cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9s4mw6mkf
title: Species-specific effects and the ecological role of Programmed cell Death in the microalgae Ankistrodesmus (Sphaeropleales, Selenastraceae)

description: Reports of programmed cell death (PCD) in phytoplankton raise questions
 about the ecological evolutionary role of cell death in these organisms.
 We induced PCD by nitrogen deprivation and unregulated cell death
 (non-PCD) in one strain of the green microalga Ankistrodesmus densus and
 investigated the effects of the cell death supernatants on
 phylogenetically related co-occurring organisms using growth rates and
 maximum biomass as proxies of fitness. PCD-released materials from A.
 densus CCMA-UFSCar-3 significantly increased growth rates of two
 conspecific strains compared to healthy culture (HC) supernatants and
 improved the maximum biomass of all A. densus strains compared to related
 species. Although growth rates of non-A. densus with PCD supernatants were
 not statistically different from HC treatment, biomass gain was
 significantly reduced. Thus, the organic substances released by PCD,
 possibly nitrogenous compounds, could promote conspecific growth. These
 results support the argument that PCD may differentiate species or
 subtypes and increases inclusive fitness in this model unicellular
 chlorophyte. Further research, however, is needed to identify the
 responsible molecules and how they interact with cells to provide the PCD
 benefits.
description: Methods and statistical analysis are described fully in the
 associated main manuscript. The README.docx file provides all the
 instructions needed to replicate data analysis.
description: R (v4.02) (to run the scripts) and Microsoft office (to open the
 data files).
DOI: 10.5281/zenodo.18256763
title: The Climate Opportunities of Risks of Contrail Avoidance - Output Climate Data Cases 19-27

description: This repository contains climate data that is outputted to the Aviation Climate and Air Quality Impacts model to generate the climate outputs for the journal publication titled The Climate Opportunities and Risks of Contrail Avoidance. The output files in this repository are files 19 to 27 of 36, denoted by the two-digit number at the start of the file.

The climate data that has been deposited relates to the effective radiative forcing and global surface temperature rise due to carbon dioxide emissions from aviation and contrails, produced using Monte Carlo simulations of uncertain parameters, under various contrail avoidance and modified fuel composition scenarios. The data is separated and labelled with respect to these scenarios. Levels of contrail avoidance effectiveness of 0%, 25%, 50% and 75% are labelled as “no_action”, “eff=25%”, “eff=50%”, “eff=75%” respectively. The scenario with a of contrail avoidance effectiveness of 100% is unlabelled. The aviation growth projections (AGPs) of AGP 0.36, AGP 0.29, AGP 0.21 and AGP 0.14 are labelled as “exp_no_sat”, “exp_sat”, “lin” and “no_growth”, respectively. Scenarios that assume a modified fuel composition have the label “SAF”. Fuel burn penalties of 0.35%, 5% and 10% have the labels “0035”, “0500” and “1000”, respectively. Please see The Climate Opportunities and Risks of Contrail Avoidance for more information.
DOI: 10.5061/dryad.c2fqz61c8
title: The effects of exploratory behavior on physical activity in a common animal model of human disease, zebrafish (Danio rerio)

description: Zebrafish (Danio rerio) are widely accepted as a multidisciplinary
 vertebrate model for neurobehavioral and clinical studies, and more
 recently have become established as a model for exercise physiology and
 behavior. Individual differences in activity level (e.g., exploration)
 have been characterized in zebrafish, however, how different levels of
 exploration correspond to differences in motivation to engage in swimming
 behavior has not yet been explored. We screened individual zebrafish in
 two tests of exploration: the open field and novel tank diving tests. The
 fish were then exposed to a tank in which they could choose to enter a
 compartment with a flow of water (as a means of testing voluntary
 motivation to exercise). After a 2-day habituation period, behavioral
 observations were conducted. We used correlative analyses to investigate
 the robustness of the different exploration tests. Due to the complexity
 of dependent behavioral variables, we used machine learning to determine
 the personality variables that were best at predicting swimming behavior.
 Our results show that contrary to our predictions, the correlation between
 novel tank diving test variables and open field test variables was
 relatively weak. Novel tank diving variables were more correlated with
 themselves than open field variables were to each other. Males exhibited
 stronger relationships between behavioral variables than did females. In
 terms of swimming behavior, fish that spent more time in the swimming zone
 spent more time actively swimming, however, swimming behavior was
 inconsistent across the time of the study. All relationships between
 swimming variables and exploration tests were relatively weak, though
 novel tank diving test variables had stronger correlations. Machine
 learning showed that three novel tank diving variables (entries
 top/bottom, movement rate, average top entry duration) and one open field
 variable (proportion of time spent frozen) were the best predictors of
 swimming behavior, demonstrating that the novel tank diving test is a
 powerful tool to investigate exploration. Increased knowledge about how
 individual differences in exploration may play a role in swimming behavior
 in zebrafish is fundamental to their utility as a model of exercise
 physiology and behavior.
DOI: 10.5281/zenodo.18256762
title: The Climate Opportunities of Risks of Contrail Avoidance - Output Climate Data Cases 19-27

description: This repository contains climate data that is outputted to the Aviation Climate and Air Quality Impacts model to generate the climate outputs for the journal publication titled The Climate Opportunities and Risks of Contrail Avoidance. The output files in this repository are files 19 to 27 of 36, denoted by the two-digit number at the start of the file.

The climate data that has been deposited relates to the effective radiative forcing and global surface temperature rise due to carbon dioxide emissions from aviation and contrails, produced using Monte Carlo simulations of uncertain parameters, under various contrail avoidance and modified fuel composition scenarios. The data is separated and labelled with respect to these scenarios. Levels of contrail avoidance effectiveness of 0%, 25%, 50% and 75% are labelled as “no_action”, “eff=25%”, “eff=50%”, “eff=75%” respectively. The scenario with a of contrail avoidance effectiveness of 100% is unlabelled. The aviation growth projections (AGPs) of AGP 0.36, AGP 0.29, AGP 0.21 and AGP 0.14 are labelled as “exp_no_sat”, “exp_sat”, “lin” and “no_growth”, respectively. Scenarios that assume a modified fuel composition have the label “SAF”. Fuel burn penalties of 0.35%, 5% and 10% have the labels “0035”, “0500” and “1000”, respectively. Please see The Climate Opportunities and Risks of Contrail Avoidance for more information.
DOI: 10.5068/d15960
title: Genetic structure and historic demography of endangered unarmored threespine stickleback at southern latitudes signals a need for new management directives

description: Habitat loss, flood control infrastructure, and drought have left most of
 southern California and northern Baja California’s native freshwater fish
 fauna on the brink of extinction, including the endangered unarmored
 threespine stickleback (Gasterosteus aculeatus williamsoni). This
 subspecies, an unusual morph lacking the typical lateral bony plates of
 the G. aculeatus complex, occurs at arid southern latitudes in the eastern
 Pacific Ocean and survives in only three inland locations. Managers have
 been stymied by a lack of molecular data to prioritize conservation
 efforts, including basic questions about the ancestry and genetic
 distinctiveness of unarmored populations. We sampled G. aculeatus from 36
 localities and used microsatellites and whole genome data to place
 unarmored populations within the broader evolutionary context of G.
 aculeatus across southern California/northern Baja California. We
 identified three genetic groups, with none consisting solely of unarmored
 populations. Unlike G. aculeatus at northern latitudes, where Pleistocene
 glaciation has produced similar historical demographic profiles across
 populations, we found markedly different demographies depending on
 sampling location, with inland unarmored populations tending to show
 steeper declines and lower heterozygosity compared to low armored
 populations in coastal lagoons. One exception involved the only
 high-elevation population in the region, where the demography and alleles
 of unarmored fish were similar to low-armored populations near the coast,
 exposing one of several cases of artificial translocation. Our results
 suggest that the current ‘management-by-phenotype’ approach is
 incidentally protecting the most imperiled populations; however,
 redirecting efforts toward the evolutionary units, regardless of
 phenotype, may be more effective at preserving adaptive potential.
DOI: 10.5061/dryad.x69p8czmz
title: Data on: Climate drives the spatiotemporal dynamics of scrub typhus in China

description: This dataset is the data used in the paper of Global change biology
 entitled "Climate drives the spatiotemporal dynamics of scrub typhus
 in China". We incorporate Chinese national surveillance data on scrub
 typhus from 2010 to 2019 into a climate-driven generalized additive mixed
 model to explain the spatiotemporal dynamics of this disease and predict
 how it may be affected by climate change under various representative
 concentration pathways (RCPs) for three future time periods (the 2030s,
 2050s, and 2080s). This dataset provides important information on the
 projected cases of scrub typhus in mainland China under various RCPs
 (RCP4.5, RCP6.0, and RCP8.5) for three future time periods, which can help
 public health authorities refine their prevention and control measures to
 reduce the disease risk.
description: See the Materials and methods section in the original paper.
description: Microsoft Excel are required to open the data files.
DOI: 10.15468/dl.kggsb2
title: Occurrence Download

description: A dataset containing 338 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dolichos trilobus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 338 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003238-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7m0cfxpxr
title: Data for: Mapping the ecological resilience of Atlantic postglacial heaths

description: Anthropogenic heathlands are semi-cultural ecosystems with a unique
 cultural and biodiversity value, considered worthy of preservation across
 most of the world. Their rate of loss, however, is alarming. Currently, we
 know little about the heathlands’ actual span of instability and their
 association with abiotic and anthropogenic factors, including how much
 additional intervention they need to persist. Consequently, we are missing
 out on vital knowledge for conservation, management, and the historical
 persistence of heathlands. This paper develops a method to assess the
 ecological resilience of Atlantic inland heaths in the absence of human
 management. We use 12 existing cases of heathland succession to establish
 a four-step resilience grade for each site, which we regress onto a series
 of explaining factors and use in predicting postglacial heath resilience
 across Atlantic Northern Europe. We find that temperature, humidity,
 elevation and sandiness have a positive correlation with high heathland
 resilience. Our predictive mapping shows an uneven distribution of
 ecological heath resilience across Atlantic Northern Europe within an area
 of 1000x1200 km of 5x5 km resolution. Compared with archaeological and
 palaeoecological evidence, prehistoric heathland distributions far exceed
 areas that afford high heath resilience, suggesting that heath
 distribution and persistence depends on both abiotic and anthropogenic
 factors. Policy implications: The predictive map can be used as an initial
 screening tool for managers working towards heath preservation and
 restoration to predict resilience, prioritize conservation, and to plan
 management practices across Atlantic Northern Europe. The developed model
 and predictive map provide an important initial screening tool to assess
 heathland resilience for ecologists and will help managers to prioritize
 conservation efforts of heathland ecosystems. The results are equally
 relevant for scholars who are interested in humans’ role in increasing and
 decreasing ecosystem resilience. Moreover, we speculate that our
 predictive method can be applied in other regions across the world by
 adding regionally-specific variables.
DOI: 10.5061/dryad.x95x69pmz
title: Data from: Comparison of macro-molluscan assemblages in a protected and a non-protected tropical seagrass ecosystem

description: Humans benefit from a variety of ecosystem services provided by seagrass
 meadows. However, seagrass conservation efforts appear to be insufficient,
 as evidenced by its low representation in marine protected areas around
 the world. Protecting seagrasses benefits not just the seagrass itself,
 but also the macrobenthic invertebrate assemblages that dwell beside it
 and contribute indirectly to the various environmental services through
 their functions. Studies comparing seagrass-associated invertebrate
 assemblages and functional trait composition within and outside marine
 protected areas are uncommon, so the current study compares invertebrate
 assemblages and functional trait composition from a marine protected area
 (Gulf of Mannar Marine National Park) and an adjacent non-marine protected
 area (Palk Bay) along the southeast coast of India. The species richness
 (mean S = 83.3) and density (mean D = 6276.6) of seagrass-associated
 macromolluscs were higher in marine protected areas than in non-marine
 protected areas (mean S = 54.6, mean D = 5264.0), but not the species
 diversity (mean H’ = 2.1 for marine protected areas, mean H’ = 2.0 for
 non-marine protected areas). Protected seagrass ecosystems, on the other
 hand, exhibited much higher species richness within functional groups
 (i.e., deposit feeders (mean S = 5.5), micro-/macro-grazers (21.7),
 predators (34.8), ectoparasites (2.1) and suspension feeders (19.3)),
 suggesting that the protection status supports functional redundancy. The
 study's findings reveal the importance of protection status in
 enhancing macromollusc assemblages in seagrass ecosystems, which improves
 the ecosystem's resilience and function.
description: We conducted field studies to compare protected and unprotected
 seagrass ecosystems in a tropical setting in terms of the richness of the
 macrofauna that is associated with seagrass, particularly macromolluscan
 assemblages. Using quadrats, seagrass diversity and density were
 evaluated. Using modified dredge-trawl and push-net, macromolluscan
 diversity and density were measured and compared between protected and
 unprotected areas. To assess the functional species richness, abundance,
 and diversity between the protection status, the identified macromolluscan
 species were assigned to trophic categories (herbivores, carnivores, and
 omnivores) as well as feeding guild types (deposit feeders,
 micro-/macro-grazers, predators, ectoparasites and suspension
 feeders).
DOI: 10.5061/dryad.n8pk0p2zk
title: Data: Detecting preservation and reintroduction sites for endangered plant species using a two-step modelling and field approach

description: To withstand the surge of species loss worldwide, (re)introduction of
 endangered plant species has become an increasingly common technique in
 conservation biology. Successful (re)introduction plans, however, require
 identifying sites that provide the optimal ecological conditions for the
 target species to thrive. In this study, we propose a two-step approach to
 identify appropriate (re)introduction sites. The first step involves
 modelling the niche and distribution of the species with bioclimatic and
 topographical predictors, both at continental and at national scales. The
 second step consists of refining these bioclimatic predictions by
 analysing stationary ecological parameters, such as soil conditions, and
 relating them to population-level fitness values. We demonstrate this
 methodology using Swiss populations of the lady’s slipper orchid
 (Cypripedium calceolus L., Orchidaceae), for which conservation plans have
 existed for years but have generally been unfruitful. Our workflow
 identified sites for future (re)introductions based on the species
 requirements for mid-to-sunny light conditions and specific soil
 physico-chemical properties, such as basic to neutral pH and low soil
 organic matter content. Our findings show that by combining wide-scale
 bioclimatic modelling with fine scale field measurements it is possible to
 carefully identify the ecological requirements of a target species for
 successful (re)introductions.
description: Data was collected from the field, on natural populations
 of <em>C. calceolus.</em>
DOI: 10.5061/dryad.3r2280gk8
title: Raw data and R code for: Negative effects of urbanisation on diurnal and nocturnal pollen-transport networks

description: Pollinating insects are declining due to habitat loss and climate change,
 and cities with limited habitat and floral resources may be particularly
 vulnerable. The effects of urban landscapes on pollination networks remain
 poorly understood, and comparative studies of taxa with divergent niches
 are lacking. Here, for the first time, we simultaneously compare nocturnal
 moth and diurnal bee pollen-transport networks using DNA metabarcoding and
 ask how pollination networks are affected by increasing urbanisation. Bees
 and moths exhibited substantial divergence in the communities of plants
 they interact with. Increasing urbanisation had comparable negative
 effects on pollen-transport networks of both taxa, with significant
 declines in pollen species richness. We show that moths are an important,
 but overlooked, component of urban pollen-transport networks for wild
 flowering plants, horticultural crops, and trees. Our findings highlight
 the need to include both bee and non-bee taxa when assessing the status of
 critical plant-insect interactions in urbanised landscapes.
description: This is an R markdown file that will use the datasets attached to
 this project. It will reproduce all the analysis (in the order it appears
 in the methods of this manuscript).
DOI: 10.5061/dryad.dz08kps0x
title: Ecology and evolution of competitive trait variation in natural phytoplankton communities under selection

description: Competition for limiting resources is a major force structuring ecological
 communities. Species minimum resource requirements (R*s) can predict
 competitive outcomes and evolve under selection in simple communities
 under controlled conditions. However, whether R*s predict competitive
 outcomes or demonstrate adaptive evolution in naturally complex
 communities is unknown. We subjected natural phytoplankton communities to
 three types of resource limitation (nitrogen, phosphorus, light) in
 outdoor mesocosms over ten weeks. We examined the community composition
 weekly and isolated 21 phytoplankton strains from seven species to
 quantify responses to selection of R* for these resources. We investigated
 evolutionary change in R*s in the dominant species, Desmodesmus armatus.
 R*s were good predictors of species changes in relative abundance, though
 this was largely driven by the success of D. armatus across several
 treatments. This species also demonstrated evolutionary change in R*s
 under resource limitation, supporting the potential for adaptive trait
 change to modify competitive outcomes in natural communities.
description: Data were collected experimentally, in outdoor mesocosms and in
 laboratory-controlled experiments The folder
 "DATA" includes six files: Three files with
 growth curves and growth rates of 21 strains that were isolated from
 outdoor mesocosms, and grown under 10 different levels of a given resource
 (light, nitrogen, phosphorous) One file with Monod
 parameters and R* values for each resource (light, nitrogen, phosphorous),
 calculated at the species level (7 species). One file
 with additional traits measured under laboratory-controlled experiments,
 at the species level: size, maximum growth rate across all resources,
 stoichiometry internal ratios, and R* values. One file
 with taxonomic identification of all phytoplankton taxa grown in the
 outdoor mesocosms, and their abundances.
DOI: 10.5061/dryad.rr4xgxdc0
title: Supplementary materials: Return of the pika: American pikas re-occupy long-extirpated, warm locations

description: To accompany: Return of the pika: American pikas re-occupy
 long-extirpated, warm locations by Constance I. Millar and Andrew T.
 Smith, Nature Notes. American pika re-colonization sites identified in
 this study  Bodie State Historic Park – Noonday Mine 38.004 N;
 -119.1005 W; 2,615 m Site also clearly identified in maps in Smith
 (1974a), Smith & Gilpin (1997), Smith & Nagy (2015). North
 Mono Craters Site 37.9116 N; -118.9985 W; 2,145-2,250 m
description: The primary data include temperatures (deg C) from
 mini-thermochron units placed in American pika habitats. These include
 temperature data from pika haypile surfaces and ~0.5 m below the haypile
 in talus matrices. 
description: Comparative temperature data The following
 four .txt files contain thermochron temperature data (Maxim iButtons) for
 summer 2019 through summer 2020 at two pika sites: 1) North Mono Craters
 (recently re-colonized) and 2) Virginia Canyons (long extant). The files
 represent a thermochron placed on the surface of the haypiles and a
 thermochron in the matrix (0.5 m depth) of the talus below the
 haypile. Table SM1. North Mono Craters, haypile surface
 temperature. Table SM2. North Mono Craters, haypile
 matrix temperature. Table SM3. Virginia Canyon, haypile
 surface temperature. Table SM4. Virginia Canyon,
 haypile matrix temperature.