cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ksn02v71t
title: Multi-scale habitat assessment of pronghorn migration routes

description: We studied the habitat selection of pronghorn (Antilocapra americana)
 during seasonal migration; an important period in an animal’s annual cycle
 associated with broad-scale movements. We further decompose our
 understanding of migration habitat itself as the product of both broad-
 and fine-scale behavioral decisions and take a multi-scale approach to
 assess pronghorn spring and fall migration across the transboundary
 Northern Sagebrush Steppe region. We used a hierarchical habitat selection
 framework to assess a suite of natural and anthropogenic features that
 have been shown to influence selection patterns of pronghorn at both broad
 (migratory neighborhood) and fine (migratory pathway) scales. We then
 combined single-scale predictions into a scale-integrated step selection
 function (ISSF) map to assess its effectiveness in predicting migration
 route habitat. During spring, pronghorn selected for native grasslands,
 areas of high forage productivity (NDVI), and avoided human activity
 (i.e., roads and oil and natural gas wells). During fall, pronghorn
 selected for native grasslands, larger streams and rivers, and avoided
 roads. We detected avoidance of paved roads, unpaved roads, and wells at
 broad spatial scales, but no response to these features at fine scales. In
 other words, migratory pronghorn responded more strongly to anthropogenic
 features when selecting a broad neighborhood through which to migrate than
 when selecting individual steps along their migratory pathway. Our results
 demonstrate that scales of migratory route selection are hierarchically
 nested within each other from broader (second-order) to finer scales
 (third-order). In addition, we found other variables during particular
 migratory periods (i.e., native grasslands in spring) were selected for
 across scales indicating their importance for pronghorn. The mapping of
 ungulate migration habitat is a topic of high conservation
 relevance.  In some applications, corridors are mapped according
 to telemetry location data from a sample of animals, with the assumption
 that the sample adequately represents habitat for the entire population.
 Our use of multi-scale modelling to predict resource selection during
 migration shows promise and may offer another relevant alternative for use
 in future conservation planning and land management decisions where
 telemetry-based sampling is unavailable or incomplete.
description: The following databases were recorded using GPS-radio collars
 deployed on female pronghorn. Collars took GPS locations either every 2 or
 4 hours. Important variables were intersected and added to both use and
 available locations for each scale of selection. Here are the names of the
 two databases:
 Pronghorn_NSS_3rd_Order_Data_PlosOne_Paper
 Pronghorn_NSS_2nd_Order_Data_PlosOne_Paper
description: Please see the READ ME file which contains contact information
 and definitions for both databases.
DOI: 10.5061/dryad.sbcc2fr3t
title: Loss of ecologically important genetic variation in late generation hybrids reveals links between adaptation and speciation

description: Adaptation to contrasting environments occurs when advantageous alleles
 accumulate in each population, but it remains largely unknown whether
 these same advantageous alleles create genetic incompatibilities that can
 cause intrinsic reproductive isolation leading to speciation. Identifying
 alleles that underlie both adaptation and reproductive isolation is
 further complicated by factors such as dominance and genetic interactions
 among loci, which can affect both processes differently and obscure
 potential links between adaptation and speciation. Here, we use a
 combination of field and glasshouse experiments to explore the connection
 between adaptation and speciation while accounting for dominance and
 genetic interactions. We created a hybrid population with equal
 contributions from four contrasting ecotypes of Senecio lautus
 (Asteraceae), which produced hybrid genomes both before (F1 hybrid
 generation) and after (F4 hybrid generation) recombination among the
 parental ecotypes. In the glasshouse, plants in the second generation (F2
 hybrid generation) showed reduced fitness as a loss of fertility, but
 fertility was recovered in subsequent generations suggesting that genetic
 variation underlying fertility reduction was lost in subsequent
 generations. To quantify the effects of losing genetic variation at the F2
 generation on the fitness of later generation hybrids, we used a
 reciprocal transplant to test for fitness differences between parental
 ecotypes, and F1 and F4 hybrids in all four parental habitats. Compared to
 the parental ecotypes and F1 hybrids, variance in F4 hybrid fitness was
 lower, and lowest in habitats that showed stronger native-ecotype
 advantage, suggesting that stronger natural selection for the native
 ecotype reduced fitness variation in the F4 hybrids. Fitness trade-offs
 that were present in the parental ecotypes and F1 hybrids were absent in
 the F4 hybrid. Together, these results suggest that the genetic variation
 lost after the F2 generation was likely associated with both adaptation
 and intrinsic reproductive isolation among populations adapted to
 contrasting environments.
description: These data are from two experiments. Experiment 1 measured leaf
 phenotypes of an F4 hybrid and the four parental ecotypes. Experiment 2
 involved a large reciprocal transplant of the four ecotypes, their F1
 hybrids and the F4 hybrids. All data are raw, and no processing has
 occurred.
DOI: 10.5061/dryad.w0vt4b8nk
title: Radical change: Temporal patterns of oxidative stress during social ascent in a dominance hierarchy

description: Dominant individuals have priority access to mates and resources. However,
 high rank can be costly too, especially when it is maintained by intense
 agonistic behavior. Oxidative stress has been proposed as a potential cost
 of social dominance. However, social dominance hierarchies can be dynamic,
 and few studies have examined the cost of social dominance when males are
 changing status. We studied temporal changes in markers of oxidative
 stress during social ascent in the East African cichlid fish Astatotilapia
 burtoni. After removing the dominant male, males ascended from subordinate
 to dominant status. On the first day of social ascent, immediately after
 the dominant male removal, the newly dominant male showed lower levels of
 plasma total antioxidant capacity (TAC). However, we found that liver TAC
 and liver superoxide dismutase, an enzymatic antioxidant, were
 significantly upregulated on day 1 and 2 of social ascent, respectively.
 By day 14, all markers of oxidative stress were similar to those observed
 in stable dominant males, which has higher levels of reactive oxygen
 metabolites (ROM) compared to subordinate males. We conclude that markers
 of oxidative stress vary dramatically during social ascent in a time- and
 tissue-sensitive manner. Our study provides a more nuanced look at the
 oxidative cost of social dominance and highlights the importance of
 considering temporal changes in markers of oxidative stress during
 important life-history events.
DOI: 10.7280/d12h4m
title: Floral scent dynamics of Schiedea kaalae and Schiedea hookeri

description: Floral scent often intensifies during periods of pollinator activity, but
 the degree of this synchrony may vary among scent compounds depending on
 their function. Related plant species with the same pollinator may exhibit
 similar timing and composition of floral scent. We compared timing and
 composition of floral volatiles for two endemic Hawaiian plant species,
 Schiedea kaalae and S. hookeri (Caryophyllaceae). For S. kaalae, we also
 compared the daily timing of emission of floral volatiles to evening
 visits of their shared pollinator, an endemic Hawaiian moth
 (Pseudoschrankia brevipalpis; Erebidae). The identity and amount of floral
 volatiles were measured in the greenhouse during day and evening periods
 with dynamic headspace sampling and GC-MS (gas chromatography – mass
 spectrometry). The timing of emissions (daily rise, peak, and fall) was
 measured by sampling continuously for multiple days in a growth chamber
 with PTR-MS (proton transfer reaction mass spectrometry). Nearly all
 volatiles detected underwent strong daily cycles in emission. Timings of
 floral volatile emissions were similar for S. kaalae and S. hookeri, as
 expected for two species sharing the same pollinator. For S. kaalae, many
 volatiles known to attract moths, including several linalool oxides and
 2-phenylacetaldehyde, peaked within 2 h of the peak visitation time of the
 moth which pollinates both species. Floral volatiles of both species that
 peaked in the evening were also emitted several hours before and after the
 brief window of pollinator activity. Few volatiles followed a daytime
 emission pattern, consistent with increased apparency to visitors only at
 night. The scent blends of the two species differed in their major
 components and were most distinct from each other in the evening. The
 qualitative difference in evening scent composition between the two
 Schiedea species may reflect their distinct evolutionary history and may
 indicate that the moth species uses several different floral cues to
 locate rewards.
description: An included readme file describes the format of the GC-MS and
 PTR-MS datasets.
DOI: 10.5061/dryad.5x69p8d10
title: Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau

description: The Tibetan Plateau (TP) and surrounding regions have one of the most
 complex biotas on Earth. However, the evolutionary history of these
 regions in deep time is poorly understood. In this study, we quantified
 the temporal changes in beta dissimilarities among zoogeographical regions
 during the Cenozoic using 4,966 extant terrestrial vertebrates and 1,278
 extinct mammal genera. We identified ten present-day zoogeographical
 regions and found that they underwent a striking change over time.
 Specifically, the fauna on the TP was close to the Oriental realm in deep
 time, while it became more similar to the Palearctic realms towards the
 present day. The present-day zoogeographical regions generally emerged
 during the Miocene/Pliocene boundary (ca. 5 Ma). These results indicate
 that geological events such as the Indo-Asian Collision, the TP uplift,
 and the aridification of the Asian interior underpinned the evolutionary
 history of the zoogeographical regions surrounding the TP over different
 time periods.
DOI: 10.5281/zenodo.11433205
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - ALMERIA - (June 23 - May 24)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) the andalusian agroclimatic information network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2023, to May 31, 2024, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Almería:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5281/zenodo.11433206
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - ALMERIA - (June 23 - May 24)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) the andalusian agroclimatic information network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2023, to May 31, 2024, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Almería:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5061/dryad.gxd2547hz
title: Data from: Chemical structure predicts the effect of plant-derived low-molecular weight compounds on soil microbiome structure and pathogen suppression

description: 1. Plant-derived low molecular weight compounds play a crucial role in
 shaping soil microbiome functionality. While various compounds have been
 demonstrated to affect soil microbes, most data are case-specific and do
 not provide generalizable predictions on their effects. Here we show that
 the chemical structural affiliation of low molecular weight compounds
 typically secreted by plant roots – sugars, amino acids, organic acids and
 phenolic acids – can predictably affect microbiome diversity, composition
 and functioning in terms of plant disease suppression. 2. We amended soil
 with single or mixtures of representative compounds, mimicking carbon
 deposition by plants. We then assessed how different classes of compounds,
 or their combinations, affected microbiome composition and the protection
 of tomato plants from the soil-borne Ralstonia solanacearum bacterial
 pathogen. 3. We found that chemical class predicted well the changes in
 microbiome composition and diversity. Organic and amino acids generally
 decreased the microbiome diversity compared to sugars and phenolic acids.
 These changes were also linked to disease incidence, with amino acids and
 nitrogen-containing compound mixtures inducing more severe disease
 symptoms connected with a reduction in bacterial community diversity. 4.
 Together, our results demonstrate that low molecular weight compounds can
 predictably steer rhizosphere microbiome functioning providing guidelines
 to engineer microbiomes based on root exudation patterns by specific plant
 cultivars or crop regimes.
DOI: 10.5061/dryad.wdbrv15kr
title: Developmental plasticity in Nephilingis cruentata

description: This dataset contains four tabs with the information used to analyse the
 role of developmental plasticity in adult male size in a spider. The first
 tab contains the overall developmental data per individual. The
 second tab contains the data for the animal model, the third tab the
 pedigree, and the fourth tab contains the summary of mortality data per
 family. 
description: The
 spiders for this study were taken from a laboratory population that was
 established in 2015. The seed population (females = 40, males = 22) was
 collected in South Africa in January of 2015. For this study, a total of
 16 females were mated with 16 different males in a full-sib breeding
 design. When the spiderlings were around 14 – 16 days old, they were
 separated individually in upside down plastic cups (200 ml). In a
 split-brood design, they were assigned to two different feeding regimes:
 low feeding regime (2 fruit flies a week) (n = 21 per egg-sac) and ad
 libitum (more fruit flies than they can eat) (n = 21 per egg-sac).
 Subadult males were further exposed to two sex-biased environments, either
 to environment with female silk cues (presence of females) (n = 123) or to
 environment with male silk cues (presence of males) (n = 134), while
 maintaining the feeding regime and split-brood design. We checked
 spiderlings five times a week and recorded the duration of the subadult
 stage and the size (i.e. carapace width) and mass of the males at
 maturation. Body size was
 obtained by measuring carapace width. For measuring carapace width at both
 the sub-adult and the adult stages, we photographed each spider using a
 Canon Eos 7D camera equipped with a Canon 50 mm macro lens. For all
 photography of spiders, we used a standardized fixed focal length and
 calculated carapace width by converting the pixel distance. Growth at the
 sub-adult stage was obtained by subtracting the size at the sub-adult
 stage from the size at maturation. Mass of adult individuals was measured
 a day or two after moulting using an electronic laboratory scale (KERN GI,
 220-3NM; min = 0.02, d = 0.001 mg). Body condition was calculated as
 standardized residuals from regression with carapace width and body mass
 as independent and dependent variable, respectively. Developmental time
 was estimated by counting the days from the hatching date until the day of
 the last moult to maturation. The duration of the sub-adult stage was
 obtained by subtracting the dates between ultimate and penultimate
 moults.
description: The file contains the raw data and there are missing values.
 Complete cases of the variables are needed to analyse the data.
DOI: 10.5061/dryad.w3r2280nd
title: Data from: Direct effects of nitrogen addition on seed germination of eight semi-arid grassland species

description: Seed germination plays an important role in mediating plant species
 composition of grassland communities under nitrogen (N) enrichment. Shifts
 of plant community structure with N-enhanced deposition in terrestrial
 ecosystems have occurred globally. Despite numerous studies about the
 effects of enhanced N deposition on mature plant communities, few studies
 have focused on seed germination. Using a laboratory experiment, we report
 the effects of five N concentrations, including 0, 5, 10, 20, and 40 mM N
 (NH4NO3) on seed germination of eight semi-arid grassland species. Results
 showed that low N concentrations (5- and 20-mM N) promoted mean final
 germination proportion of all eight species by 4.4% and 6.4%, but high
 concentrations (40 mM N) had no effect. The mean germination rate was
 decreased 2.1% and 5.1% by higher N concentration (20- and 40-mM N)
 levels, but germination start time showed the opposite trend, delayed by
 0.7, 0.9, and 1.8 d for the 10, 20, and 40 Mm N treatments. Final
 germination proportion, mean germination rate, and germination start time
 were significantly different among species in response to N concentration
 treatments. The final germination proportion of Allium tenuissimum and
 Chenopodium glaucum were suppressed by increased N concentration, whereas
 it increased for Potentilla bifurca, Plantago asiatica and Setaria
 viridis. Our findings provide novel insights into N-deposition-induced
 species loss based on seed germination factors in semi-arid grassland
 communities.
description: Figures
DOI: 10.5061/dryad.5tb2rbp29
title: Data from: Experimental demonstration of the importance of keystone communities for maintaining metacommunity biodiversity and ecosystem functioning

description: As local communities within a metacommunity may differ considerably in
 their contributions to biodiversity and ecosystem functioning, it has been
 suggested that conservation priority should be given to disproportionately
 important local communities (i.e., keystone communities). However, we know
 little about what characterizes a keystone community. Using laboratory
 protist microcosms as the model system, we examined how the environmental
 uniqueness and location of a local community affect its contributions to
 the metacommunities. We found that the removal of local communities with
 unique environmental conditions, which supported endemic species, reduced
 regional-scale diversity, qualifying them as regional-scale keystone
 communities. In addition, the local communities possessing unique
 environmental conditions had greater impacts on ecosystem functions,
 including biovolume production and particulate organic matter
 decomposition. We also found that keystone communities for biovolume
 production were not keystone for organic matter decomposition, and vice
 versa. Our study, therefore, demonstrates the important role of keystone
 communities in maintaining biodiversity and functioning of
 metacommunities.
DOI: 10.5061/dryad.44j0zpcbj
title: A little damping goes a long way: code and data

description: It is currently unclear if damping plays a functional role in legged
 locomotion, and simple models often do not include damping terms. We
 present a new model with a damping term that is isolated from other
 parameters: that is, the damping term can be adjusted without retuning
 other model parameters for nominal motion. We systematically compare how
 increased damping affects stability in the face of unexpected
 ground-height perturbations. Unlike most studies, we focus on task-level
 stability: that is, instead of observing whether trajectories converge
 back towards a nominal limit-cycle, we quantify the ability to avoid falls
 using a recently developed mathematical measure. This measure allows
 trajectories to be compared quantitatively instead of only being separated
 into a binary classification of “stable” or “unstable”. Our simulation
 study shows that increased damping contributes significantly to task-level
 stability; however, this benefit quickly plateaus after only a small
 amount of damping. These results suggest that the low intrinsic damping
 values observed experimentally may have stability benefits, and are not
 simply minimized for energetic reasons. All Python code and data needed to
 generate our results are available open-source.
description: This is a simulation study of the effect of damping in a simple
 model of running, with large amounts of data generated by simulation. Both
 the simulation-generated data used in the paper, as well as the code to
 generate the data is provided. Code to process and visualize the data is
 also provided.
description: A readme and guide is included in the zip file.
 This codebase is also hosted online at
 https://github.com/sheim/vibly. If you wish to use the tools for new
 studies, we recommend using this, as it will be kept more up to date,
 including potential bugfixes and new features.