cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16265273
title: Tunable simultaneous propulsion by two distinct motility motors drives surface motility in Myxococcus xanthus

description: This deposit contains all of the processed data and analysis scripts supporting the findings in “Tunable simultaneous propulsion by two distinct motility motors drives surface motility in Myxococcus xanthus.”

/Data.zip

Contains all processed cells trajectories and focal-adhesion datasets used to generate figures and quantitative analyses in the manuscript.

/Cells_data





Agar_0p75: pickle files with per‐cell, per‐frame (x,y) trajectories for leading pole, lagging pole, and center on 0.75 % agar.




Ibidi_chitosan: same format for trajectories recorded on chitosan-coated coverslips.




Umap: two-dimensional embeddings of the 48 motility features for all strains.



/FACS_data





Agar_predation: detected focal-adhesion complexes (FACS) from AglZ-YFP in predation assays; one .pkl per time‐lapse.




Ibidi_chitosan: FACS spot coordinates for both A⁺S⁻ and WT strains on chitosan substrates.



/Scripts.zip

Includes all code and configuration files required to reproduce data processing, analysis, and figure generation:





config/parameters.jsonDefines data paths and processing and analysis settings.




modules/Python modules implementing image preprocessing, segmentation, tracking, feature extraction (kymographs, pole detection), FACS detection, and trajectory feature computation.




run_pipeline.pyOrchestrates raw data ingestion, processing through most modules for cell tracking, and exports the final .pkl datasets.
DOI: 10.15468/dl.g9ggxg
title: Occurrence Download

description: A dataset containing 462 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Curcuma aromatica"
 ]
}

 The dataset includes 462 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001395-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6502mg2
title: Data from: Intraspecific trait variation and trade-offs within and across populations of a toxic dinoflagellate

description: Intraspecific trait diversity can promote the success of a species, as
 complementarity of functional traits within populations may enhance its
 competitive success and facilitates resilience to changing environmental
 conditions. Here, we experimentally determined the variation and
 relationships between traits in 15 strains of the toxic dinoflagellate
 Alexandrium ostenfeldii derived from two populations. Measured traits
 included growth rate, cell size, elemental composition, nitrogen uptake
 kinetics, toxin production and allelochemical potency. Our results
 demonstrate substantial variation in all analyzed traits both within and
 across populations, particularly in nitrogen affinity, which was even
 comparable to interspecific variation across phytoplankton species. We
 found distinct trade-offs between maximum nitrogen uptake rate and
 affinity, and between defensive and competitive traits. Furthermore, we
 identified differences in trait variation between the genetically similar
 populations. The observed high trait variation may facilitate development
 and resilience of harmful algal blooms under dynamic environmental
 conditions.
description: Trait measurements of 15
 Alexandrium ostenfeldii strains isolated from two distinct
 locationsTraitsAlexandriumostenfeldii.csv
DOI: 10.5061/dryad.2pp12mt
title: Data from: Juvenile survival, competing risks, and spatial variation in mortality risk of a marine apex predator

description: Reliable estimates of mortality have been a major gap in our understanding
 of population ecology for marine animals. This is especially true for
 juveniles, which are often the most vulnerable age class and whose
 survival can strongly influence population growth. Thousands of pop‐up
 archival satellite tags (PAT) have been deployed on a variety of marine
 species, but analysis of these data has mainly been restricted to movement
 ecology and post‐handling survival following fisheries bycatch. We used
 PAT data to provide empirical estimates of annual survival and
 cause‐specific mortality for juveniles of a marine top predator. We tagged
 and tracked juvenile white sharks in the north eastern Pacific Ocean to
 (1) estimate survival rates and competing risks and (2) investigate
 intrinsic and environmental influences on mortality risk. We also
 evaluated the use of PAT data with respect to meeting assumptions of
 known‐fate survival models. Annual juvenile survival rate was 0.632 (SE =
 0.15) and annual natural mortality rate (0.08, SE = 0.06) was lower than
 the rate of gillnet interactions (0.48, SE = 0.15). Mortality risk
 decreased with greater body length and was significantly greater (hazard
 ratio = 9.05, SE = 0.70) for juvenile sharks in Mexican waters, relative
 to California waters. The PAT data allowed for unambiguous determination
 of fate in most cases, aided by collaborative relationships with fishers
 and secondary tags deployed on a subset of sharks. Although caution must
 be exercised to establish whether assumptions are met, our work
 demonstrates that PAT data represent a widely available, untapped data
 source that could dramatically increase our understanding of marine
 population ecology. Synthesis and applications. Our research shows
 fisheries bycatch to be the main source of mortality for juvenile white
 sharks in the northeastern Pacific Ocean, highlighting the need for best
 practices, such as releasing sharks quickly following incidental capture.
 Furthermore, mortality risk for juveniles was greater in Mexican waters,
 such that survival may be lower in colder years when juveniles are likely
 to move south seeking warmer water. This could increase stochasticity in
 juvenile survival and negatively influence population growth for this apex
 predator.
description: Benson et al. juvenile
 white shark shark survival dataSurvival monitoring data
 from tracking satellite tagged juvenile white sharks. Data includes ID
 numbers, start and end dates of tracking data, fate of sharks at end of
 tracking period, total length in cm at tagging, location (Mexico or US),
 and sex.Bensonetal.JuvenileWhiteSharkSurvivalData.xlsx
DOI: 10.5061/dryad.j26k3
title: Data from: A theoretical approach to the size-complexity rule

description: The so-called size-complexity rule claims the existence of a positive
 correlation between organism size and number of cell types. In this
 spirit, here we address the relationship between organism size and number
 of potential tasks that can be performed. The modeling relies on the
 assumption that the states of the cells within the aggregates are such
 that the maximum fitness is realized, but also relies on the existence of
 tradeoffs among the distinct functions. For group sizes larger than the
 number of potential tasks, fitness maximization is attained when all cells
 in group specialize in a given task. Under this scenario, the number of
 potential tasks equals the number of cell types. We have found that the
 morphology and the topology of aggregates, as well as the developmental
 mode, strongly influence the dynamics of body formation. Particularly, it
 has been observed that more compact structures, such as sphere-like
 structures, are more likely to follow the claim of the size-complexity
 rule, whereas more fragile structures such as linear chains, which are
 more vulnerable to drastic changes due to division mechanisms, can, in a
 broad scenario, violate the size-complexity rule.
description: A theoretical approach
 to the size-complexity ruleThis repository provides
 the code necessary to reproduce the results in the paper "A
 theoretical approach to the size-complexity rule". It comprises two
 codes: one for the spherical and linear geometries, in C++11, and the
 other for the snowflake geometry, in python3.size_complexity_rule.zip
DOI: 10.5061/dryad.7kd12bg
title: Data from: No support for cryptic choice by ovarian fluid in an external fertilizer

description: Whether the ovarian fluid represents a selective environment influencing
 cryptic female choice was tested using an external fertilizer experiencing
 intense sperm competition and large effects of ovarian fluid on sperm
 swimming behaviour - the Arctic charr (Salvelinus alpinus). We physically
 separated the ovarian fluid from the eggs of reproductively active females
 and reintroduced either their own ovarian fluid or fluid from another
 female to the eggs. The eggs were then fertilized in vitro in a replicated
 split-brood design with sperm from two males under synchronized sperm
 competition trials, while also measuring sperm velocity of the individual
 males in the individual ovarian fluids. We found large effects of males,
 but no effect of females (i.e., eggs) on paternity, determined from
 microsatellites. More important, we found no effect of ovarian fluid
 treatments on the relative paternity of the two competing males in each
 pair. This experimental setup does not provide support for the hypothesis
 that ovarian fluid plays an important role as medium for cryptic female
 choice in charr. Power-analyses revealed that our sample size is large
 enough to detect medium sized changes in relative paternity (medium-sized
 effect-sizes), but not large enough to detect small changes in relative
 paternity. More studies are needed before a conclusion can be drawn about
 ovarian fluid’s potential influence on paternity under sperm competition -
 even in charr.
description: Kleppe et al Final Data
 - sperm velocity 10s Table 2SpermVelocity.txtKleppe et al Final Data - paternity Table 3Paternity.txt
DOI: 10.5061/dryad.3bd65
title: Data from: Colony-level differences in the scaling rules governing wood ant compound eye structure

description: Differential organ growth during development is essential for adults to
 maintain the correct proportions and achieve their characteristic shape.
 Organs scale with body size, a process known as allometry that has been
 studied extensively in a range of organisms. Such scaling rules, typically
 studied from a limited sample, are assumed to apply to all members of a
 population and/or species. Here we study scaling in the compound eyes of
 workers of the wood ant, Formica rufa, from different colonies within a
 single population. Workers’ eye area increased with body size in all the
 colonies showing a negative allometry. However, both the slope and
 intercept of some allometric scaling relationships differed significantly
 among colonies. Moreover, though mean facet diameter and facet number
 increased with body size, some colonies primarily increased facet number
 whereas others increased facet diameter, showing that the cellular level
 processes underlying organ scaling differed among colonies. Thus, the
 rules that govern scaling at the organ and cellular levels can differ even
 within a single population.
description: Perl_Niven_2016_colony_level_ant_scaling
DOI: 10.5061/dryad.3113c
title: Data from: Seasonal changes in starch content in trophopods of Matteuccia struthiopteris

description: Trophopods are modified stipe bases that function as starch-storage organs
 in a wide variety of mainly temperate ferns. Ever since they were first
 observed, the presence of trophopods has been explained by reference to
 seasonality and they have been assumed to provide nutrition for the
 rapidly expanding fern leaves in spring. We present the results of an
 analysis of the annual variation in starch content in Matteuccia
 struthiopteris (L.) Todaro, cultivated in the Leiden botanical garden. Our
 results show a distinct seasonal variation in starch content, suggesting
 that the presence of trophopods is indeed functionally linked to
 seasonality, but we do not find a decrease in starch content corresponding
 to the period of leaf expansion that would clearly link the depletion of
 stored starch to the expansion of new leaves.
description: Seasonal changes in
 starch content in Matteuccia struthiopterisStarch content in
 samples from trophopods, sampled over one year (233 samples) and in leaf
 tissue sampled in expanded leaves (2 samples)Hovenkamp et al changes in
 starch content in Matteuccia.csv
DOI: 10.5061/dryad.1qf3s
title: Data from: Allee effects in ants

description: 1. Allee effects occur when the aggregation of individuals result in
 mutually beneficial intraspecific interactions whereby individual fitness,
 or per capita growth rate, increases with the number of individuals. Allee
 effects are common in social species due to their cooperative behaviours,
 such as breeding, feeding, or defence. Allee effects have important
 implications for many aspects of basic and applied ecology. Over the past
 decades, the study of Allee effects has influenced population dynamics,
 community ecology, endangered species management, and invasion biology. 2.
 Despite the fact that cooperation is the basis of their social structure,
 Allee effects have received little attention among eusocial insects.
 Extreme cooperation is common and reproductive specialization of
 individuals occurs due to division of labour. These life history traits
 suggest that the potential contribution of each caste to reproduction and
 survival may be differential and nonadditive. 3. We studied Allee effects
 in the invasive Argentine ant (Linepithema humile). In this species, many
 queens and workers are present in colonies, which allowed us to explore
 the differential effects of castes on the presence of Allee effects. In
 the laboratory, we measured brood production and individual survival in
 experimental colonies that differed in the initial numbers of queens and
 workers. 4. Our results highlight the differential effect of queens and
 workers on survival and productivity. We found three positive
 density-dependent relationships indicative of component Allee effects at
 the colony level: both workers and queens had a positive effect on the
 productivity of the other caste, and queens had a positive effect on
 worker survivorship. 5. Our experimental results suggest a potential
 positive feedback between worker and queen abundance, which may have
 contributed to the evolution of large colony sizes. Our study provides the
 first evidence of Allee effects in eusocial insects, and highlights the
 need to consider castes separately in population dynamics. Division of
 labour and differential reproductive rates are factors that should be
 integrated into the study of Allee effects.
description: AE_in_antsDataQueen_MortalityScript for queen mortality analysisQueen_ProductivityScript for Queen productivity analysisWorker_MortalityScript for worker mortality analysisWorker_ProductivityScript for worker productivity analysis
DOI: 10.5061/dryad.5hs50
title: Data from: Response of the red fox to expansion of human habitation in the Trans-Himalayan mountains

description: Habitat modification through rural and urban expansions negatively impacts
 most wildlife species. However, anthropogenic food sources in habitations
 can benefit certain species. The red fox Vulpes vulpes can exploit
 anthropogenic food, but human subsidies sometimes also sustain populations
 of its potential competitor, the free-ranging dog Canis familiaris. As
 human habitations expand, populations of free-ranging dog are increasing
 in many areas, with unknown effects on wild commensal species such as the
 red fox. We examined occurrence and diet of red fox along a gradient of
 village size in a rural mountainous landscape of the Indian
 Trans-Himalaya. Diet analyses suggest substantial use of anthropogenic
 food (livestock and garbage) by red fox. Contribution of livestock and
 garbage to diet of red fox declined and increased, respectively, with
 increasing village size. Red fox occurrence did not show a clear
 relationship with village size. Red fox occurrence showed weak positive
 relationships with density of free-ranging dog and garbage availability,
 respectively, while density of free-ranging dog showed strong positive
 relationships with village size and garbage availability, respectively. We
 highlight the potential conservation concern arising from the strong
 positive association between density of free-ranging dog and village size.
description: Red fox data_Ghoshal et
 al, 2016The data consists
 information on red fox use (tracks per hectare) across ten sampled
 villages in Trans-Himalaya, village sizes, density of free-ranging dog and
 diet of red fox.Red
 fox_PlotLevelData_Ghoshal et al, 2016This data file contains
 information on number of red fox tracks per plot (5mX5m) across ten
 villages of different sizes.
DOI: 10.5281/zenodo.18384924
title: Maps of total and active CaCO3 content (0-30 cm) of the soils of Emilia-Romagna (NE Italy)

description: The two datasets contain the maps of total and active limestone (reference depth 0-30 cm) for the soils of Emilia-Romgna (NE Italy). The maps are in raster format (GEOTIF) and have a spatial resolution of 100 m; the Rs system is EPSG 7791. For both total and active limestone,  maps of estimation uncertainty are provided; uncertainty classes (low, medium and high) were based on the width of the interquartile ranges (P75-P25) assessed via Digital Soil Mapping (DSM) via Quantile Random Forest. A raster map of the difference between total and active CaCO3 is also provided (in CALATT_0_30.zip).

Details on the methdology can be found  in the Technical Note (in Italian):

Ungaro, F., Tarocco, P., & Severi, P. (2026). Maps of total and active CaCO3 content in the sois of Emilia-Romagna (NE Italy) (v.1.1.2025). Scale 1:50.000, Note illustrative (First Ed.). Regione Emilia Romagna, Direzione Generale cura del territorio e dell'ambiente, Area Geologia, Suoli e Sismica. Zenodo. https://doi.org/10.5281/zenodo.18384552
DOI: 10.5281/zenodo.18384925
title: Maps of total and active CaCO3 content (0-30 cm) of the soils of Emilia-Romagna (NE Italy)

description: The two datasets contain the maps of total and active limestone (reference depth 0-30 cm) for the soils of Emilia-Romgna (NE Italy). The maps are in raster format (GEOTIF) and have a spatial resolution of 100 m; the Rs system is EPSG 7791. For both total and active limestone,  maps of estimation uncertainty are provided; uncertainty classes (low, medium and high) were based on the width of the interquartile ranges (P75-P25) assessed via Digital Soil Mapping (DSM) via Quantile Random Forest. A raster map of the difference between total and active CaCO3 is also provided (in CALATT_0_30.zip).

Details on the methdology can be found  in the Technical Note (in Italian):

Ungaro, F., Tarocco, P., & Severi, P. (2026). Maps of total and active CaCO3 content in the sois of Emilia-Romagna (NE Italy) (v.1.1.2025). Scale 1:50.000, Note illustrative (First Ed.). Regione Emilia Romagna, Direzione Generale cura del territorio e dell'ambiente, Area Geologia, Suoli e Sismica. Zenodo. https://doi.org/10.5281/zenodo.18384552
DOI: 10.15468/dl.c98n6e
title: Occurrence Download

description: A dataset containing 10727 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "TaxonKey is Psammotettix"
 ]
}

 The dataset includes 10727 records from 146 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001396-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5nd50
title: Data from: Phylogenetic comparative methods for evaluating the evolutionary history of function-valued traits

description: Phylogenetic comparative methods offer a suite of tools for studying trait
 evolution. However, most models inherently assume fixed trait values
 within species. Although some methods can incorporate error around species
 means, few are capable of accounting for variation driven by environmental
 or temporal gradients, such as trait responses to abiotic stress or
 ontogenetic trajectories. Such traits, often referred to as
 function-valued or infinite-dimensional, are typically expressed as
 reaction norms, dose–response curves, or time plots and are described by
 mathematical functions linking independent predictor variables to the
 trait of interest. Here, I introduce a method for extending ancestral
 state reconstruction to incorporate function-valued traits in a
 phylogenetic generalized least squares (PGLS) framework, as well as
 extensions of this method for testing phylogenetic signal, performing
 phylogenetic analysis of variance (ANOVA), and testing for correlated
 trait evolution using recently proposed multivariate PGLS methods.
 Statistical power of function-valued comparative methods is compared to
 univariate approaches using data simulations, and the assumptions and
 challenges of each are discussed in detail.
description: Goolsby_EW_SystBiol_2015Zip file containing 5 R scripts for performing function-valued ancestral curve reconstruction, and all simulations conducted in the Syst Biol paper. Also included is a README file explaining use of each R script.DemoScriptsTo reproduce simulations in paper, source ICA_functions_SHOWCASE.R and cxxFunctions_OU_Generic_SHOWCASE.cxx from
DOI: 10.5061/dryad.4846b
title: Data from: Seed to seedling transitions in successional habitats across a tropical landscape

description: Recognition that tree recruitment depends on the balance between seed
 arrival and seedling survival has led to a surge of interest in
 seed-dispersal limitation and seedling-establishment limitation in primary
 forests. Virtually unaddressed are comparisons of this balance in mature
 and early successional habitats. We assessed seed rain and seedling
 recruitment dynamics of tree species in primary forest, secondary forest
 and pasture released from grazing in a tropical agricultural landscape.
 Seed to seedling ratios (seed effectiveness; Φi) for 43 species in
 southern Mexico determined differences in the extent to which seeds
 produced seedlings by habitat, life history, and dispersal mode.
 Reproductive potential as estimated by the transition from seed rain to
 seedling recruitment, differed by habitats, and varied dramatically by
 life history and dispersal mode. Expected recruit densities (Eit) were
 higher for animal-dispersed than wind-dispersed species, and for
 non-pioneer than pioneer species. Non-pioneers and animal-dispersed
 species had higher expected relative recruit abundance (εit) in primary
 forest (median of 4 seeds recruit−1) whereas in secondary forest
 wind-dispersed pioneers had the highest expected relative recruit
 abundance (median of 16 seeds per recruit). In pastures, wind-dispersed
 pioneer species were most successful with many more seeds per recruit
 (median of 291) than both forest habitats. Seeds per recruit (Φi) appeared
 to decrease with increase in seed mass for 43 species for which data were
 available (r = –0.55, P &lt; 0.001). This was associated with a
 negative correlation of Φi with seed size in primary forest (r = –0.50, P
 = 0.08 for 13 species); Φi was not correlated with seed size in secondary
 forest (n = 16) or pasture (n = 14). Metrics of seeds per recruit,
 expected recruit density and expected relative recruit abundance
 dramatically illustrate differences in barriers to recruitment in
 successional habitats.
description: de la Pena Domene et al.
 2016. Oikos. Data BaseData description of
 species, seeds number, recruit number, seeds per recruit, life history,
 dispersal mode and habitat