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openCustomJan 2020View details →

Effects of ribbed mussel aggregation size on marsh invertebrate community structure and multiple eocsystem functions

Ribbed mussels (Geukensia demissa) were added in aggregations containing 0, 1, 3, 5, 10, 20, 40 or 80 mussels (N=3 replicates per aggregation size) in Spring of 2012 in a high marsh platform at the Airport Marsh on Sapelo Island, GA. In summer of 2013, we measured the response of invertebrate communities and six ecosystem functions. Specifically, we counted the number of Littoraria irrorata, Sesarma reticulatum burrows, Uca pugnax burrows (those > and <5mm in diameter were counted separately), and mud crab (Eurythium limosum and Panopeus herbstii) in 50cm x 50cm sampling frames. And, we measured aboveground cordgrass biomass, benthic algae biomass, invertebrate biomass, decomposition rate, infiltration rate, and soil accretion in the same size sampling frames in August of 2013.

openCustomJan 2020View details →

Effects of marsh periwinkle (Littoraria irrorata) size and density on cordgrass (Spartina aterniflora) biomass and dead standing material

Marsh periwinkles (Littoraria irrorata) are common in southeastern US salt marshes, including those on Sapelo Island, GA. They are known to affect the productivity of cordgrss (Spartina alterniflora) and also contribute to its decomposition following senescence. The population struture of Littoraria, in terms of the size and densities of individuals, varies widely in space and time. No previous experiments have, however, attempted to manipulate the density and body size of populations of Littoraria and assessd the response of Spartina. We perforned such an experiment in Airport Marsh on Sapelo Island, using small experimental enclosures and measured Spartina biomass and dead standing material after 3 months (mid July - mid Oct, 2012). We assessed response variables by removing all Spartina material from plots before seperating and drying them in the lab.

openCustomJan 2020View details →

Experimental manipulation of predatory crab species identity (Panopeus obesus vs. Eurytium limosum) and size-structure and assessment of effects on invertebrate densities, sediment properties and plant biomass.

Predatory mud crabs (Panopeus obesus and Eurytium limosum) are two of the main resident infaunal predators in southeastern US salt marshes. Little is known, however, about their effects on important prey species, or their influences on sediment or plant properties. These influences are likely to be dependent on the identity of species and the size-stucture of the population. We therefore manipulated the species identity (Panopeus or Eurtium) and size-structure. The size-structure treatrment had four levels: small [9 individuals, each 18-22mm carapace diameter], medium [6 ind. 24 -28mm], large [3 ind. 32-36mm], mixed (3 small, 2 medium, 1 large, all within same cage). The numbers of crabs in each size-structure treatment were chosen to capture natural size-abundance relationships. The treatments were maintained in experimental cages (70 x 70 x 100 cm, length, width, height) in the mid-Spartina zone at Dean Creek, Sapelo Island, GA. We maintained the treatments over 4 months (July - October 2010), before assessing impacts on prey densitities (mud fiddler crabs, ribbed mussels and marsh periwinkles), and ecosystem properties (aboveground plant biomass, sediment redox potential, sediment water content).

openCC (other)Oct 2024View details →

Effects of long-term nitrogen addition on Solidago altissima stem morphology, size, and herbivory at Kellogg Biological Station 2016-2022

We surveyed naturally occurring tall goldenrod (Solidago altissima) plants in a long-term nitrogen addition field experiment at the Kellogg Biological Station's T7 untilled succession plots in the Main Cropping System Experiment (https://lter.kbs.msu.edu/research/long-term-experiments/main-cropping-system-experiment/). We collected data on the defensive stem nodding morph (which helps plants evade apex-galling herbivores) and presence of galls in 2016, 2021, and 2022.

opencc-by-4.0Nov 2018View details →

Integrated pedagogical methods effectiveness in Physics' preliminary undergraduate education within the context of large size lectures.

Three files relating the first round of analysis testing active methods for large size lectures. The Presentation including the research design, methods, main results in synthesis is available here: https://www.researchgate.net/project/Getting-started-with-Physics-preliminary-undergraduated-strategies/update/5a44cac6b53d2f0bba475104 2- Dataset on Students' Learning Outcomes. Dataset adopted in the first experimental round. The dataset includes data used for the first type of analysis (learning outcomes) carried out for the ICEM2017 Conference presentation "Integrating MOOCs in Physics preliminary undergraduate education: beyond large size lectures". The data includes the results of the initial, baseline Test, the final Test, and two other variables that could be used to analyse covariance: Sex and Type of Group (Large/Small). 3- Dataset on Students' Opinion. Dataset adopted in the first experimental round. The dataset includes data used for the second type of analysis (students' opinion) carried out for the ICEM2017 Conference presentation "Integrating MOOCs in Physics preliminary undergraduate education: beyond large size lectures". The data includes the results of a final questionnaire gathering the students opinion on the four types of pedagogical factors affecting their experience within a large size lecture: MOOCs, Active Learning, Self-Assessment tools, Tutors’ guidance. 4- Codes and analysis adopted in the first experimental round. The Document includes two analysis carried on for the ICEM2017 Conference presentation "Integrating MOOCs in Physics preliminary undergraduate education: beyond large size lectures". These are: Test (measuring students' knowledge on the subject taught) and Students' Opinion/satisfaction on the several pedagogical methods adopted along the experimental intervention.

opencc-by-4.0Feb 2019View details →

Group size effects and critical mass in public goods games

<pre>This dataset accompanies the paper "Group size effects and critical mass in public goods games", https://doi.org/10.1038/s41598-019-41988-3 It records participant decisions in a set of binary one-shot Public Goods Games with curvilinear payoff function (see details in the paper). The explanation of the data fields is present also in the metadata of the file: # Cooperation: 0=defection, 1=cooperation, 99=the participant did not make the decision # Group: interacting group size (N) # Treatment: Critical Mass Nc # dropout: 1=the participant did not make the decision, 0=the participant made the decision # incompleted: 1=participant did not make all the decisions of the experiment; 0=participant did made all the decisions of the experiment # female: 1=female, 0=male </pre>

opencc-by-4.0Oct 2024View details →

Size-dependent effects of oxo-degradable plastic contamination on soil quality and Zea mays L. performance

Agricultural plastic mulch films represent a significant source of microplastic contamination in soils, raising concerns about soil health and food security. Oxo-degradable plastics (ODPs) have emerged as a potentially more eco-friendly alternative to conventional plastic mulch films, however, uncertainty remains around the degradation rate of ODPs in soil and their impacts on soil quality and crop health. Using a controlled mesocosm experiment, we evaluated the behaviour and impact of different concentrations of oxo-biodegradable macro- (>10 mm) or micro-plastic (<5 mm) (0.01, 0.1, 1, and 10% w/w) on the performance of Zea mays L. grown in an agricultural soil over a 6-week period. Contrary to expectation, no major fragmentation or degradation of ODP was observed during the experimental period, however, FTIR revealed the formation of carbonyl groups indicative of oxidation. Overall, our results showed that typical levels of plastic contamination (0.01% w/w) had very little effect on soil physicochemical properties, microbial activity or plant performance. However, higher levels of plastic contamination resulted in significant changes in soil pH, EC, NO3-, bulk density, and soil moisture. At extreme plastic loading rates (10% Can you write w/w), both micro- and macro-sized ODPs caused significant reductions in plant height and foliar chlorophyll content, with microplastic treatments showing consistently greater effects than macroplastics. None of the plastic loading rates had an effect on shoot and root biomass or soil NH4+ and P concentrations or microbial community structure in comparison to the unamended controls. Our findings indicate that at realistic field concentrations, ODPs are likely to have little effect on agroecosystem functioning but that they may persist in soil for long periods of time leading to their progressive accumulation in agricultural soils if used over repeated cropping cycles. Further research is needed to evaluate the longer-term impacts of ODPs on soil quality and crop health under field conditions.

opencc-by-4.0May 2023View details →

Supplementary Material of the Manuscript: "The effects of blank size and knapping strategy on the estimation of core's reduction intensity"

This repository hosts the R-markdown and dataset that allow reproducibility and replicability of the statistical analyses implemented in the paper: Lombao, D., Cueva-Temprana, A., Rabuñal, J.R., Morales, J.I., Mosquera, M.  The effects of blank size and knapping strategy on the estimation of core’s reduction intensity. Archaeol Anthropol Sci 11, 5445–5461 (2019). https://doi.org/10.1007/s12520-019-00879-4 For further information, please open first the readme.txt. document.

opencc-by-4.0May 2023View details →

Dataset of the article "A new and almost perfectly accurate approximation of the eigenvalue effective population size of a dioecious population: comparisons with other estimates and detailed proofs"

Dataset of the article "A new and almost perfectly accurate approximation of the eigenvalue effective population size of a dioecious population: comparisons with other estimates and detailed proofs"  (https://doi.org/10.5281/zenodo.7927968), recommended by PCI Evol Biol (https://evolbiol.peercommunityin.org/articles/rec?id=651)

edi44/100

PSC01 Exploring effects on stream ecosystem properties by two size classes of prairie stream cyprinids

Losses in freshwater fish diversity might produce a loss in important ecological services provided by fishes in particular habitats. An important gap in our understanding of ecosystem services by fishes is the influence of individuals from different size classes, which is predicted based on known ontogenetic shifts in habitat and diet. I used twenty experimental stream mesocosms located on Konza Prairie Biological Station (KPBS), KS, USA to assess the influence of fish size on ecosystem properties. Mesocosms included two macrohabitats: one riffle upstream from one pool filled with consistent pebble and gravel substrate. There were four experimental and one control treatment, each replicated four times (N = 20). I used two size classes of Central Stonerollers (Campostoma anomalum) and Southern Redbelly Dace (Chrosomus erythrogaster). Five ecosystem properties were assessed: algal filament length (cm), benthic chlorophyll a (µg/cm2), benthic organic matter (g/m2), macroinvertebrate biomass (g/m2), and stream metabolism (g O2/m2/day1). Size structure of fish populations affected some, but not all, ecosystem properties and these effects were dependent upon species identity. Size structure of both species had effects on algal filament lengths where stonerollers of both size classes reduced algal filaments, but only small redbelly dace kept filaments short. A better understanding of the relationship between these prairie stream minnows and their small stream habitats could be useful to both predict changes in stream properties if species are lost or size structure shifts, and to redbelly dace populations, a Species In Need of Conservation.

openCC0Jul 2023View details →

opencc-by-4.0Dec 2020View details →

Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees

Data and results of the paper "Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees". - data_table_species.csv: contains life-history and geographical range descriptors, terminal branch length and genomic estimated values for each substitution category, for each species in the dataset. Contains results obtained with both the complete data set and the subsampled dataset with 88 species. - data_table_genes.csv: contains values of substitution count that are sums of the values obtained for every species in the alignment. Also contains the results of HyPhy RELAX analyses for each alignment. - data_table_genes_species.csv: contains estimated values for each substitution category for each species in each alignment. Contains results obtained with both the complete data set and the subsampled dataset with 88 species.

openmit-licenseNov 2023View details →

Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex

When using the data or code from this manuscript, please cite it as:Leiva FP, Santos M, Rezende E, & Verberk WCEP. 2021. Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex. Zenodo. <a href="https://doi.org/10.5281/zenodo.5120028">https://doi.org/10.5281/zenodo.5120028</a>.

opencc-zeroJan 2024View details →

Data from: Promoting success in thin layer sediment placement: effects of sediment grain size and amendments on salt marsh plant growth and greenhouse gas exchange

Thin layer sediment placement (TLP) is a method to mitigate factors resulting in loss of elevation and severe alteration of hydrology, such as sea level rise and anthropogenic modifications, and prolong the lifespan of drowning salt marshes. However, TLP success may vary due to plant stress associated with reductions in nutrient availability and hydrologic flushing or through the creation of acid sulfate soils. This study examined the influence of sediment grain size and soil amendments on plant growth, soil and porewater characteristics, and greenhouse gas exchange for three key US salt marsh plants: Spartina alterniflora, Spartina patens, and Salicornia pacifica. We found that bioavailable nitrogen concentrations (measured as extractable NH4+-N) and porewater pH and salinity were found to have an inverse relationship with grain size, while soil redox was more reducing in finer sediments. This suggests that utilizing finer sediments in TLP projects will result in a more reduced environment with higher nutrient availability, while larger grain-sized sediments will be better flushed and oxidized. We further found that grain size had a significant effect on vegetation biomass allocation and rates of gas exchange, although these effects were species-specific. We found that soil amendments (biochar and compost) did not subsidize plant growth but were associated with increases in soil respiration and methane emissions. Biochar amendments were additionally ineffective in ameliorating acid sulfate conditions. This study uncovers complex interactions between sediment type and vegetation, emphasizing limitations of soil amendments. The findings aid restoration project managers in making informed decisions regarding sediment type, target vegetation, and soil amendments for successful TLP projects.

opencc-zeroJan 2024View details →

Data for: Effective population size mediates the impact of pollination services on pollen limitation

Inadequate pollen receipt limits flowering plant reproduction worldwide. Ecological causes of pollen limitation ('PL'), like pollinator scarcity and low plant abundance, have been a primary focus of research. The genetic diversity of plant populations could impact both quantity and quality components of PL in concert with ecological factors, yet empirical examples are lacking. We evaluated joint effects of ecological factors (flower abundance, pollinator visitation) and genetic effective population size (NE) on PL across 13 populations of a common herb. We used a histological approach with 5504 styles from 1137 flowers to separate quantity and quality components of PL, and link these to reproductive output. NE and pollinator visitation interacted to shape PL, but NE had stronger direct effects. Effectively smaller populations experienced stronger quantity PL, and controlled crosses in a pollinator-free environment revealed that pollen quantity was an intrinsic population-level attribute that increased with NE. Pollinator visitation enhanced pollen quality, but only in effectively larger populations. Quantity and quality PL negatively impacted fruit and seed set, respectively. Results highlight that PL is dictated by plant population genetic diversity in addition to commonly evaluated ecological factors. Efforts to support pollinators will only enhance plant reproduction in genetically diverse plant populations.

opencc-zeroMar 2024View details →

Data for: Harvest and decimation affect genetic drift and the effective population size in wild reindeer

Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long-term viability. The effective population size (Ne) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate Ne of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The Ne/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14-year period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2 % in 2005-2018 and 44.8 % in 2021). Increased harvest rates decreased Ne in the simulations, but less sex-biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased Ne. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long-term genetic viability of wildlife populations subject to disease will also depend on the population impacts of the disease and how these interact with management actions.

opencc-zeroMar 2022View details →

Datasets and R code for: Brood as booty: The effect of colony size and resource value in social insect contests

From the Manuscript: Animals engage in contests for access to resources like food, mates, and space. Intergroup contests between groups of organisms have received little attention, and it remains unresolved what information groups might use collectively to make contest decisions. We staged whole-colony contests using ant colonies (Temnothorax rugatulus), which perceive conspecific colonies as both a threat and resource from which to steal brood. We recorded individual behaviors and used demographic characteristics as proxies for resource value (number of brood items) and fighting ability (number of workers). We found that ants altered their fighting effort depending on the relative number of workers of their opponent. While the proximate mechanism for this ability remains uncertain, we found that colonies increased fighting when their opponent had relatively more brood, but not if opposing colonies had relatively many more workers. This suggests that ant colonies can use information about opposing colonies that shapes contest strategies. Further, the behavior of opposing colonies were strongly correlated with each other despite colony size differences ranging from 4-51%, consistent with the hypothesis that colonies can use opponent information. The behavior of a distributed, collective system of many individuals, like a eusocial insect colony, thus fits several predictions of contest models designed for individuals if we consider the gain and loss of worker ants analogous to energetic costs accrued during typical dyadic contests.

opencc-by-4.0Apr 2022View details →

Dataset and R code: Effects of temperature and air pollution on emergency ambulance dispatches: a time series analysis in a medium-sized city in Germany

Dataset and R script to replicate results in the manuscript "Effects of temperature and air pollution on emergency ambulance dispatches: a time series analysis in a medium-sized city in Germany", currently under review.

opencc-zeroApr 2022View details →

Negotiating mutualism: a locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts

In mutualisms, variation at genes determining partner fitness provides the raw material upon which coevolutionary selection acts, setting the dynamics and pace of coevolution. However, we know little about variation in the effects of genes that underlie symbiotic fitness in natural mutualist populations. In some species of legumes that form root nodule symbioses with nitrogen-fixing rhizobial bacteria, hosts secrete nodule-specific cysteine-rich (NCR) peptides that cause rhizobia to differentiate in the nodule environment. However, rhizobia can cleave NCR peptides through the expression of genes like the plasmid-borne Host range restriction peptidase (hrrP), whose product degrades target NCR peptides. Although hrrP activity can confer host exploitation by depressing host fitness and enhancing symbiont fitness, the effects of hrrP on symbiosis phenotypes depend strongly on the genotypes of the interacting partners. However, the effects of hrrP have yet to be characterized in a natural population context, so its contribution to variation in wild mutualist populations is unknown. To understand the distribution of effects of hrrP in wild rhizobia, we measured mutualism phenotypes conferred by hrrP in 12 wild Ensifer medicae strains. To evaluate context dependency of hrrP effects, we compared hrrP effects across two Medicago polymorpha host genotypes and across two experimental years for five E. medicae strains. We show for the first time in a natural population context that hrrP has a wide distribution of effect sizes for many mutualism traits, ranging from strongly positive to strongly negative. Furthermore, we show that hrrP effect size varies across both host genotype and experiment year, suggesting that researchers should be cautious about extrapolating the role of genes in natural populations from controlled laboratory studies of single genetic variants.