cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fqz612jq7
title: Data from: Combining stable isotopes, morphological, and molecular analyses to reconstruct the diet of free-ranging consumers

description: 1. Accurate estimates of animal diet composition are essential to untangle
 complex interactions in food webs. Biomarkers and molecular tools are
 increasingly used to estimate diet, sometimes alongside traditional
 dietary tracing methods. Yet only a few empirical studies have compared
 the outcomes and potential gains of using a combination of these methods,
 especially using free-ranging animals with distinct foraging preferences.
 2. We used stable isotopes, morphological and molecular analyses to
 investigate the diet of free-ranging consumers with two distinct diet
 types, i.e. carnivore and omnivore. By combining the three analytical
 methods to assess the diet of consumers during the same period, we aimed
 to identify the limits of each method and to assess the potential benefits
 of their combined use to derive diet estimates. 3. Our results showed that
 the different methods led to a consistent diet description for carnivores,
 which have a relatively simple diet mixture, but their outcomes somewhat
 differed for omnivore, which have a more complex diet. Still, the combined
 use of morphological and molecular analyses enhanced the diversity of food
 sources detected compared to the use of a single method independently of
 diet types. Precision of diet estimates derived from stable isotope
 analyses was improved by the addition of priors obtained from
 morphological and molecular diet analyses of the same population.
 4.Although we used free-ranging animals without a known diet, our
 empirical testing of three of the most widely used methods of diet
 determination highlights the limits of relying over a single approach,
 especially in systems with few or no a priori information about the
 foraging habits of consumers. The choice of an appropriate approach of
 diet description should be a key step when planning dietary studies of
 free-ranging populations. We recommend using more than one dietary
 determination methods especially for species with complex diet mixtures.
description: README_for_Bonin_et_al_EcoEvo
DOI: 10.5061/dryad.hhmgqnkdf
title: Phylogenetic data for the lichen genus Bacidia originally used to describe a new species, Bacidia gigantensis

description: Bacidia gigantensis, a green to greenish-brown, sorediate, crustose to
 microsquamulose lichen is described a new to science. It is corticolous on
 mature Thuja occidentalis trees throughout Sleeping Giant Provincial Park
 on the Sibley Peninsula along the north shore of Lake Superior, Ontario.
 The species is unusual within Bacidia due to the production of asexual
 propagules and homosekikaic acid. Placement in Bacidia is based on the
 characters of the sexual reproductive structures (biatorine apothecia with
 a true exciple, Bacidia-type asci, sigmoid, acicular, ascospores), ITS
 sequence data and molecular phylogenetic analyses of mtSSU sequence data.
 The latter also inferred a relationship to Bacidiopsora, a tropical genus
 that has been proposed for synonymy with Bacidia and includes other
 species with similar chemistries.
description: New sequence data for Bacidia gigantensis were added to
 pre-exisitng DNA sequence data for the lichen genus Bacidia. All sequence
 data were aligned manually and a phylogenetic tree was built using mtSSU
 sequence data.
DOI: 10.5061/dryad.prr4xgxj4
title: New Age of Fishes initiated by the Cretaceous−Paleogene mass extinction

description: Ray-finned fishes (Actinopterygii) comprise nearly half of all modern
 vertebrate diversity, and are an ecologically and numerically dominant
 megafauna in most aquatic environments. Crown teleost fishes diversified
 relatively recently, during the Late Cretaceous and early Paleogene,
 although the exact timing and cause of their radiation and rise to
 ecological dominance is poorly constrained. Here we use microfossil teeth
 and shark dermal scales (ichthyoliths) preserved in deep-sea sediments to
 study the changes in the pelagic fish community in the latest Cretaceous
 and early Paleogene. We find that the Cretaceous−Paleogene (K/Pg)
 extinction event marked a profound change in the structure of ichthyolith
 communities around the globe: Whereas shark denticles outnumber ray-finned
 fish teeth in Cretaceous deep-sea sediments around the world, there is a
 dramatic increase in the proportion of ray-finned fish teeth to shark
 denticles in the Paleocene. There is also an increase in size and
 numerical abundance of ray-finned fish teeth at the boundary. These
 changes are sustained through at least the first 24 million years of the
 Cenozoic. This new fish community structure began at the K/Pg mass
 extinction, suggesting the extinction event played an important role in
 initiating the modern “age of fishes.”
description: Samples were processed using a standard ImageJ protocol to clean
 the images and find individual light "particles" on a dark
 background. Due to their often semi-transparent nature, often teeth had to
 be "filled in" to ensure that ImageJ found their correct
 borders. This was done iteratively and by hand, until all objects visible
 in the image were captured by the "Analyze Particles" function
 corretly.
description: Open the 4th ("*_BW") image in ImageJ to see the
 particle IDs found using "Analyze Particles" protocol. For some
 reason, the outlines and numbers aren't readable by regular image
 viewers, but are saved in the image and will appear if opened with
 ImageJ. The first number indicates which IODP sample
 the fossils are from, while the second indicates which hole on the
 physical slide they are in - some samples included more fossils than fit
 in a single hole, thus multiple holes were used and imaged. (See
 "Age-Depth Key" files)
DOI: 10.5281/zenodo.18392968
title: SuperDARN data in netCDF format (2006-Feb)

description: 2006-Feb SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5281/zenodo.6632719
title: SuperDARN data in netCDF format (2006-Feb)

description: 2006-Feb SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5061/dryad.f4qrfj6t2
title: The role of habitat diversity in generating the small-island effect

description: The small-island effect (SIE) has become a widespread pattern in island
 biogeography and biodiversity research. However, in most previous studies
 only area is used for the detection of the SIE, while other causal factors
 such as habitat diversity is rarely considered. Therefore, the role of
 habitat diversity in generating SIEs is poorly known. Here, we compiled 86
 global datasets that included the variables of habitat diversity, area and
 species richness to systematically investigate the prevalence and
 underlying factors determining the role of habitat diversity in generating
 SIEs. For each dataset, we used both path analysis and breakpoint
 regressions to identify the existence of an SIE. We collected a number of
 system characteristics and employed logistic regression models and an
 information-theoretic approach to determine which combination of variables
 was important in determining the role of habitat diversity in generating
 SIEs. Among the 61 datasets with adequate fits, habitat diversity was
 found to influence the detection of SIEs in 32 cases (52.5%) when using
 path analysis. By contrast, SIEs were detected in 26 of 61 cases (42.6%)
 using breakpoint regressions. Model selection and model-averaged parameter
 estimates showed that Number of sites, Habitat range and Species range
 were three key variables that determined the role of habitat diversity in
 generating SIEs. However, Area range, Taxon group and Site type received
 considerably less support. Our study demonstrates that the effect of
 habitat diversity on generating SIEs is quite prevalent. The inclusion of
 habitat diversity is important because it provides a causal factor for the
 detection of SIEs. We conclude that for a better understanding of the
 causes of SIEs, habitat diversity should be included in future studies.
DOI: 10.5061/dryad.hhmgqnkdg
title: Using naturalistic incubation temperatures to demonstrate how variation in the timing and continuity of heat wave exposure influences phenotype

description: Most organisms are exposed to bouts of warm temperatures during
 development, yet we know little about how variation in the timing and
 continuity of heat exposure influences biological processes. If heat waves
 increase in frequency and duration as predicted, it is necessary to
 understand how these bouts could affect thermally sensitive species,
 including reptiles with temperature-dependent sex determination (TSD). In
 a multi-year study using fluctuating temperatures, we exposed Trachemys
 scripta embryos to cooler, male-producing temperatures interspersed with
 warmer, female-producing temperatures (heat waves) that varied in either
 timing during development or continuity and then analyzed resulting sex
 ratios. We also quantified the expression of genes involved in testis
 differentiation (Dmrt1) and ovary differentiation (Cyp19A1) to determine
 how heat wave continuity affects the expression of genes involved in
 sexual differentiation. Heat waves applied during the middle of
 development produced significantly more females compared to heat waves
 that occurred just 7 days before or after this window, and even short gaps
 in the continuity of a heat wave decreased the production of females.
 Continuous heat exposure resulted in increased Cyp19A1 expression while
 discontinuous heat exposure failed to increase expression in either gene
 over a similar time course. We report that even small differences in the
 timing and continuity of heat waves can result in drastically different
 phenotypic outcomes. This strong effect of temperature occurred despite
 the fact that embryos were exposed to the same number of warm days during
 a short period of time, which highlights the need to study temperature
 effects under more ecologically relevant conditions where temperatures may
 be elevated for only a few days at a time. In the face of a changing
 climate, the finding that subtle shifts in temperature exposure result in
 substantial effects on embryonic development becomes even more critical.
DOI: 10.5061/dryad.2jm63xskx
title: Data from: Fitness outcomes in relation to individual variation in constitutive innate immune function

description: Although crucial for host survival when facing persistent parasite
 pressure, costly immune functions will inevitably compete for resources
 with other energetically expensive traits such as reproduction.
 Optimising, but not necessarily maximising, immune function might
 therefore provide net benefit to overall host fitness. Evidence for
 associations between fitness and immune function is relatively rare,
 limiting our potential to understand ultimate fitness costs of immune
 investment. Here, we assess how measures of constitutive immune function
 (haptoglobin, natural antibodies, complement activity) relate to
 subsequent fitness outcomes (survival, reproductive success, dominance
 acquisition) in a wild passerine (Malurus coronatus). Surprisingly,
 survival probability was not positively linearly predicted by any immune
 index. Instead, both low and high values of complement activity (quadratic
 effect) were associated with higher survival, suggesting that different
 immune investment strategies might reflect a dynamic disease environment.
 Positive linear relationships between immune indices and reproductive
 success suggest that individual heterogeneity overrides potential resource
 reallocation trade-offs within individuals. Controlling for body condition
 (size-adjusted body mass) and chronic stress (heterophil-lymphocyte ratio)
 did not alter our findings in a sample subset with available data.
 Overall, our results suggest that constitutive immune components have
 limited net costs for fitness and that variation in immune maintenance
 relates to individual differences more closely.
description: These data were collected as part of the long-term purple-crowned
 fairy-wren research project established in 2005 by Anne Peters.
 The code in the accompanying R markdown file was used to analyse
 the dataset for this publication.
description: Individual Band-ID numbers registered with the Australian Bird
 and Bat Banding Scheme (ABBBS) have been de-identified for online
 publication. These Band-ID numbers have been replaced with a 6-character
 alphanumeric string, unique to each individual. Identities of individual
 Band-ID numbers are kept on record with Michael J. Roast and Anne Peters
 and can be re-identified if necessary. Missing row numbers
 constitute records of nestling and fledgling immature birds from the
 long-term dataset that were not included as part of this study. Missing
 data values are noted with NA.
DOI: 10.25345/c53776831
title: MassIVE MSV000100607 - GNPS - MC637 Positive Mode_January_2026
title: Mouse cecum samples. Untargeted LC-MS/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q Exactive-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.1 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA)
DOI: 10.25349/d9w02c
title: Data from: Mechanisms of severe dieback and mortality in a classically drought-tolerant shrubland species (Arctostaphylos glauca)

description: PREMISE Mortality events involving drought and pathogens in natural plant
 systems are on the rise due to global climate change. In the Santa Ynez
 mountain range in Santa Barbara County, California, USA, big berry
 manzanita (Arctostaphylos glauca) has experienced canopy dieback related
 to both a multi-year drought, and infection from fungal pathogens in the
 Botryosphaeriaceae family. METHODS A full factorial greenhouse experiment
 with four treatment groups (drought + inoculation; drought – inoculation;
 watering + inoculation; and control: watering – inoculation) was conducted
 using N. australe to test the specific influences of drought and fungal
 infection on A. glauca. Data were collected on stress symptoms, changes in
 leaf fluorescence and photosynthesis, and mortality. KEY RESULTS A two-way
 ANOVA showed significant effects of watering and inoculation treatments on
 net photosynthesis, dark-adapted fluorescence, and disease symptom
 severity (P &lt; 0.05), and a strong correlation was found between
 physiological decline and visible stress (P &lt; 0.0001). Mortality
 differed between treatments, with all groups except for the control
 experiencing mortality (43% mortality in drought – inoculation, 83% in
 watering – inoculation, and 100% in drought + inoculation). A Kaplan-Meier
 survival analysis showed drought + inoculation to have the least estimated
 survivorship compared to all other treatment groups. CONCLUSIONS In
 addition to a possible synergistic interaction between drought and fungal
 infection in disease onset and mortality rates in A. glauca, these results
 indicate that young, non-drought stressed plants are susceptible to
 mortality from N. australe infection, with important implications for the
 future of wildland shrub communities.
DOI: 10.5281/zenodo.18395221
title: pH-dependent structural dynamics of the neuropeptide Y in aqueous solution

description: All input and parameter files for Molecular Dynamics simulations, Constant pH Molecular Dynamics simulations and all python codes used for analysis can be found here.
DOI: 10.5061/dryad.xsj3tx9bv
title: Data from: Shifts in plant community composition weaken the negative effect of nitrogen addition on community-level arbuscular mycorrhizal fungi colonization

description: Nitrogen addition affects plant-arbuscular mycorrhizal fungi (AMF)
 association greatly. However, although the direct effect of nitrogen
 addition on AMF colonization has received investigation, its indirect
 effect through shifts in plant community composition has never been
 quantified. Based on a 7-year nitrogen addition experiment in an alpine
 meadow of Qinghai-Tibetan Plateau, we investigated the effects of nitrogen
 addition on both plant community, AMF diversity and colonization, and
 disentangled the direct and indirect effects of nitrogen addition on
 community AMF colonization. At plant species level, nitrogen addition
 significantly decreased root colonization rate and altered AMF community
 composition, but with no significant effect on AMF richness. At plant
 community level, plant species richness and AMF colonization rate
 decreased with nitrogen addition. Plant species increasing in abundance
 after nitrogen addition were those with higher AMF colonization rates in
 natural conditions, resulting in an increased indirect effect induced by
 alternation in plant community composition with nitrogen addition, whereas
 the direct effect was negative and decreased with nitrogen addition.
 Overall, we illustrated the effect of nitrogen addition and plant species
 in influencing the AMF diversity, and demonstrated how shifts in plant
 community composition (indirect effect) weakened the negative direct
 effect of nitrogen addition on community-level AMF colonization rate, and
 emphasized the importance of plant community-mediated mechanisms in
 regulating ecosystem functions.
DOI: 10.5061/dryad.dfn2z34xp
title: Concurrent shifts in wintering distribution and phenology in migratory swans

description: Range shifts and phenological change are two processes by which organisms
 respond to environmental warming. Understanding the mechanisms that drive
 these changes is key for optimal conservation and management. Here we
 study both processes in the migratory Bewick’s swan (Cygnus columbianus
 bewickii) using different methods, analysing nearly 50 years of resighting
 data (1970-2017). In this period the wintering area of the Bewick’s swans
 shifted eastwards (“short-stopping”) at a rate of &gt;12.5 km y-1,
 thereby shortening individual migration distance on average by 353 km.
 Concurrently, the time spent at the wintering grounds has reduced
 (“short-staying”) by ~38 days since 1989. We show that individuals are
 consistent in their migratory timing in winter, indicating that the
 frequency of individuals with different migratory schedules has changed
 over time (a generational shift). In contrast, for short-stopping we found
 evidence for both individual plasticity (individuals decrease their
 migration distances over their lifetime) and generational shift.
 Additional analysis of swan resightings with temperature data showed that,
 throughout the winter, Bewick’s swans frequent areas where air
 temperatures are c. 5.5˚C. These areas have also shifted eastwards over
 time, hinting that climate warming is a contributing factor behind the
 observed changes in the swans’ distribution. The occurrence of winter
 short-stopping and short-staying suggests that this species is to some
 extent able to adjust to climate warming, but benefits or repercussions at
 other times of the annual cycle need to be assessed. Furthermore, these
 phenomena could lead to changes in abundance in certain areas, with
 resulting monitoring and conservation implications. Understanding the
 processes and driving mechanisms behind population changes therefore is
 important for population management, both locally and across the species
 range.
description: Data has been collected by a &gt;50 year ring-resighting
 project of both legrings (1970-present) and neckbands
 (1989-present).
DOI: 10.5061/dryad.z08kprr9b
title: Data from: Sick plants in grassland communities: a growth-defense trade-off is the main driver of fungal pathogen abundance

description: Aboveground fungal pathogens can substantially reduce biomass production
 in grasslands. However, we lack a mechanistic understanding of the drivers
 of fungal pathogen infection and impact. Using a grassland global change
 and biodiversity experiment we show that the trade-off between plant
 growth and defense is the main determinant of infection incidence. In
 contrast, nitrogen addition only indirectly increased incidence via
 shifting plant communities towards faster growing species. Plant diversity
 did not decrease incidence, likely because spillover of generalist
 pathogens or dominance of susceptible plants counteracted negative
 diversity effects. A fungicide treatment increased plant biomass
 production and high levels of infection incidence were associated with
 reduced biomass. However, pathogen impact was context dependent and
 infection incidence reduced biomass more strongly in diverse communities.
 Our results show that a growth-defense trade-off is the key driver of
 pathogen incidence, but pathogen impact is determined by several
 mechanisms and may depend on pathogen community composition.