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opencc-zeroOct 2020View details →

The effects of age on the demography of a perennial plant depend on interactions with size and environment

Age-dependence of the demographic rates survival, fecundity and individual growth is a fundamental aspect of population biological theory. Knowledge about plant ageing can also be important for conservation and agriculture as it will improve the accuracy of population viability assessments and long-term performance assessments in perennial crops. Recent studies show age effects on demographic rates for several plant species, yet much remains to be learned about the patterns and mechanisms of plant ageing, particularly about how age effects interact with the environment and with plant size. We collected age-and-size-based demographic data, as well as individual-based environmental data, for the perennial herb Plantago lanceolata in Denmark over three annual transitions (four years). We combined frequent field monitoring of carefully mapped individuals with the underused technique of root histology to determine age of herbaceous plants. We used generalized linear mixed effects models to assess how age, soil properties, and year influenced survival, growth, and reproduction. Our results show no strong evidence of consistent age declines, rather, we found mostly positive effects of age on vital rates. For all vital rates, i.e. survival, growth, flowering, and reproductive output, age effects also differed significantly among years. Additionally, we detected an interactive effect of age and size in the growth model. Size, and temporal and spatial environmental variation also affected vital rates independently of age. Synthesis: Our study shows that age-dependence of demographic rates can depend both on individual size and environmental variation. These results suggest that a consideration of potential age-interactions may improve the accuracy of comparative studies of ageing and population projections. Moreover, this study shows that much is still unknown about how plant ageing can be affected by the environment, and illustrates how age determination using herb chronology provides an opportunity to increase our knowledge about ageing in herbaceous plants.

opencc-zeroOct 2020View details →

Size-dependent aggression towards kin in a cannibalistic species

In juveniles extreme intraspecies aggression can seem counter-intuitive, as it might endanger their developmental goal of surviving until reproductive stage. On the other hand, aggression can be vital for survival, although the factors (e.g. genetic or environmental) leading to the expression and intensity of this behavior vary across taxa. Attacking (and sometimes killing) related individuals may reduce inclusive fitness; as a solution to this problem, some species exhibit kin discrimination and preferentially attack unrelated individuals. Here, we used both experimental and modeling approaches to consider how physical traits (e.g. size in relation to opponent) and genetic relatedness mediate aggression in dyads of cannibalistic Dendrobates tinctorius tadpoles. We paired full-sibling, half-sibling, and non-sibling tadpoles of different sizes together in an arena and recorded their aggression and activity. We found that the interaction between relative size and relatedness predicts aggressive behavior: large individuals in non-sibling dyads are significantly more aggressive than large individuals in sibling dyads. Unexpectedly, although siblings tended to attack less overall, in size mismatched pairs they attacked faster than in non-sibling treatments. Using a theoretical model to complement these empirical findings, we propose that larval aggression reflects a balance between relatedness and size where individuals trade-off their own fitness with that of their relatives.

opencc-by-4.0Nov 2020View details →

Temperature-dependent Raman, FTIR data and breakdown temperature of phlogopite

This dataset contains all new data corresponding to figures in the manuscript and the supporting information, including temperature-dependent FTIR, Raman data, and breakdown temperature from previous studies and this study.

opencc-zeroNov 2020View details →

Data from: Density-dependent adaptive topography in a small passerine bird, the collared flycatcher

The adaptive topography is a central concept in evolutionary biology, describing how the mean fitness of the population changes with gene frequencies or mean phenotypes. We use expected population size as quantity to be maximized by natural selection to show that selection on pairwise combinations of reproductive traits of collared flycatchers caused by fluctuations in population size generated an adaptive topography with distinct peaks often located at intermediate phenotypes. This occurred because r- and K-selection made phenotypes favored at small densities different from those with higher fitness at population sizes close to the carrying capacity K. The fitness decreased rapidly with a delay in the timing of egg-laying with a density-dependent effect especially occurring among early-laying females. The number of fledglings maximizing fitness was larger at small population sizes than close to K. Finally, there was directional selection for large fledglings independent of population size. We suggest that these patterns can be explained by increased competition for some limiting resources or access to favorable nest sites at high population densities. Thus, r- and K-selection based on expected population size as evolutionary maximization criterion may influence life history evolution and constrain the selective responses to changes in the environment.

Weed dataset - Crop diversity Experiment - Crop-weed relationships are context-dependent and cannot fully explain the positive effects of intercropping on yield

This shows the weed mass per species and crop yield per species of each plot described in the experiment.

opencc-by-4.0Oct 2020View details →

Supporting data for "Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription"

Supporting data for Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription Grace A. Rosena,1, Inwha Baekb,1, Larry J. Friedmana, Yoo Jin Joob, Stephen Buratowskib,2, Jeff Gellesa,2 aDepartment of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA. bDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA. 1Equal contributions 2Corresponding authors:  <a href="mailto:steveb@hms.harvard.edu">steveb@hms.harvard.edu</a>; +1 (617) 432-0696 (S.B.) and <a href="mailto:gelles@brandeis.edu">gelles@brandeis.edu</a>; +1 (781) 736-2377 (J.G.) See Source data index.pdf for description of files.

Amyloid burden quantification depends on PET and MR image processing methodology

The enclosed datasets refer to the work developed at the University Medical Center Groningen and consist of the minimally required PET image data to replicate the results of the study entitled "Amyloid burden quantification depends on PET and MR image processing methodology" which abstract can be found below: <blockquote> Quantification of amyloid load with positron emission tomography can be useful to assess Alzheimer’s Disease in-vivo. However, quantification can be affected by the image processing methodology applied. This study’s goal was to address how amyloid quantification is influenced by different semi-automatic image processing pipelines. Images were analysed in their Native Space and Standard Space; non-rigid spatial transformation methods based on maximum a posteriori approaches and tissue probability maps (TPM) for regularisation were explored. Furthermore, grey matter tissue segmentations were defined before and after spatial normalisation, and also using a population-based template. Five quantification metrics were analysed: two intensity-based, two volumetric-based, and one multi-parametric feature. Intensity-related metrics were not meaningfully affected by spatial normalisation and did not significantly depend on the grey matter segmentation method, with an impact similar to that expected from test-retest studies (≤10%). Yet, volumetric and multi-parametric features were sensitive to the image processing methodology, with an overall variability up to 45%. Therefore, the analysis should be carried out in Native Space avoiding non-rigid spatial transformations. For analyses in Standard Space, spatial normalisation regularised by TPM is preferred. Volumetric-based measurements should be done in Native Space, while intensity-based metrics are more robust against differences in image processing pipelines. </blockquote>

Real-time benchmark dynamics of the Ohmic Spin-Boson Model computed with Time-Dependent Variational Matrix Product States. (TDVMPS) coupling strength and temperature parameter space

Data describing the complete propagators (maps) for the evolution of the Ohmic Spin-Boson Model are made available, here. Using a time-dependent variotnal matrix product states (TDVMPS) respresentation of the complete spin-environment wave function, non -perturbative results are presented over a wide range of coupling strengths, temperatures and initial conditions. The results in this repository are associated with the article:  https://www.preprints.org/manuscript/202012.0016/v1   A mathematica notebook that allows the data to be visualised and manipulated is also provided.

Numerosity adaptation partly depends on the allocation of implicit numerosity-contingent visuo-spatial attention

The folder Dataset contains five subfolders. Each subfolder contains the single subjects’ data for each experiment (three experiments) and each control experiment (two control experiments). Each file contains two Matlab tables called “TBase” and “TAdapt”. Each row of the table is a trial.    In Experiment 1 and 2 the columns contain the following information: 1st: Numerosity of the test stimulus 2nd: Response 3rd: Reaction Times 4th: Accuracy  5th: Test/Adapt side 6th: N° of presented Adaptors   In Experiment 3 the columns contain the following information: 1st: Numerosity of the test stimulus 2nd: Cue position 3rd: Response 4th: Reaction Times 5th: Accuracy  6th: Test/Adapt side

The evolutionary advantage of fitness-dependent recombination in diploids: a deterministic mutation–selection–balance model

Recombination's omnipresence in nature is one of the most intriguing problems in evolutionary biology. The question of why recombination exhibits certain general features is no less interesting than that of why it exists at all. One such feature is recombination's fitness dependence (FD). The so far developed population-genetics models have focused on the evolution of FD recombination mainly in haploids, although the empirical evidence for this phenomenon comes mostly from diploids. Using numerical analysis of modifier models for infinite panmictic populations, we show here that FD recombination can be evolutionarily advantageous in diploids subjected to purifying selection. We ascribe this advantage to the differential rate of disruption of lower- vs higher-fitness genotypes, which can be manifested in selected systems with at least three loci. We also show that if the modifier is linked to such selected system, it can additionally benefit from modifying this linkage in a fitness-dependent manner. The revealed evolutionary advantage of FD recombination appeared robust to crossover interference within the selected system, either positive or negative. Remarkably, FD recombination was often favored in situations where any constant non-zero recombination was evolutionarily disfavored, implying a relaxation of the rather strict constraints on major parameters (e.g., selection intensity and epistasis) required for the evolutionary advantage of non-zero recombination formulated by classical models.

Size-selective exclusion of mammals and invertebrates differently affects grassland plant communities depending on vegetation type

Human-caused loss of vertebrate and invertebrate animals, defaunation, is increasing, and potentially affects plant community structure of diverse grassland ecosystems worldwide. We experimentally simulated defaunation using size-selective fences to progressively exclude large-, medium- and small-sized mammals, and invertebrates from two subalpine vegetation types in the Swiss National Park (SNP): intensively grazed short-grass and moderately grazed tall-grass vegetation. We assessed plant community properties yearly from 2009 to 2013, and examined treatment effects on plant community structure in the two grassland types. In the short-grass vegetation, the exclusion of large mammals increased total plant biomass, while the exclusion of large and medium-sized mammals increased total, grass and forb biomass compared to when all animals had access. These increases became stronger when also invertebrates were excluded. The exclusion of all mammals and invertebrates increased biomass of grasses by 205%, forbs by 100% and total plant biomass by 118% compared to when all animals had access, hence enhancing relative biomass of grasses from 43.6% to 60%, changing plant species composition and lowering richness of forbs by 16%, the number of plant families by 13% and family-level Shannon diversity by 23%. In contrast to these significant community-level responses found in the short-grass vegetation, there was no evidence that the size-selective exclusion of animals altered the plant community structure of the tall-grass vegetation. The contrasting results were due to the difference in plant community composition prior to our experiment, which were related to differences in quantity and quality of forage and in grazing intensities of herbivores between the two grassland types. Synthesis. Our results showed that different-sized animals, in particular large mammals and invertebrates, contributed to maintain the plant community structure in the short-grass vegetation, highlighting the importance of multiple, functionally different animal groups for ecosystem functioning and stability. In contrast to the short-grass vegetation, we could not detect such a top-down control by animals in the tall-grass vegetation. Our results suggest that potential defaunation effects on grassland plant community structure depend on the degree of grazing pressure release and grassland vegetation type.

Exact Spin-Boson-Model Tunneling Dynamics with Time Dependent Variation Matrix Product States (TDVMPS). Barrier height and temperature parameter space

Spin-Boson tunnelling data acquired using the T-TEDOA method for Time-Dependent-Variational-Matrix-Product-States (TDVMPS) accompanying the paper <a href="https://doi.org/10.3389/fchem.2020.600731">https://doi.org/10.3389/fchem.2020.600731</a>.

Floral spectral reflectance data for: Floral color properties of serpentine seep assemblages depend on community size and species richness

Functional traits, particularly those that impact fitness, can shape the ecological and evolutionary relationships among coexisting species of the same trophic level. Thus, examining these traits and properties of their distributions (underdispersion, overdispersion) within communities can provide insights into key ecological interactions (e.g., competition, facilitation) involved in community assembly. For instance, the distribution of floral colors in a community may reflect pollinator-mediated interactions between sympatric plant species, and the phylogenetic distribution of color can inform how evolutionary contingencies can continue to shape extant community assemblages. Additionally, the abundance and species richness of the local habitat may influence the type or strength of ecological interactions among co-occurring species. To evaluate the impact of community size and species richness on mechanisms shaping the distribution of ecologically relevant traits, we examined how floral color (defined by pollinator color vision models) is distributed within co-flowering assemblages. We modeled floral reflectance spectra of 55 co-flowering species using honeybee (Apis mellifera) and syrphid fly (Eristalis tenax) visual systems to assess the distributions of flower color across 14 serpentine seep communities in California. We found that phylogenetic relatedness had little impact on the observed color assemblages. However, smaller seep communities with lower species richness were more overdispersed for flower color than larger, more species-rich communities. Results support that competitive exclusion could be a dominant process shaping the species richness of flower color in smaller-sized communities with lower species richness, but this is less detectable or overwhelmed by other processes at larger, more speciose communities.

Sensitive dependence of ultrarelativistic electron precipitation on EMIC wave frequency

This is the data set used to create the figures in the paper by Lee (2021) in Journal of Geophysical Research as obtained from numerical calculations of equations of motion for ultrarelativistic electrons under electromagnetic ion cyclotron waves in the Earth's inner magnetosphere.

Data for the paper: An energetic view on the geographical dependence of the fast aerosol radiative effects on precipitation

This is the data presented in "An energetic view on the geographical dependence of the fast aerosol radiative effects on precipitation", Dagan et al 2021 JGR. names of files: *aqua* is for aqua-planet simulations, while *AMIP* is for AMIP simulations. *id* is for the simulations with the idealised aerosol perturbations in AMIP type of simulations. sur* are for surface variables, while d_*zonal* and d_mar* present the devotion zonal and  meridional cross-sections as in the paper    The names of the variables are as in the paper.

Data associated to the manuscript "Size-dependence of hydrophobic hydration at electrified gold/water interfaces"

Contains input files and data used to generate the figures of the article: Size-dependence of hydrophobic hydration at electrified gold/water interfaces Alessandra Serva, Mathieu Salanne, Martina Havenith and Simone Pezzotti, arXiv, 2011.08825, 2020 <a href="https://arxiv.org/abs/2011.08825">https://arxiv.org/abs/2011.08825</a> The folder typical_input_files contains typical MetalWalls input files used to perform the simulations. The folder DATA_ASCII_FIGURES contains the processed data used to plot all the figures of the paper.

Data from: Negative density dependence in the mortality and growth of tropical tree seedlings is strong, and primarily caused by fungal pathogens

<ol> <li class="Body">Natural enemies have been implicated as agents of negative density dependence (NDD) in tropical forests, but their relative contributions to NDD, and thus to the maintenance of diversity, are largely unknown.</li> <li class="Body">We monitored the rates of survival and relative growth rates on seedlings for ten years in tropical moist forest in Manu National Park, Peru. We then experimentally manipulated the plots to exclude fungal pathogens, insects, small mammals, and large mammals for an additional 31 months to assess the influence of these natural enemies on density-dependent interactions among tropical seedlings.</li> <li class="Body">Fungal pathogens made the most important contribution to negative density dependence. The application of fungicide led to lower mortality rates, faster growth rates, and decreased species diversity. Other taxa of natural enemies had at most minor effects on seedling performance.</li> <li class="Body"> Synthesis. We conclude that fungal pathogens are the strongest contributors to the widely observed NDD that occurs among seedlings. Moreover, the presence of fungal pathogens augments the species diversity of seedlings, indicating their critical contribution to the maintenance of species coexistence and the structure of tropical tree communities.</li> </ol>

opencc-by-4.0Feb 2021View details →

IDEA Dataset: Inter-parameter DEpendencies in web Apis

Dataset of inter-parameter dependencies found in real-world web APIs.

Short-Tandem-Repeat (STR) marker set for Eurasian lynx for article: Genetic analysis indicates spatial-dependent patterns of sex-biased dispersal in Eurasian lynx in Finland

Conservation and management of large carnivores requires knowledge of female and male dispersal. Such information is crucial to evaluate the population's status and thus management actions. This knowledge is challenging to obtain, often incomplete and contradictory at times. The size of the target population and the methods applied can bias the results. Also, population history and biological or environmental influences can affect dispersal on different scales within a study area. We have genotyped Eurasian lynx (180 males and 102 females, collected 2003-2017) continuously distributed in southern Finland (~23,000 km2) using 21 short tandem repeats (STR) loci and compared statistical genetic tests to infer local and sex-specific dispersal patterns within and across genetic clusters as well as geographic regions. We tested for sex-specific substructure with individual-based Bayesian assignment tests and spatial autocorrelation analyses. Differences between the sexes in genetic differentiation, relatedness, inbreeding, and diversity were analysed using population-based AMOVA, F-statistics, and assignment indices. Our results showed two different genetic clusters that were spatially structured for females but admixed for males. Similarly, spatial autocorrelation and relatedness was significantly higher in females than males. However, we found weaker sex-specific patterns for the Eurasian lynx when the data were separated in three geographical regions than when divided in the two genetic clusters. Overall, our results suggest male-biased dispersal and female philopatry for the Eurasian lynx in Southern Finland. The female genetic structuring increased from west to east within our study area. In addition, detection of male-biased dispersal was dependent on analytical methods utilized, on whether subtle underlying genetic structuring was considered or not, and the choice of population delineation. Conclusively, we suggest using multiple genetic approaches to study sex-biased dispersal in a continuously distributed species in which population delineation is difficult.