cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18353694
title: Global multi-crop agricultural trial data supported by citizen science

description: Global multi-crop agricultural trial data supported by citizen science

The triadic comparison of technologies (tricot) is a citizen science approach for testing technology options in their target environments, which has been applied to on-farm testing of crop varieties. ‘Triadic’ refers to the sets of three technology options that are compared by each participant. In the approach, participants are invited to test an anonymous set of three technologies (out of a larger number, generally between 5 to 20) randomly assigned. Between 2011 and 2025 the tricot approach was applied in more than 25 countries across Africa, Asia, Europe and Latin America with more than 30 crops.tricot data v1

This release consolidates standardized trial outputs from participatory on-farm evaluations implemented through the tricot (triadic comparison of technology options) approach. This dataset supports re-use for variety evaluation, genotype-by-environment research, target population of environments (TPE) analyses, farmer preference modeling, and broader work on data-driven crop improvement and climate adaptation.

Number of new studies: 41 Countries covered: 5 (BJ, ML, TZ, NG, RW)Crops covered: 10 Total participant observations added: ~12,355 participants
DOI: 10.5061/dryad.gr61mv4
title: Data from: A residence time theory for biodiversity

description: From microorganisms to the largest macroorganisms, much of Earth’s
 biodiversity is subject to forces of physical turnover. Residence time is
 the ratio of an ecosystem’s size to its rate of flow and provides a means
 for understanding the influence of physical turnover on biological
 systems. Despite its use across scientific disciplines, residence time has
 not been integrated into the broader understanding of biodiversity, life
 history, and the assembly of ecological communities. Here, we propose a
 residence time theory for the growth, activity, abundance, and diversity
 of traits and taxa in complex ecological systems. Using thousands of
 stochastic individual-based models to simulate energetically constrained
 life history processes, we show that our predictions are conceptually
 sound, mutually compatible, and support ecological relationships that
 underpin much of biodiversity theory. We discuss the importance of
 residence time across the ecological hierarchy and propose how residence
 time can be integrated into theories ranging from population genetics to
 macroecology.
description: Simulation data from
 residence time modelingThis compressed file is
 a directory that contains four files, each containing data from 10,000
 individual-based models (IBMs). The file active.RAD-Data.csv contains
 simulated species rank-abundance data from the active portions of
 communities. The file RAD-Data.csv contains simulated species
 rank-abundance data from entire communities (active + dormant). Finally,
 the SimData.csv file contains all other simulated data resulting from
 residence time IBMs and needed to reproduce all figures for the associated
 manuscript.data.zip
DOI: 10.5281/zenodo.17112491
title: Global multi-crop agricultural trial data supported by citizen science

description: Global multi-crop agricultural trial data supported by citizen science

The triadic comparison of technologies (tricot) is a citizen science approach for testing technology options in their target environments, which has been applied to on-farm testing of crop varieties. ‘Triadic’ refers to the sets of three technology options that are compared by each participant. In the approach, participants are invited to test an anonymous set of three technologies (out of a larger number, generally between 5 to 20) randomly assigned. Between 2011 and 2025 the tricot approach was applied in more than 25 countries across Africa, Asia, Europe and Latin America with more than 30 crops.tricot data v1

This release consolidates standardized trial outputs from participatory on-farm evaluations implemented through the tricot (triadic comparison of technology options) approach. This dataset supports re-use for variety evaluation, genotype-by-environment research, target population of environments (TPE) analyses, farmer preference modeling, and broader work on data-driven crop improvement and climate adaptation.

Number of new studies: 41 Countries covered: 5 (BJ, ML, TZ, NG, RW)Crops covered: 10 Total participant observations added: ~12,355 participants
DOI: 10.5061/dryad.30326v6
title: Data from: The molecular biogeography of the Indo-Pacific: testing hypotheses with multispecies genetic patterns

description: Aim: To test hypothesized biogeographic partitions of the tropical
 Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate
 the strength and nature of barriers emerging from this test. Location: The
 Indo-Pacific Ocean. Time Period: Pliocene through the Holocene. Major Taxa
 Studied: 56 marine species. Methods: We tested eight biogeographic
 hypotheses for partitioning of the Indo-Pacific using a novel modification
 to analysis of molecular variance. Putative barriers to gene flow emerging
 from this analysis were evaluated for pairwise ΦST, and these ΦST
 distributions were compared to distributions from randomized datasets and
 simple coalescent simulations of vicariance arising from the Last Glacial
 Maximum. We then weighed the relative contribution of distance vs.
 environmental or geographical barriers to pairwise ΦST with a
 distance-based redundancy analysis (dbRDA). Results: We observed a
 diversity of outcomes, although the majority of species fit a few broad
 biogeographic regions. Repeated coalescent simulation of a simple
 vicariance model yielded a wide distribution of pairwise ΦST that was very
 similar to empirical distributions observed across five putative barriers
 to gene flow. Three of these barriers had median ΦST that were
 significantly larger than random expectation. Only 21 of 52 species
 analyzed with dbRDA rejected the null model. Among these, 15 had overwater
 distance as a significant predictor of pairwise ΦST, while 11 were
 significant for geographical or environmental barriers other than
 distance. Main Conclusions: Although there is support for three previously
 described barriers, phylogeographic discordance in the Indo-Pacific oceans
 indicates incongruity between processes shaping the distributions of
 diversity at the species and population levels. Among the many possible
 causes of this incongruity, genetic drift provides the most compelling
 explanation: given massive effective population sizes of Indo-Pacific
 species, even hard vicariance for tens of thousands of years can yield ΦST
 values that range from 0 to nearly 0.5.
description: Indo-Pacific mtDNA
 database 2019_01_08This is the full
 database that we used in the paper. Sequence data are contained in the
 "sequence" field, and are aligned within each species. The
 bioregion that each sample fell into under the various regionalizations
 are in columns named for that regionalization. Most other columns are self
 explanatory, or are defined as part of DarwinCore:
 https://dwc.tdwg.org/terms/. All of these data and metadata are also
 available in GeOMe -https://geome-db.orgindo_pacific_mtDNA_database_2019_01_08.csvIPDB_UPPER-OverWater_LOWER-EuclideanThese are the overwater and Euclidean distances that were calculated for dbRDA analysis. Methods can be found in the readme file.
DOI: 10.5061/dryad.950km35
title: Data from: Earthworms and cadmium – heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils?

description: Preservation of the soil resources stability is of high importance for
 ecosystems, particularly in the current era of environmental change, which
 presents a severe pollution burden (e.g. by heavy metals) to soil fauna.
 Gut microbiomes are becoming recognized as important players in organism
 health, with comprehension of their perturbations in the polluted
 environment offering new insights into the nature and extent of heavy
 metal effects on the health of soil biota. Our aim was to investigate the
 effect of environmentally relevant heavy metal concentrations of cadmium
 (Cd) on the earthworm (Lumbricus terrestris) gut microbiota. Our results
 revealed that Cd exposure led to perturbations of earthworm gut microbiota
 with an increase in bacteria previously described as heavy metal resistant
 or able to bind heavy metals, revealing the potential of the earthworm-gut
 microbiota system in overcoming human-caused heavy metal pollution.
 Furthermore, an ‘indicator species analysis’ linked the bacterial genera
 Paenibacillus, Flavobacterium and Pseudomonas, with Cd treatment,
 suggesting these bacterial taxa as biomarkers of exposure in earthworms
 inhabiting Cd-stressed soils. The results of this study help to understand
 the impact of anthropogenic disturbance on soil fauna health and will have
 implications for environmental monitoring and protection of soil
 resources.
description: Raw fastq files of 16S
 rRNA gene sequencesThe folder contains the
 sequencing data (raw 16S rRNA gene fastq sequences from a paired-end run
 on an Illumina MiSeq) used in analyses of the respective
 publication.earthworm_microbiota.tar.gz
DOI: 10.5061/dryad.sg2637q
title: Data from: Adsorption of Cd(II) in water by mesoporous ceramic functional nanomaterials

description: Mesoporous Ceramic Functional Nanomaterials (MCFN) is a self-assembled
 environmental adsorbent with a monolayer molecular which is widely used in
 the treatment of industrial wastewater and contaminated soil. This work
 aimed to study the relationship between the adsorption behavior of Cd(II)
 by MCFN and contact time, initial concentration, MCFN dosage, pH,
 oscillation rate, and temperature through a batch adsorption method. The
 adsorption kinetic and isotherm behaviors were well described by the
 pseudo-second-order and Langmuir models. The batch characterization
 technique revealed that MCFN had several oxygen-containing functional
 groups. Using Langmuir model the maximum adsorption capacity of MCFN for
 Cd(II) was 97.09 (mg/g) at pH 6, 25, dosage of 0.2 g, and contact time of
 180. Thermodynamic study indicated that the present adsorption process was
 feasible, spontaneous and endothermic at the temperature ranging 25 - 55℃.
 The results of this study provide an important enlightenment for Cd
 removal or preconcentration of porous ceramic nanomaterials adsorbents for
 environmental applications.
description: Full
 MetadataDesign, calculation,
 fitting and analysis of different models for adsorption of new
 nanomaterials
DOI: 10.5061/dryad.8md5419
title: Data from: Bees use anthropogenic habitats despite strong natural habitat preferences

description: Aim: Habitat loss and alteration are widely considered one of the main
 drivers of current pollinator diversity loss. Yet little is known about
 habitat importance and preferences for major groups of pollinators,
 although this information is crucial to anticipate and mitigate the
 current decline of their populations. We aim to rank and assess the
 importance of different habitats for bees, to determine the preference for
 and avoidance of particular habitat types by different bees, and to
 quantify the diversity of bees within and among habitats. Location:
 Northeastern US. Time period: The sampling was done over 15 years
 (2001-2015). Major taxa studied: Apoidea Methods: We used an unprecedented
 extensive dataset of &gt;15,000 bee specimens, comprising more than
 400 species collected across northeast USA. We extracted habitat
 information from the points and used network analyses, null models
 comparisons and beta-diversity analysis to assess habitat importance,
 habitat preference, use and diversity. Results: We found that natural
 habitats sustain higher bee diversity and a different set of species than
 agricultural and urban areas. Although many bee species can use
 human-altered habitats, most species exhibited strong preferences for
 forested habitats and only a few preferred altered habitats over more
 natural habitats. In contrast to previous studies, landscape composition
 only had moderate buffer effects on diversity loss. The loss of
 biodiversity in human-altered environments could have been higher had not
 been partially compensated by the presence of human commensals and exotic
 species. Main conclusions: Although human-altered environments may harbor
 a substantial number of species, our work reveals that preserving natural
 areas is still essential to guarantee the conservation of bee
 biodiversity.
description: Bee
 habitatsA big data frame
 collected by Sam Droeges' team, containing information about
 individual bee species, the coordinates where they were found and the
 habitat extracted from the USGS land use raster layerDatos1.csv
DOI: 10.5061/dryad.m4s45t4
title: Data from: Patterns of modern pollen and plant richness across northern Europe

description: 1. Sedimentary pollen offers excellent opportunities to reconstruct
 vegetation changes over past millennia. Number of different pollen taxa or
 pollen richness is used to characterise past plant richness. To improve
 the interpretation of sedimentary pollen richness, it is essential to
 understand the relationship between pollen and plant richness in
 contemporary landscapes. This study presents a regional-scale comparison
 of pollen and plant richness from northern Europe and evaluates the
 importance of environmental variables on pollen and plant richness. 2. We
 use a pollen dataset of 511 lake-surface pollen samples ranging through
 temperate, boreal, and tundra biomes. To characterise plant diversity, we
 use a dataset formulated from the two largest plant atlases available in
 Europe. We compare pollen and plant richness estimates in different groups
 of taxa (wind-pollinated vs non-wind-pollinated, trees and shrubs vs herbs
 and grasses) and test their relationships with climate and landscape
 variables. 3. Pollen richness is significantly positively correlated with
 plant richness (r=0.53). The pollen–plant richness correlation improves
 (r=0.63) when high pollen-producers are downweighted prior to estimating
 richness minimising the influence of pollen-production on the pollen
 richness estimate. This suggests that methods accommodating
 pollen-production differences in richness estimates deserve further
 attention and should become more widely used in Quaternary pollen
 diversity studies. 4. The highest correlations are found between pollen
 and plant richness of trees and shrubs (r=0.83) and of wind-pollinated
 taxa (r=0.75) suggesting that these are the best measures of broad-scale
 plant richness over several thousands of square kilometres. 5. Mean annual
 temperature is the strongest predictor of both pollen and plant richness.
 Landscape openness is positively associated with pollen richness but not
 with plant richness. Pollen-richness values from extremely open and/or
 cold areas where pollen production is low, should be interpreted with
 caution because low local pollen production increases the proportion of
 extra-regional pollen. 5. Synthesis. Our results confirm that pollen data
 can provide insights into past plant richness changes in northern Europe,
 and with careful consideration of pollen production differences and
 spatial scale represented, pollen data make it possible to investigate
 vegetation diversity trends over long timescales and under changing
 climatic and habitat conditions.
description: Dryad-dataInformation on pollen sample location, plant dataset used for richness calculations and richness data in Open Document Format. Metadata included on the last sheet of the file.Reitalu-etal_JEcol_Modern_pollen_plants_Europe.ods
DOI: 10.5061/dryad.vv7s70m
title: Data from: Simulation-based validation of spatial capture-recapture models: a case study using mountain lions

description: Spatial capture-recapture (SCR) models have improved the ability to
 estimate densities of rare and elusive animals. However, SCR models have
 seldom been validated even as model formulations diversify and expand to
 incorporate new sampling methods and/or additional sources of information
 on model parameters. Information on the relationship between encounter
 probabilities, sources of additional information, and the reliability of
 density estimates, is rare but crucial to assessing reliability of
 SCR-based estimates. We used a simulation-based approach that incorporated
 prior empirical work to assess the accuracy and precision of density
 estimates from SCR models using spatially unstructured sampling. To assess
 the consequences of sparse data and potential sources of bias, we
 simulated data under six scenarios corresponding to three different levels
 of search effort and two levels of correlation between search effort and
 animal density. We then estimated density for each scenario using four
 models that included increasing amounts of information from harvested
 individuals and telemetry to evaluate the impact of additional sources of
 information. Model results were sensitive to the quantity of available
 information: density estimates based on low search effort were biased high
 and imprecise, whereas estimates based on high search effort were unbiased
 and precise. A correlation between search effort and animal density
 resulted in a positive bias in density estimates, though the bias
 decreased with increasingly informative datasets. Adding information from
 harvested individuals and telemetered individuals improved density
 estimates based on low and moderate effort but had negligible impact for
 datasets resulting from high effort. We demonstrated that density
 estimates from SCR models using spatially unstructured sampling are
 reliable when sufficient information is provided. Accurate density
 estimates can result if empirical-based simulations such as those
 presented here are used to develop study designs with appropriate amounts
 of effort and information sources.
description: DryadMiminalDataSetThis .csv file contains the results of all the simulations used in our analysis. The file consists of 4800 rows and 11 columns. The columns are: 1) the effort (in km), 2) the model used to generate an estimate (encounter only, encounter and harvest, encounter and harvest and information from collars), 3) the average number of recaptures per individual, 4) the average number of spatial recaptures, 5) baseline probability of detection, 6) median effort per cell, 7) observed correlation with animal density, 8) number of individuals seen, 9) estimated density, 10) true density, and 11) whether the effort was induced to be correlated with animal density.
DOI: 10.5061/dryad.5p9m3q2
title: Data from: Inferring longitudinal hierarchies: framework and methods for studying the dynamics of dominance

description: 1. Social inequality is a consistent feature of animal societies, often
 manifesting as dominance hierarchies, in which each individual is
 characterized by a dominance rank denoting its place in the network of
 competitive relationships among group‐members. Most studies treat
 dominance hierarchies as static entities despite their true longitudinal,
 and sometimes highly dynamic, nature. 2. To guide study of the dynamics of
 dominance, we propose the concept of a longitudinal hierarchy: the
 characterization of a single, latent hierarchy and it's dynamics over
 time. Longitudinal hierarchies describe the hierarchy position (r) and
 dynamics (∆) associated with each individual as a property of its
 interaction data, the periods into which these data are divided based on a
 period delineation rule (p), and the method chosen to infer the hierarchy.
 Hierarchy dynamics result from both active (∆a) and passive (∆p)
 processes. Methods that infer longitudinal hierarchies should optimize
 accuracy of rank dynamics as well as of the rank orders themselves, but no
 studies have yet evaluated the accuracy with which different methods infer
 hierarchy dynamics. 3. We modify three popular ranking approaches to make
 them better suited for inferring longitudinal hierarchies. Our three
 ‘informed’ methods assign ranks that are informed by data from the prior
 period rather than calculating ranks de novo in each observation period,
 and use prior knowledge of dominance correlates to inform placement of new
 individuals in the hierarchy. These methods are provided in an R package.
 4. Using both a simulated dataset and a long‐term empirical dataset from a
 species with two distinct sex‐based dominance structures, we compare the
 performance of these methods and their unmodified counterparts. We show
 that choice of method has dramatic impacts on inference of hierarchy
 dynamics via differences in estimates of ∆a. Methods that calculate ranks
 de novo in each period overestimate hierarchy dynamics, but incorporation
 of prior information leads to more accurately inferred ∆a. Of the modified
 methods, Informed MatReorder infers the most conservative estimates of
 hierarchy dynamics and Informed Elo infers the most dynamic hierarchies.
 5. This work provides crucially needed conceptual framing and
 methodological validation for studying social dominance and its dynamics.
description: Code and data for
 Strauss & Holekamp (2019) Inferring longitudinal hierarchies
 paperFiles are numbered
 according to the order of their appearance in the analysis. File paths in
 the scripts will need to be changed in order for the code to run properly.
 Please see the README file for details.FinalSubmissionDryad.zip