relational analogies is still debated. We tested such abilities in two groups of budgerigars with a diverse set of item categories in which the figures of the stimuli were quite different in nature (size, color, shape, geometric type, and number). Budgerigars trained to discriminate two identical figures from the same two figures differing in size, generalized the discrimination to test stimuli belonging to the novel categories, demonstrating the spontaneous use of analogical relations. In contrast, budgerigars trained to discriminate two circles that were either the same or different in color seemed to generalize to novel stimuli by perceptual rather than conceptual similarity. The results thus demonstrate the spontaneous emergence of perceiving analogical relations in budgerigars of a nature beyond that demonstrated in previous studies of non-primate species. However, the results also show that whether budgerigars generalize a relationship by perceptual or conceptual similarity seems dependent on the nature of the training stimuli.

Density-dependent changes of mating system and family structure in Brandt's voles (Lasiopodomys brandtii)

A mating system is an important life history for animals dealing with changing environments. Population density affects the plasticity of a mating system and subsequently the family structure of animals, but its impacts on mating systems and social structures are rarely investigated by using molecular markers in field conditions. In this study, using microsatellite genetic markers, we examined the changes in the social and genetic mating system and family structure of Brandt's voles in the grassland of Inner Mongolia, China, under low-, medium-, and high-density enclosures (each enclosure 0.48-ha with 4 replicates.) We found, that with the increase in population density of the founder voles introduced into the enclosure in early spring, both sexes increased their number of genetic mating partners, while males increased their social partners, resulting in a more promiscuous mating system. The number of genetic fathers and mothers per family, the number of social offspring per founder male or female, and the proportion of extra-group offspring increased with increased density, indicating that the response of the family structure to density change which is consistent with the change in mating system observed in our study. Both male and female voles had multiple mates, but males had a larger number of social and genetic mates, the number of social and genetic offspring, and the number of social and genetic families. Our study highlights the significance of density-dependent plasticity of a mating system and family structure in affecting the population change of small mammals.

The condition-dependence of male genital size and shape

The male genitals of internal fertilizers evolve rapidly and divergently, and sexual selection is generally responsible for this. Many sexually selected traits are condition-dependent - with their expression dependent upon the resources available to be allocated to them - as revealed by genetic or environmental manipulations of the condition. However, it is not clear whether male genitals are also condition-dependent. Here we manipulate the condition in two ways (via inbreeding and diet) to test the condition-dependence of the genital arch of Drosophila simulans. We found that genital size but not genital shape suffered from inbreeding depression, whereas genital size and shape were affected by dietary manipulation of the condition. The differential effects of these treatments likely reflect the underlying genetic architecture that has been shaped by past selection: inbreeding depression is only expected when traits have a history of directional selection, while diet impacts traits regardless of historical selection. Nonetheless, our results suggest genitals can be condition-dependent like other sexually selected traits.

Distance-dependence seed set of Vasconcellea chilensis

Plant reproductive failure is a critical concern for conserving rare and endangered species that typically have low-density and sparse populations. One important factor contributing to reproductive failure is the spatial arrangement of plants within a population, which can lead to isolation and negatively affect seed output, particularly in obligate outcrosses. Additionally, this effect can be compounded by plant size. Here, we investigate how plants' spatial distribution and size influence the reproductive success of Vasconcellea chilensis, a threatened papaya species from northern Chile. Using flower exclusion experiments, we first examined whether V. chilensis can produce seeds via apomixis. We then used Spatial Point Pattern Analysis (SPPA) in three populations to examine the spatial arrangement of plants in three populations, and, finally, we assessed whether plant size and mate distance influence the reproductive success of this plant species. V. chilensis is a dioecious shrub unable to produce fruits through apomixis. The SPPA revealed significant clustering of female and male plants at different spatial scales, indicating a non-random distribution. Moreover, a significant attraction between the sexes suggested a preference for proximity. In two populations, closer proximity to male plants was linked to higher seed production. Our study revealed that the absence of apomixis in V. chilensis makes it prone to experiencing distance-dependent reproductive failure. In particular, the seed set was compromised in female plants isolated from male neighbors. This link between isolation and seed production was especially significant in the driest site, and we discussed how environmental factors can exacerbate this effect.

Data from: ESCRT-III-dependent adhesive and mechanical changes are triggered by a mechanism detecting alteration of Septate Junction integrity in Drosophila epithelial cells

Barrier functions of proliferative epithelia are constantly challenged by mechanical and chemical constraints. How epithelia respond to and cope with disturbances of barrier functions to allow tissue integrity maintenance is poorly characterized. Cellular junctions play an important role in this process and intracellular traffic contribute to their homeostasis. Here, we reveal that, in Drosophila pupal notum, alteration of the bi- or tricellular septate junctions (SJs) triggers a mechanism with two prominent outcomes. On one hand, there is an increase in the levels of E-cadherin, F-Actin and non-muscle Myosin II in the plane of adherens junctions. On the other hand, β-integrin/Vinculin-positive cell contacts are reinforced along the lateral and basal membranes. We found that the weakening of SJ integrity, caused by the depletion of bi- or tricellular SJ components, alters ESCRT-III/Vps32/Shrub distribution, reduces degradation, and instead favours recycling of SJ components, an effect that extends to other recycled transmembrane protein cargoes including Crumbs, its effector β-Heavy Spectrin Karst, and β-integrin. We propose a mechanism by which epithelial cells, upon sensing alterations of the septate junction, reroute the function of Shrub to adjust the balance of degradation/recycling of junctional cargoes and thereby compensate for barrier junction defects to maintain epithelial integrity.

Can livestock grazing dampen density dependent fluctuations in wild herbivore populations?

Conservation policy for the high mountains of Asia increasingly recognises the need to encompass large multi-use landscapes beyond the protected area network. Due to limited long-term research in this region, our understanding of even fundamental processes, such as factors regulating large mammal populations is poor. Understanding the factors that regulate animal populations, especially those generating cyclicity, is a long-standing problem in ecology. Long-term research across multiple taxa (mainly from Europe and North America) has focused on the relative roles of food and predation in generating cyclicity in population dynamics. It remains unclear how trophic interactions that are influenced by anthropogenic stressors can affect population dynamics in human-modified landscapes. We present a 10-year study to compare the effects of livestock grazing on density dependent dynamics in two populations of bharal, Pseudois nayaur, in the Himalaya. We combine this with a mechanistic understanding of whether density dependence in these two sites acts predominantly by affecting adult survival or recruitment. We compared and quantified density dependence in the bharal population by fitting Bayesian Gompertz state‐space (GSS) models. We found evidence for negative density dependence which indicates possible cyclic dynamics in the bharal population of the site (Tabo) with low livestock density. The population dynamics of this site were driven by recruited offspring – with a 2-year density dependent lag effect – rather than adult survival. In the site with high livestock density (Kibber), this density dependence was not detected. We postulate the potential role of excessive grazing by livestock in affecting offspring recruitment, thereby affecting the bharal population in Kibber. Synthesis and applications: Our results suggest that conservation action to facilitate wild herbivore population recovery, such as the development of protected areas and village reserves, needs to account for density dependent regulation. Sites with trophy hunting require continuous monitoring to understand the effects of density dependence so that appropriate hunting quotas can be formulated.

The effects of microplastics on crop variation depend on polymer types and their interactions with soil nutrient availability and weed competition

Microplastics pollution of agricultural soil is a global environmental concern because of its potential risk to food security and human health. Although many studies have tested the direct effects of microplastics on growth of Eruca sativa Mill., little is known about whether these effects are regulated by fertilization and weed competition in field management practices. Here, we performed a greenhouse experiment growing E. sativa as target species in a three-factorial design with two levels of fertilization (low versus. high), two levels of weed competition treatments (weed competition versus no weed competition) and five levels of microplastic treatments (no microplastics, Polybutylene adipateco-terephthalate [PBAT], Polybutylene succinate [PBS], Polycaprolactone [PCL] or Polypropylene [PP]). Compared to the soil without microplastics, PBS and PCL reduced aboveground biomass and leaf number of the E. sativa. PBS also resulted in increased root allocation and thicker roots in E. sativa. In addition, fertilization significantly mitigated the negative effects of PBS and PCL on aboveground biomass of E. sativa, but weed competition significantly promoted these effects. Although fertilization alleviated the negative effect of PBS on aboveground biomass, such alleviation became weaker under weed competition than when E. sativa grew alone. The results indicate that the effects of specific polymer types on E. sativa growth could be regulated by fertilization, weed management, and even their interactions. Therefore, reasonable on-farm management practices may help in mitigating the negative effects of microplastics pollution on E. sativa growth in agricultural fields.

opencc-zeroDec 2023View details →

Data from: Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside

Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive for local adaptation with gene flow. Local adaptation is widespread in marine species despite generally high connectivity and is often associated with tightly linked genomic architectures, such as chromosomal inversions. To investigate gene regulatory evolution under gene flow and the role of inversions associated with local adaptation to a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (Menidia menidia) from two locally adapted populations and their F1 hybrids, reared under two temperatures. We found substantial divergence in gene expression and thermal plasticity between populations, with up to 31% of genes being differentially expressed. Reduced thermal plasticity, temperature-dependent gene misexpression and the disruption of co-expression networks in hybrids point towards a role of regulatory incompatibilities in local adaptation, particularly under colder temperatures. Chromosomal inversions show an accumulation of regulatory incompatibilities but are not consistently enriched for differentially expressed genes. Together, these results suggest that gene regulation can diverge substantially among populations despite gene flow, partly due to the accumulation of temperature-dependent regulatory incompatibilities within inversions.

opencc-by-4.0Oct 2023View details →

Size-Dependent Dynamics of the Internal Carbon Pool Drive Isotopic Vital Effects in Calcifying Phytoplankton

Isotopic offsets in biogenic calcite from equilibrium values can provide unique insights into the physiology and mechanisms of carbon regulation in calcifying phytoplankton. This study examines the impact of varying CO2 (controlled via pH) on five coccolithophore species chosen for varied cell sizes, physiology, and calcification. The study investigates isotopic offsets in coccolith calcite and organic matter, in relation to carbon demand and supply (µ/CO2). Species-specific CO2/pH optima for growth (µopt) were derived from variations in growth rates with varying CO2 concentrations. Growth rates for all species declined with rising CO2 (decreasing pH) due to H+-driven inhibition. C. braarudii and C. leptoporus exhibited high µopt values (suggesting high carbon-demand) and limited growth under low CO2 (high pH) suggesting carbon limitation. Under low CO2 supply, when growth rates were CO2-limited, both species exhibited coincident isotopic depletion in calcite and organic matter as a consequence of CO2 diffusion into the cell that experienced no equilibration as a result of a highly depleted internal carbon pool. In these two species, isotopic values in calcite  remained unaffected by growth rates and CO2 concentration (µ/CO2) when CO2 was sufficient for optimal growth. G. huxleyi and G. oceanica displayed optima for growth (µopt) at low CO2 concentrations and showed no growth limitation under low CO2 (indicating low carbon-demand). Both species experienced depleted (negative) vital effects caused by an excess of CO2 diffusion into the small internal carbon pool of the cell when diffusive carbon supply outpaced low demand (low µ/CO2). Enriched (positive) vital effects were observed under low carbon supply and high demand, likely due to diffusive loss of CO2 from the cell's intracellular carbon pool due to a lower intracellular pH. C. carterae exhibited an intermediate µopt and isotopically equilibrated intracellular carbon pool such that δ13C values in calcite and organic matter suggested a shared carbon pool. This study illustrates that pH-CO2 driven vital effects and fractionation into organic matter indicate the residence time for carbon in the intracellular carbon pool, and the size of this pool is proportional to cell size. C. leptoporus and C. carterae can elevate intracellular pH to minimise CO2 leakage, whereas vital effects in G. huxleyi and G. oceanica are caused by diffusive CO2 due to the small size of their internal carbon pool.

opencc-zeroApr 2024View details →

Data from: Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability

Prophages, viral sequences integrated into bacterial genomes, can confer fitness benefits and costs. Despite the risk of prophage activation and subsequent bacterial death, active prophages are present in most bacterial genomes. However, our understanding about the selective forces that maintain prophages in bacterial populations is scarce. Combining experimental evolution with stochastic modelling we found that prophage maintenance and loss are primarily determined by environmental conditions that amplify the net fitness effect of the prophage. Whole genome sequencing revealed that prophage loss occurs through environment-specific sequences of selective sweeps, leading to rapid prophage loss when prophages are costly. However, conflicting selection pressures that select against the prophage but for a prophage-encoded accessory gene can prolong prophage maintenance. The extent of prolonged maintenance depends on the sociality of this accessory gene. Selection for non-cooperative genes is more effective for prophage maintenance as cooperative genes allow for protection of phage-free 'cheaters' that may emerge if prophage costs outweigh their benefits. Our mathematical model suggests that environmental variation plays a larger role than mutation rates in determining prophage maintenance. This challenges our understanding of the role of random chance events relative to environmental factors in shaping the evolutionary trajectory of bacterial populations.

Raw data for journal article: "Wave propagation across the skull under bone conduction: Dependence on coupling methods"

This is a data set containing the raw data for figures 3-6 from the journal article: "Wave propagation across the skull under bone conduction: Dependence on coupling methods" Original article DOI: 10.1121/10.0009676 Original article link: https://pubmed.ncbi.nlm.nih.gov/35364950/   The Fig 3 and 4 data are contained within MATLAB  figure (.fig) files, all saved with MATLAB version R2020a. Fig 5 and 6 data are  3D velocity data for 5 cadaver heads (CH1-5) and FEM predictions. This data are stored within a folder structure indicating the stimulation condition (defined in the journal article). For example "Cadaver head data\CH1\Attract" contains cadaver head data for cadaver head 1 (CH1) with stimulation "Attract", as defined in the journal article above. For each combination  of cadaver head (or FEM) and stimulation condition there is a TXT file (comma delimited) for the real and imaginary data at each stimulation frequency, and orthogonal velocity axis (X,Y,Z based on the anatomical coordinate system defined in the journal article) as well as the combined (maximum) velocity vector. The data set also includes a TXT file with the position (in same coordinate system the velocity data) of each measurement point and a list of stimulation frequencies.

opencc-by-4.0Nov 2023View details →

Data from: Higher-order species interactions cause time-dependent niche and fitness differences: experimental evidence in plant-feeding arthropods

trajectories.csv (the raw data) id: replicate identifier variant: co-existence status ("competition" or "monoculture") day: day of experiment species: mite species ("CRM" or "WCM") n: population density   model.R The R script with the GAMM fitted to the trajectory data (the GAMM model is saved as model.RData); also produces simulations from this model (saved as sim.csv).   model.RData The GAMM for growth rates.   sim.csv (simulations from the GAMM) day: day of experiment spec_var: combination of co-existence status ("competition" or "monoculture") and species ("CRM" or "WCM") X1:X1000: population densities simulated from the fitted GAMM (on the log scale)   NFD_over_time_monte_carlo_gam.py Python script to compute niche and fitness differences. Takes sim.csv (densities over time for different instantiations) and model.RData (stores the GAMM from R for the growth rates) as input and generates the file Data_NFD_monte_carlo_multi_c.csv which stores the niche and fitness differences computed for these communities.   figures.R The R script that produces Figures 2-4.   plot_biotic_model.py Python code to generate the figures S3 and S4 showing the simulations of a biotic resource competition model.    plot_abiotic_model.py Python code to generate the figures S1 and S2 showing simulations of an abiotic resource competition model.

Dataset for "Understanding Wavelength-dependent Synergies between Morphology and Photonic Design in TiO2-based Solar Powered Redox Cells"

Open the record for dataset details and reuse information.

The data for Time-dependent Stellar Flare Models of Deep Atmospheric Heating

This repository contains model output (within two .tar.gz files) and a pdf document (analysis_tools_mdwarfradyngrid-v1.0.pdf) that explains the contents and use.  The models are described in Kowalski, A.F., Allred, J.C., & Carlsson, M. Time-dependent Stellar Flare Models of Deep Atmospheric Heating, published 2024 July 5 in The Astrophysical Journal Volume 969, Number 2 (DOI: <a href="https://iopscience.iop.org/article/10.3847/1538-4357/ad4148">10.3847/1538-4357/ad4148</a>). The Jupyter notebook demo, radyn_xtools_Demo.ipynb is included in the PyPI package installation that is described in analysis_tools_mdwarfradyngrid-1.0.pdf.

Material Dependent Influence of Ring/Spot Beam Profiles in Laser Powder Bed Fusion

Raw data associated with a paper submission. "Material Dependent Influence of Ring/Spot Beam Profiles in Laser Powder Bed Fusion" Contained are all the Matlab scripts used for the simulations, as well as csv's of any data plotted in graphs.

opencc-zeroApr 2024View details →

Data from: Sensory perception of rivals has trait-dependent effects on plasticity in Drosophila melanogaster

The social environment has myriad effects on individuals, altering reproduction, immune function, cognition, and aging. Phenotypic plasticity enables animals to respond to heterogeneous environments such as the social environment but requires that they assess those environments accurately. It has been suggested that combinations of sensory cues allow animals to respond rapidly and accurately to changeable environments, but it is unclear whether the same sensory inputs are required in all traits that respond to a particular environmental cue. Drosophila melanogaster males, in the presence of rival males, exhibit a consistent behavioral response by extending mating duration. However, exposure to a rival also results in a reduction in their lifespan, a phenomenon interpreted as a trade-off associated with sperm competition strategies. D. melanogaster perceive their rivals by using multiple sensory cues; interfering with at least two of olfactory, auditory, or tactile cues eliminates the extension of mating duration. Here we assessed whether these same cues were implicated in the lifespan reduction. Removal of combinations of auditory and olfactory cues removed the extended mating duration response to a rival, as previously found. However, we found that these manipulations did not alter the reduction in lifespan of males exposed to rivals or induce any changes in activity patterns, grooming or male-male aggression. Therefore, our analysis suggests that lifespan reduction is not a cost associated with the behavioral responses to sperm competition. Moreover, this highlights the trait-specific nature of the mechanisms underlying plasticity in response to the same environmental conditions.

opencc-zeroFeb 2024View details →

Insect root feeders incur negative density-dependent damage across plant species in an alpine meadow

Although herbivores are well known to incur positive density-dependent damage and mortality, thereby likely shaping plant community assembly, the response of belowground root feeders to changes in plant density has seldom been addressed. Locally rare plant species (with lower plant biomass per area) are often smaller with shallower roots than common species (with higher plant biomass per area) in competition-intensive grasslands. Likewise, root feeders are often distributed in the upper soil layers. We hypothesized therefore that root feeders would incur a negative density (biomass) dependent damage across plant species. To test this hypothesis, we investigated the diversity and abundance of plant and root feeder species in an alpine meadow, and determined the diet of the root feeders using metabarcoding. Across all species, root feeder load decreased with increasing aboveground plant biomass, root biomass, and total plant biomass per area, indicating negative density dependence of damage across plant species. Aboveground plant biomass per area increased with increasing individual plant biomass and root depth per area across species, suggesting that rare plant species were smaller in size and had shallower root systems compared to common plant species. Both root biomass per area and root feeder biomass per area decreased with soil depth, but the root feeder biomass decreased disproportionally faster compared to root biomass with increasing root depth. Root feeder load decreased with increasing root depth, but was not correlated with the feeding preference of root feeder species. Moreover, the prediction derived from a random process incorporating vertical distributions of root biomass and root feeder biomass significantly accounted for interspecific variation in root feeder load. In conclusion, the data indicate that root feeders incur negative density-dependent damage across plant species. On this basis, we suggest that manipulative experiments should be conducted to determine the effect of the negative density-dependent damage on plant community structure, and that different types of plant-animal interactions should be concurrently examined to fully understand the effect of plant density on overall herbivore damage across plant species.

opencc-zeroApr 2024View details →

Local reflects global: Life-stage dependent changes in the phenology of coastal habitat use by North Sea herring

Climate warming is affecting the suitability and utilisation of coastal habitats by marine fishes around the world. Phenological changes are an important indicator of population responses to climate-induced changes but remain difficult to detect in marine fish populations. The design of large-scale monitoring surveys does not allow fine-grained temporal inference of population responses, while the responses of ecologically and economically important species groups such as small pelagic fish are particularly sensitive to temporal resolution. Here, we use the longest, highest-resolution time series of species composition and abundance of marine fishes in northern Europe to detect possible phenological shifts in the small pelagic North Sea herring. We detect a clear forward temporal shift in the phenology of nearshore habitat use by small juvenile North Sea herring. This forward shift can best be explained by changes in water temperatures in the North Sea. We find that reducing the temporal resolution of our data to reflect the resolution typical of larger surveys makes it difficult to detect phenological shifts and drastically reduces the effect sizes of environmental covariates such as seawater temperature. Our study therefore shows how local, long-term, high-resolution time series of fish catches are essential to understand the general phenological responses of marine fishes to climate warming and to define ecological indicators of system-level changes.

Data and code for: Suppression of nitrogen deposition on global forest soil CH4 uptake depends on nitrogen status

Methane (CH4) is the second most important atmospheric greenhouse gas (GHG) and forest soils are a significant sink for atmospheric CH4. Uptake of CH4 by global forest soils is affected by nitrogen (N) deposition; clarifying the effect of N deposition helps to reduce uncertainties of the global CH4 budget. However, it remains an unsolved puzzle why N input stimulates soil CH4 flux (RCH4) in some forests while suppressing it in others. Combining previous findings and data from N addition experiments conducted in global forests, we proposed and tested a “stimulating-suppressing-weakened effect” (“three stages”) hypothesis on the changing responses of RCH4 to N input. Specifically, we calculated the response factors (f) of RCH4 to N input for N-limited and N-saturated forests across biomes; the phased changes in f values supported our hypothesis. We also estimated the global forest soil CH4 uptake budget to be approximately 11.2 Tg yr–1. CH4 uptake hotspots were located predominantly in temperate forests. Furthermore, we quantified that current level of N deposition reduced global forest soil CH4 uptake by ~3%. This suppression effect was more pronounced in temperate forests than in tropical or boreal forests, likely due to differences in N status. The proposed “three stages” hypothesis in this study generalizes the diverse effects of N input on RCH4, which could help improve experimental design. Additionally, our findings imply that by regulating N pollution and reducing N deposition, soil CH4 uptake can be significantly increased in the N-saturated forests in tropical and temperate biomes. Specifically, Data Set S1 (CH4_exp dataset in main text) was used to derive the response factors of soil CH4 flux to N input in global forests; Data Set S2 (CH4_obs dataset in main text) was used to estimate the soil CH4 fluxes in global forests; Data Sets S3–S7 were used to classify the N-limited and N-saturated forests on global level; Data Set S8 contains environmental factors (MAT, MAP, soil texture, etc.) for global estimations on grid level; Data Set S9 contains global forest soil CH4 budgets reported in previous studies. The data analysis process and produced figures can be replicated with the uploaded R script (Code S1).

Velocity and temperature dependence of steady-state friction of natural gouge controlled by competing healing mechanisms

The empirical rate- and state-dependent friction law is widely used to explain the frictional resistance of rocks. However, the constitutive parameters vary with temperature and sliding velocity, preventing extrapolation of laboratory results to natural conditions. Here, we explain the frictional properties of natural gouge from the San Andreas Fault, Alpine Fault, and the Nankai Trough from room temperature to $\sim300^\circ$C for a wide range of slip-rates with constant constitutive parameters by invoking the competition between two healing mechanisms with different thermodynamic properties. A transition from velocity-strengthening to velocity-weakening at steady-state can be attained either by decreasing the slip-rate or by increasing temperature. Our study provides a framework to understand the physics underlying the slip-rate and state dependence of friction and the dependence of frictional properties on ambient physical conditions.