cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ns1rn8pzz
title: Data for: Host infection dynamics and disease induced mortality modify species contributions to the environmental reservoir

description: Environmental pathogen reservoirs exist for many globally important
 diseases and can fuel epidemics, influence pathogen evolution, and
 increase the threat of host extinction. Species composition can be an
 important factor that shapes reservoir dynamics and ultimately determines
 the outcome of a disease outbreak. However, disease-induced mortality can
 change species communities, indicating that species responsible for
 environmental reservoir maintenance may change over time. Here we examine
 reservoir dynamics of Pseudogymnoascus destructans, the
 fungal pathogen that causes white-nose syndrome in bats. We quantified
 changes in pathogen shedding, infection prevalence and intensity, host
 abundance, and the subsequent propagule pressure imposed by each species
 over time. We find that highly shedding species are important during
 pathogen invasion, but contribute less over time to environmental
 contamination as they also suffer the greatest declines. Less infected
 species remain more abundant, resulting in equivalent or higher propagule
 pressure. More broadly, we demonstrate that high infection intensity and
 subsequent mortality during disease progression can reduce the
 contributions of high-shedding species to long-term pathogen maintenance.
DOI: 10.5061/dryad.05qfttf85
title: Long-term seedling and small sapling census data from the Barro Colorado Island 50 ha Forest Dynamics Plot, Panama

description: Tropical forests are well known for their high woody plant diversity.
 Processes occurring at early life stages are thought to play a critical
 role in maintaining this high diversity and shaping the composition of
 tropical tree communities. To evaluate hypothesized mechanisms promoting
 tropical tree species coexistence and influencing composition, we
 initiated a census of woody seedlings and small saplings in the permanent
 50-ha Forest Dynamics Plot (FDP) on Barro Colorado Island (BCI), Panama.
 Situated in old-growth, lowland tropical moist forest, the BCI FDP was
 originally established in 1980 to monitor trees and shrubs ≥1 cm diameter
 at 1.3 m above ground (dbh) at ca. 5-yr intervals. However, critical data
 on the dynamics occurring at earlier life stages were initially lacking.
 Therefore, in 2001 we established a 1-m2 seedling plot in the center of
 every 5 x 5 m section of the BCI FDP. All freestanding woody individuals
 ≥20 cm tall and &lt;1 cm dbh (hereafter referred to as seedlings) were
 tagged, mapped, measured, and identified to species in 19,313 1-m2
 seedling plots. Because seedling dynamics are rapid, we censused these
 seedling plots every 1–2 years. Here we present data from the 14 censuses
 of these seedling plots conducted between the initial census in 2001 to
 the most recent census, in 2018. This data set includes nearly 1M
 observations of ~185,000 individuals of &gt;400 tree, shrub, and liana
 species. These data will permit spatially-explicit analyses of seedling
 distributions, recruitment, growth, and survival for hundreds of woody
 plant species. In addition, the data presented here can be linked to
 openly-available, long-term data on the dynamics of trees and shrubs ≥1cm
 dbh in the BCI FDP, as well as existing data sets from the site on
 climate, canopy structure, phylogenetic relatedness, functional traits,
 soil nutrients, and topography.
DOI: 10.5061/dryad.12jm63z3n
title: Synergism between production and soil health through crop diversification, organic amendments and crop protection in wheat-based systems

description: One of the critical challenges in agriculture is enhancing yield without
 compromising its foundation, a healthy environment, and, particularly,
 soils. Hence, there is an urgent need to identify management practices
 that simultaneously support soil health and production and help achieve
 environmentally sound production systems. To investigate how management
 influences production and soil health under realistic agronomic
 conditions, we conducted an on-farm study involving 60 wheat fields
 managed conventionally, under no-till, or organically. We assessed 68
 variables defining management, production, and soil health properties. We
 examined how management systems and individual practices describing crop
 diversification, fertiliser inputs, agrochemical use, and soil disturbance
 influenced production – quantity and quality – and soil health focusing on
 aspects ranging from soil organic matter over soil structure to microbial
 abundance and diversity. Our on-farm comparison showed marked differences
 between soil health and production in the current system: organic
 management resulted in the best overall soil health (+ 47%) but the most
 significant yield gap (- 34%) compared to conventional management. No-till
 systems were generally intermediate, exhibiting a smaller yield gap (-
 17%) and only a marginally improved level of soil health (+ 5%) compared
 to conventional management. Yet, the overlap between management systems in
 production and soil health properties was considerably large. Our results
 further highlight the importance of soil health for productivity by
 revealing positive associations between crop yield and soil health
 properties, particularly under conventional management, whereas factors
 such as weed pressure were more dominant in organic systems. None of the
 three systems showed advantages in supporting production-soil health-based
 multifunctionality. In contrast, a cross-system analysis suggests that
 multifunctional agroecosystems could be achieved through a combination of
 crop diversification and organic amendments with effective crop
 protection. Synthesis and applications: Our on-farm study implies that
 current trade-offs in managing production and soil health could be
 overcome through more balanced systems incorporating conventional and
 alternative approaches. Such multifunctionality supporting systems could
 unlock synergies between vital ecosystem services and help achieve
 productive yet environmentally sound agriculture supported by healthy
 soils.
description: On-farm survey of 60 wheat fields where management, production
 and soil parameters were assessed.
DOI: 10.17882/111834
title: COSTOF2, technical data from SeaMoN West, node of the EMSO-Azores observatory, 2024-2025

description: This dataset contains the technical log that has been done with the COSTOF2 n° 006 (COmmunication and STOrage Front-end 2), the SeaMoN West datalogger unit. This station is dedicated to geological observations on EMSO Azores.
DOI: 10.5061/dryad.9kd51c5pm
title: Factors influencing distribution of the endangered Hispid hare in Babai valley, Bardiya National Park, Nepal

description: The hispid hare, Caprolagus hispidus, is an endangered elusive mammal that
 dwells in the tall grassland of the Himalayan foothills across Nepal,
 India, Bhutan, and Bangladesh. The species has faced serious threats from
 anthropogenic activity and seasonal flooding in the various protected
 areas, leading to population decline. Most work on the species has been
 conducted in the grasslands of Shuklaphanta National Park, but only one
 study has been conducted in Bardia National Park over the past decade.
 Here, we aim to evaluate current distribution pattern of the hispid hare
 in the Babai Valley of Bardia National Park, identify the environmental
 factors that influenced distribution, and assess existing threats to the
 species. We conducted a field survey in December 2020 before grassland
 burn and May-June 2021, after a grassland burn. A total of 428 transects
 (50 m * 2 m) in a 1 km x 1 km grid were conducted across 1048.55 hectares
 of grassland in the valley. Hispid hare pellets were recorded in the
 grassland of Kalinara, Guthi, Sano Shree Phanta, Chitaale Phanta,
 Ratomate, Rhino Release Site (Babai), and Mulghat (Chepang) in Bardia
 National Park. The distribution pattern of the pellets was found to be
 clumped in the Babai Valley. We recorded higher pellet density
 post-grassland burn than the pre-burn, which indicated higher population
 density in summer in comparison to winter. The best-fit model suggested
 that grass density, grassland burning, and annual precipitation have
 influenced the distribution of hispid hare. Results suggest the species
 prefers the riverbank in winter but short grassland in summer, while the
 forest and edge between the grassland and forest were avoided. The
 grassland patches in Babai (preferred hispid hare habitat) comprised 14
 grass species in Babai dominated by Imperata cylindrica, Schharum
 spontaneum, and Cynodon doctylon. Seasonal grassland burn, summer flood,
 invasive species, vegetation succession, and predators were major threats
 in the field. Our findings can help park officials in the management and
 restoration of degraded grassland of the park and guide the developing
 management and species action plan. We recommend conservation efforts
 focus on protecting and managing grasslands that provide suitable habitat
 for the hispid hare.
description: Data data were collected in the pre and post-grassland burning in
 the park. All the data were collected in transects of the grid-based
 survey. 
description: All these data were processed in Excel, and statistical analyses
 were performed in logistic regression in R programming.
DOI: 10.5061/dryad.zs7h44jfj
title: Supporting information for: When to shed? Patterns and drivers of time to first ecdysis in snakes

description: Time from birth or hatching to the first shed (postnatal ecdysis) in
 snakes ranges from about an hour to several weeks depending upon the
 species. We assessed patterns in time to postnatal ecdysis in 102 snake
 species for which we could source appropriate information, covering 2.6%
 of all extant snake species, and related measures to various biological
 traits. Reconstruction revealed ancestral time to postnatal ecdysis to be
 eleven days. Since time to postnatal ecdysis can be shorter or longer than
 the ancestral state, we argue that there are several competing drivers for
 time to postnatal ecdysis. A reduced time to postnatal ecdysis has evolved
 in several lineages, commonly in ambush-foraging, viviparous vipers, while
 extended time to postnatal ecdysis is associated with oviparous species
 with maternal care. Of central importance is the impact of postnatal
 ecdysis on the scent levels of neonates, resulting in a reduction of time
 to postnatal ecdysis in chemically cryptic species, while the pivotal role
 of scent in mother-neonate recognition has resulted in the retention or
 extension of time to postnatal ecdysis. We showed that postnatal ecdysis
 improves chemical crypsis. The patterns revealed in this study suggest
 that measures of time to postnatal ecdysis can provide insights into the
 biology of snakes and be used as an indicator of certain life history
 traits.
description: Records of time to PNE were collected for snakes through data
 mining of the scientific literature and consultation with herpetologists
 and snake breeders. Records were mostly reported as a range of days to PNE
 observed within and across clutches or litters from one or more sources.
 The average number of days to PNE was calculated by averaging the time to
 PNE for each record for each species. Records of time
 to PNE for 102 Afrophidia species (92 Caenophidia and ten Henophidia
 species, Harrington & Reeder, 2017) were gathered, of which 17
 were collected through personal communication or unpublished data and 85
 based on available literature (S1 Table). A frequency histogram showing
 the distribution of records of time to PNE was trimodal (Figure 1).
 However, a high proportion of species were reported to shed almost
 immediately after birth and this subset was considered to be a different
 category to those that shed during subsequent days. Thus, the species were
 assigned to four categories: immediate PNE (≤1 day); early PNE (2–4 days);
 standard PNE (5–17 days); and extended PNE (&gt;17 days).
 Information related to several life history traits was collected
 from the literature and online resources (S2 Table). These included
 (categories defined below): foraging mode, body pattern, parity mode,
 maternal care, biogeographic region, and subfamily. Foraging mode was
 categorised as either ambush or active foraging.
description: Microsoft Excel, Microsoft Word.
DOI: 10.5281/zenodo.18403889
title: Data for Figure 3 of "Modular TM1 mixing in light of precision measurement in JUNO"

description: Numerical data supporting Figure 3 in the manuscript.
DOI: 10.5061/dryad.x95x69pqn
title: Dung nutrient data of rabbit, fallow deer, horse, cow, and European bison

description: Dung samples of European bison (Bison bonasus L.), cow (Bos taurus L.),
 fallow deer (Dama dama L.), horse (Equus ferus caballus L.), and rabbit
 (Oryctolagus cuniculus L.) were collected at the National Park
 Zuid-Kennemerland, the Netherlands (52.3961°N, 4.5921°E) on February 25th,
 2020. The fresh herbivore dung was placed in the oven at 70 ℃ for 72 h for
 drying to measure the moisture and then ground for the measurement of the
 nutrients (Nitrogen, Carbon, Phosphorus, C:N, N:P). Total C concentrations
 were analyzed with a dry combustion analyzer (LECO CNS-2000). Total N
 concentrations were measured on an elemental analyzer (Thermo EA Flash
 1112). Total P concentrations were analyzed using a modification of the
 combustion and hot HCl extraction procedure. Differences among species in
 dung nutrients were determined using a one-way ANOVA and Scheffe test in
 the agricolae package in R. 
description: # Dung nutrient data of rabbit, fallow deer, horse, cow and European bison
 [https://doi.org/10.5061/dryad.x95x69pqn](https://doi.org/10.5061/dryad.x95x69pqn) Nitrogen, Carbon, Phosphorus, C:N, N:P of the dung nutrient composition of five herbivore species living in the European coastal dune ecosystem. ## Description of the data structure This is a dataframe with 7 columns (moisture, TC, TN, TP, C:N, N:P, herbivore species) and 20 rows (each herbivore species has four independent individual samples). Moisture's unit is (%); TC, TN and TP's units are (g/kg). This dataframe only includes the original nutrient data without statistical analysis, if you need the final analyzed data please read the article "**Microbial community composition in the dung of five sympatric European herbivore species**" published in *Ecology and Evolution*, or conduct the R codes below in your PC. ## R Code setwd("C:/Users/...") library(agricolae) ## for scheffe.test() physico &lt;- read.csv("physicochemical characteristics.csv") run_analysis &lt;- function(data, variable) { formula &lt;- as.formula(paste(variable, "~ herbivore.species", sep = "")) model &lt;- aov(formula, data = data) summary(model) scheffe.test(model, "herbivore.species") } variables &lt;- c("moisture", "tn", "tc", "tp", "c.n", "n.p") results &lt;- lapply(variables, function(var) { cat("Analyzing", var, "\n") run_analysis(physico, var) }) results
DOI: 10.5281/zenodo.18403888
title: Data for Figure 3 of "Modular TM1 mixing in light of precision measurement in JUNO"

description: Numerical data supporting Figure 3 in the manuscript.
DOI: 10.5061/dryad.ffbg79d0s
title: Data for: A size-based perspective on the decoupling between compositional and functional changes in planktonic communities

description: Recent studies have shown a decoupling in the way community composition
 and functions respond to environmental changes. A common pattern observed
 is that aggregated functions at the community level are more stable than
 community composition, which is likely the result of functional
 compensatory dynamics driven by interspecific differences in response to
 environmental change. However, the mechanisms by which these patterns
 emerge remain largely unexplored. Here, we investigated in a mesocosm
 experiment for four weeks the compositional and functional responses of
 edible phytoplankton (&lt;64µm) and cladoceran zooplankton communities
 to climate warming (a constant increase of +3.5°C plus heat wave) and
 eutrophication (nutrient additions) from a size-based perspective. Our
 results show that warming increases small-sized taxa and decreases
 large-sized taxa within both phytoplankton and zooplankton community
 composition. We found that such opposite responses of different-sized taxa
 contributed to the stability of planktonic community functions and thereby
 resulted in a decoupling between compositional and functional changes. We
 also found that nutrient additions increased the abundance of all-sized
 algal taxa, while phytoplankton community function remained stable.
 Nutrient additions did not alter the zooplankton community, neither
 compositionally nor functionally. Under the combined stress of warming and
 nutrient additions, the compositional and functional responses of
 planktonic communities were mainly driven by warming. In a broader
 perspective, our findings reveal a size-dependent compensation mechanism
 and suggest that functional stability relies on compensatory effects among
 different-sized taxa, and it is therefore important that communities host
 a large range of taxa differing in size to withstand an increasingly more
 variable environment in the future.
description: Please contact Konghao Zhu zhukonghao@ihb.ac.cn with any questions.
DOI: 10.5281/zenodo.18385612
title: QCell: Comprehensive Quantum-Mechanical Dataset Spanning Diverse Biomolecular Fragments

description: The QCell dataset provides quantum-mechanical reference data for lipids, sugars, nucleic acids, solvated ions, water, and molecular dimers (sourced from DES370K), computed at the PBE0+MBD(-NL) level of theory using the FHI-aims code. Each HDF5 archive contains atomic structures and a set of associated energy, force, and electronic properties.  Helper script is provided to convert the data into extxyz format. Additionally, an archive containing the preconverted extxyz files with the most relevant properties is included. An example of the FHI-aims control.in settings file is also provided.

More details are available in the preprint: https://arxiv.org/abs/2510.09939. Pre-processing scripts are available in the GitHub repository: https://github.com/general-molecular-simulations/qcell.
DOI: 10.5061/dryad.r4xgxd2k4
title: Selection on weapon allometry in the wild

description: Allometry is the scaling relationship between a trait and body size. This
 relationship can often explain considerable morphological variation within
 and among species. Nevertheless, much remains unknown about the factors
 that underlie allometric patterns. For example, when different allometric
 relationships are observed amongst closely related species, these
 differences are regularly considered to be products of selection. However,
 directional selection on allometry (particularly the slope) has rarely
 been tested and observed in natural populations. Here, we investigate
 selection on the scaling relationship between weapon size and body size
 (i.e., weapon allometry) in a wild population of giant mesquite bugs,
 Pachylis neocalifornicus (previously Thasus neocalifornicus). Males in
 this species use their weapons (enlarged femurs) to compete with one
 another over access to resources and females. We found that large males
 with relatively large weapons successfully secured access to mates.
 However, we also found that small males with relatively small weapons
 could access mates as well. These two patterns together can increase the
 allometric slope of the sexually selected weapon, suggesting a
 straightforward process by which the allometric slope can evolve.
DOI: 10.5061/dryad.xsj3tx9mt
title: Recurring bleaching events disrupt the spatial properties of coral reef benthic communities across scales

description: Marine heatwaves are causing recurring coral bleaching events on tropical
 reefs that are driving ecosystem change. Yet little is known about how
 bleaching and subsequent coral mortality impacts the spatial properties of
 tropical seascapes, such as patterns of organism spatial clustering and
 heterogeneity across scales. Changes in these spatial properties can offer
 insight into ecosystem recovery potential following disturbance. Here we
 repeatedly quantified coral reef benthic spatial properties around the
 circumference of an uninhabited tropical island in the central Pacific
 over a 9-year period that included a minor and severe marine heatwave.
 Benthic communities showed increased biotic homogenisation following both
 minor and mass bleaching, becoming more taxonomically similar with less
 diverse intra-island community composition. Hard coral cover, which was
 highly spatially clustered around the island prior to bleaching, became
 less spatially clustered following minor bleaching and was indiscernible
 from a random distribution across all scales (100–2000 m) following mass
 bleaching. Interestingly, the reduced degree of hard coral cover spatial
 clustering was already evident by the onset of mass bleaching and before
 any dramatic wholesale loss in island-mean coral cover occurred.
 Reductions in hard coral spatial clustering may therefore offer an early
 indication of the ecosystem becoming degraded prior to mass coral
 mortality. In contrast, the spatial clustering of competitive fleshy
 macroalgae remained unchanged through both bleaching events, while
 crustose coralline algae and fleshy turf algae became more spatially
 clustered at larger scales (200–700 m) following mass bleaching. Overall,
 benthic community spatial patterning became less predictable following
 bleaching and was no longer reflective of gradients in long-term
 environmental drivers that typically structure these remote reefs. Our
 findings provide novel insights into how climate-driven marine heatwaves
 can impact the spatial properties of coral reef communities over multiple
 scales.