cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v0668
title: Data from: Responses of social and solitary bees to pulsed floral resources

description: Pulsed food resources lead to mismatches between distribution of consumers
 and resources in space and time. Many studies have investigated how
 pollinators and floral resources covary in space, but few have looked at
 their covariance among years. I studied responses of two bee taxa, Bombus
 (a social genus) and Anthophora (a solitary genus), to variation in
 flowering by Astragalus scaphoides, a perennial herb that flowers in
 alternate years. First, I quantified the rate at which individual plants
 were visited by bees. Anthophora showed evidence of a demographic response
 to resource pulses—that is, more individuals were seen in the year after a
 high-flowering year—whereas Bombus did not. Second, I quantified
 pollinator behavior by following individual bees and recording the
 proportion of visits to A. scaphoides within single foraging bouts. The
 proportion of visits to A. scaphoides by both taxa increased with A.
 scaphoides’s flowering density. Higher specialization in high-flowering
 years likely makes both taxa better pollinators in high-flowering years.
 If these taxa differ in effectiveness as pollinators, then these responses
 translate into variation in pollination services in space and time,
 specifically, more activity by Bombus in high-flowering years and more by
 Anthophora in years following high-flowering years. They also emphasize
 that pollinator activity depends in part on past—as well as current—floral
 resources.
description: focal bee
 dataField observations. See
 original manuscript for more information.focalbee.all.csvfocal plant dataField observations. See original manuscript for more information.focalplantALL.csv
DOI: 10.5061/dryad.nb571
title: Data from: Effects of immune challenge on the oviposition strategy of a noctuid moth

description: Infections can have detrimental effects on the fitness of an animal.
 Reproducing females may therefore be sensitive to cues of infection and be
 able to adaptively change their oviposition strategy in the face of
 infection. As one possibility, females could make a terminal investment
 and shift reproductive effort from future to current reproduction as life
 expectancy decreases. We hypothesized that females of the noctuid moth
 Heliothis virescens make a terminal investment and adapt their oviposition
 timing as well as their oviposition site selectivity in response to an
 immune challenge. We indeed found that females that were challenged with
 the bacterial entomopathogen Serratia entomophila laid more eggs than
 control females one night after the challenge. Additionally,
 bacteria-challenged females were less discriminating between oviposition
 sites than control females. Whereas control females preferred undamaged
 over damaged plants, immune-challenged females did not differentiate
 between the two. These results indicate that terminal investment is part
 of the life history of H. virescens females. Moreover, our results suggest
 that the strategy of terminal investment in H. virescens oviposition
 represents a fitness trade-off for females: in the face of infection, an
 increase in oviposition rate enhances female fitness, whereas low
 oviposition site selectivity reduces female fitness.
description: Oviposition_timing_and_siteExcel file with two sheets, one for oviposition timing, one for oviposition site.StaudacherHvOvipositionetal.xlsx
DOI: 10.5281/zenodo.17438278
title: Molecular dynamics simulation data for "Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins"

description: Molecular dynamics simulation files of the AlphaFold predicted structure of the Chi1-CBD-B interface associated with manuscript titled: "Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins". These simulations were used to validate crosslinking mass spectrometry data against the AlphaFold prediction.

"Legfoot" is an abbreviation for the Chi1 (foot) - CBD-B (leg) interface.

Included are the starting .gro file for the three replicates, the .itp, .top, .ndx and .mdp files to generate new .tpr files from the starting configuration. Additionally, the raw, unprocessed .xtc files for the three replicates are included. To correct for PBC effects for analysis of cross-linking distances, we recomend using the folloiwng GROMACS flags for trjconv: -pbc cluster, -center, -fit rot+trans.

Simulations were performed using GROMACS2022. 

Forcefield: gromos54a7

Water model: SPC216
DOI: 10.5061/dryad.q7c24
title: Data from: Maternal condition and previous reproduction interact to affect offspring sex in a wild mammal

description: Trivers and Willard proposed that offspring sex ratio should vary with
 maternal condition when condition, meant as maternal capacity to care, has
 different fitness consequences for sons and daughters. In polygynous and
 dimorphic species, mothers in good condition should preferentially produce
 sons, whereas mothers in poor condition should produce more daughters.
 Despite its logical appeal, support for this hypothesis has been
 inconsistent. Sex-ratio variation may be influenced by additional factors,
 such as environmental conditions and previous reproduction, which are
 often ignored in empirical studies. We analysed 39 years of data on
 bighorn sheep (Ovis canadensis) that fit all the assumptions of the
 Trivers–Willard hypothesis. Production of sons increased with maternal
 condition only for mothers that weaned a son the previous year. This
 relationship likely reflects a mother's ability to bear the higher
 reproductive costs of sons. The interaction between maternal condition and
 previous weaning success on the probability of producing a son was
 independent of the positive effect of paternal reproductive success.
 Maternal and paternal effects accounted for similar proportions of the
 variance in offspring sex. Maternal reproductive history should be
 considered in addition to current condition in studies of sex allocation.
description: Data used in the
 paper"Datadryad" is
 a dataframe with 9 variables: 1) idmother = mother identity, 2) year =
 year of lamb birth, 3) pws = previous maternal weaning success with 3
 modalities (0 = "no lamb weaned", 1 = "a son weaned",
 2 = "a daugther weaned"), 4) idfather = father identity, 5) sex
 = lamb sex (0 = female, 1 = male), 6) env = environmental conditions, 7)
 condition = maternal condition, 8) age = maternal age, 9) fathersuccess =
 annual paternal reproductive success. All continuous variables have been
 centered and divided by two standard deviations.datadryad.txt
DOI: 10.5061/dryad.qt4q2
title: Data from: A new ophthalmosaurid ichthyosaur from the early Cretaceous of Colombia

description: Cretaceous ichthyosaurs were relatively diverse in temperate latitudes,
 but few species have been described from the palaeotropics. Here, we
 describe a new ophthalmosaurid ichthyosaur, Muiscasaurus catheti gen. et
 sp. nov., from the Barremian–Aptian aged Paja Formation of Colombia. This
 species is known only from a partial skull and differs from all other
 ichthyosaurs in the unusual configuration of the external narial opening,
 slender rostrum, narrow postorbital region, and gracile dentition. It is
 the second ichthyosaur described from the Paja Formation, suggesting
 moderate taxonomic and ecological ichthyosaur diversity in the region
 during the Early Cretaceous.
description: Characters used in
 phylogenetic analysisMaxwelletal_Palaeo_SI.docxData matrix for phylogenetic analysisMesquite formatMaxwellea_S2.nex
DOI: 10.5061/dryad.gt2m0
title: Data from: Mycorrhizas influence functional traits of two tallgrass prairie species

description: Over the past decade, functional traits that influence plant performance
 and thus, population, community, and ecosystem biology have garnered
 increasing attention. Generally lacking, however, has been consideration
 of how ubiquitous arbuscular mycorrhizas influence plant allometric and
 stoichiometric functional traits. We assessed how plant dependence on and
 responsiveness to mycorrhizas influence plant functional traits of a
 warm-season, C4 grass, Andropogon gerardii Vitman, and the contrasting,
 cool-season, C3 grass, Elymus canadensis L. We grew both host species with
 and without inoculation with mycorrhizal fungi, across a broad gradient of
 soil phosphorus availabilities. Both host species were facultatively
 mycotrophic, able to grow without mycorrhizas at high soil phosphorus
 availability. A. gerardii was most dependent upon mycorrhizas and E.
 canadensis was weakly dependent, but highly responsive to mycorrhizas. The
 high dependence of A. gerardii on mycorrhizas resulted in higher tissue P
 and N concentrations of inoculated than noninoculated plants. When not
 inoculated, E. canadensis was able to take up both P and N in similar
 amounts to inoculated plants because of its weak dependence on mycorrhizas
 for nutrient uptake and its pronounced ability to change root-to-shoot
 ratios. Unlike other highly dependent species, A. gerardii had a high
 root-to-shoot ratio and was able to suppress colonization by mycorrhizal
 fungi at high soil fertilities. E. canadensis, however, was unable to
 suppress colonization and had a lower root-to shoot ratio than A.
 gerardii. The mycorrhiza-related functional traits of both host species
 likely influence their performance in nature: both species attained the
 maximum responsiveness from mycorrhizas at soil phosphorus availabilities
 similar to those of tallgrass prairies. Dependence upon mycorrhizas
 affects performance in the absence of mycorrhizas. Responsiveness to
 mycorrhizal fungi is also a function of the environment and can be
 influenced by both mycorrhizal fungus species and soil fertility.
description: All data from
 manuscriptDry weights, root length
 colonized, and leaf nitrogen and phosphorus concentrations for inoculated
 and non-inoculated Andropogon gerardii and Elymus
 canadensis.Dryad
 Data.xlsx
DOI: 10.5281/zenodo.17438277
title: Molecular dynamics simulation data for "Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins"

description: Molecular dynamics simulation files of the AlphaFold predicted structure of the Chi1-CBD-B interface associated with manuscript titled: "Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins". These simulations were used to validate crosslinking mass spectrometry data against the AlphaFold prediction.

"Legfoot" is an abbreviation for the Chi1 (foot) - CBD-B (leg) interface.

Included are the starting .gro file for the three replicates, the .itp, .top, .ndx and .mdp files to generate new .tpr files from the starting configuration. Additionally, the raw, unprocessed .xtc files for the three replicates are included. To correct for PBC effects for analysis of cross-linking distances, we recomend using the folloiwng GROMACS flags for trjconv: -pbc cluster, -center, -fit rot+trans.

Simulations were performed using GROMACS2022. 

Forcefield: gromos54a7

Water model: SPC216
DOI: 10.5061/dryad.843372d
title: Data from: Amino acid-specific δ15N trophic enrichment factor in fish fed with formulated diets varying in protein quantity and quality

description: Compound-specific isotope analysis (CSIA) of amino acids (AAs) in consumer
 tissues is a developing technique with wide-ranging applications for
 identifying nitrogen (N) sources and estimating animal trophic level.
 Controlled experiments are essential for determining which dietary
 conditions influence variability in N stable isotopes (δ15N) trophic
 enrichment factors in bulk tissue (TEF bulk) and AAs (TEF AA). To date,
 however, studies have not independently evaluated the effect of protein
 quantity and quality (digestibility) on TEFs, complicating the application
 of AA-15N values for estimating trophic levels. We conducted a 98-d
 feeding experiment using five formulated isoenergetic feeds prepared with
 a high-quality protein source to evaluate the effect of protein quantity
 and quality on TEFs of liver and muscle tissues of juvenile Pacific
 yellowtail (Seriola lalandi), a carnivorous fish species. We decreased
 protein digestibility using well-established protocols that do not change
 AA profiles. Growth rates were higher in diets with higher protein
 content, and isotopic equilibrium was reached for both fish tissues and
 all treatments. Protein quantity and quality influenced isotope
 discrimination depending on tissue type and AA. In liver tissue, bulk TEFs
 showed a limited but significant relationship with protein quality, but
 did not differ with protein quantity nor quality in muscle. None of the
 pre-established source-AA (Lys, Met, Phe and Gly) TEFs varied
 significantly with protein quantity or quality in liver tissue. However,
 in muscle tissue TEFPhe increased significantly with protein content and
 decreased in response to reduced digestibility, indicating it may not
 serve as proxy for baseline isotopic values used to calculate trophic
 level. Among trophic AA, TEFLeu decreased significantly with increasing
 protein quantity in liver tissue, while both Leu and Ile TEFs decreased
 with lower protein digestibility in muscle tissue. Our results indicate
 that CSIA-AA in liver tissue provide more robust source and trophic
 AA-δ15N values than in muscle.
description: NuchePascual_yellowtail_bulk_CSIA_AA_TEFsNitrogen stable isotopes data of bulk and AA-specific measurements corresponding to: (a) initial composition of the fish muscle and liver tissue prior to the start of the experiment (time 0); (b) the final composition of muscle and liver tissue (day 98); (c) the formulated feeds and the commerciaal diet that was used as a reference.
DOI: 10.5061/dryad.8032
title: Data from: Bayesian analysis of hybridization and introgression between the endangered european mink (Mustela lutreola) and the polecat (Mustela putorius)

description: Human-mediated global change will probably increase the rates of natural
 hybridization and genetic introgression between closely related species,
 and this will have major implications for conservation of the taxa
 involved. In this study, we analyse both mitochondrial and nuclear data to
 characterize ongoing hybridization and genetic introgression between two
 sympatric sister species of mustelids, the endangered European mink
 (Mustela lutreola) and the more abundant polecat (M. putorius). A total of
 317 European mink, 114 polecats and 15 putative hybrid individuals were
 collected from different localities in Europe and genotyped with 13
 microsatellite nuclear markers. Recently developed Bayesian methods for
 assigning individuals to populations and identifying admixture proportions
 were applied to the genetic data. To identify the direction of
 hybridization, we additionally sequenced mtDNA and Y chromosomes from 78
 individuals and 29 males respectively. We found that both hybridization
 and genetic introgression occurred at low levels (3% and 0.9%
 respectively) and indicated that hybridization is asymmetric, as only pure
 polecat males mate with pure European mink females. Furthermore,
 backcrossing and genetic introgression was detected only from female
 first-generation (F1) hybrids of European mink to polecats. This latter
 result implies that Haldane’s rule may apply. Our results suggest that
 hybridization and genetic introgression between the two species should be
 considered a rather uncommon event. However, the current low densities of
 European mink might be changing this trend.
description: data file
 DRYADThis file contains the
 final DNA sequence assembly. DNA sequences: Genbank accession numbers,
 FJ556592 (Mlh-DDX3Y5); FJ556591 (Mph-DDX3Y5); FJ556593-FJ556597 (mtDNA
 haplotypes: Mlh1-Mlh17, Mustela lutreola; Mph25-Mph28, Mustela putorius);
 FJ589734 (mtDNA haplotype for Mustela sibirica); FJ589735 (mtDNA haplotype
 for Neovison vison).
DOI: 10.5061/dryad.82pm0
title: Data from: Interactions between demography, genetics, and landscape connectivity increase extinction probability for a small population of large carnivores in a major metropolitan area

description: The extinction vortex is a theoretical model describing the process by
 which extinction risk is elevated in small, isolated populations owing to
 interactions between environmental, demographic, and genetic factors.
 However, empirical demonstrations of these interactions have been elusive.
 We modelled the dynamics of a small mountain lion population isolated by
 anthropogenic barriers in greater Los Angeles, California, to evaluate the
 influence of demographic, genetic, and landscape factors on extinction
 probability. The population exhibited strong survival and reproduction,
 and the model predicted stable median population growth and a 15%
 probability of extinction over 50 years in the absence of inbreeding
 depression. However, our model also predicted the population will lose
 40–57% of its heterozygosity in 50 years. When we reduced demographic
 parameters proportional to reductions documented in another wild
 population of mountain lions that experienced inbreeding depression,
 extinction probability rose to 99.7%. Simulating greater landscape
 connectivity by increasing immigration to greater than or equal to one
 migrant per generation appears sufficient to largely maintain genetic
 diversity and reduce extinction probability. We provide empirical support
 for the central tenet of the extinction vortex as interactions between
 genetics and demography greatly increased extinction probability relative
 to the risk from demographic and environmental stochasticity alone. Our
 modelling approach realistically integrates demographic and genetic data
 to provide a comprehensive assessment of factors threatening small
 populations.
description: StartingPopulationImmigrantPopulation
DOI: 10.5061/dryad.nm962
title: Data from: Physician assessment of pretest probability of malignancy and adherence with guidelines for pulmonary nodule evaluation

description: The annual incidence of pulmonary nodules is estimated at 1.57 million.
 Guidelines recommend using an initial assessment of nodule probability of
 malignancy (pCA). A previous study found that despite this recommendation,
 physicians did not follow guidelines. METHODS: Physician assessments (N =
 337) and two previously validated risk model assessments of pretest
 probability of cancer were evaluated for performance in 337 patients with
 pulmonary nodules based on final diagnosis and compared.
 Physician-assessed pCA was categorized into low, intermediate, and high
 risk, and the next test ordered was evaluated. RESULTS: The prevalence of
 malignancy was 47% (n = 158) at 1 year. Physician-assessed pCA performed
 better than nodule prediction calculators (area under the curve, 0.85 vs
 0.75; P &lt; .001 and .78; P = .0001). Physicians did not follow
 indicated guidelines when selecting the next test in 61% of cases (n =
 205). Despite recommendations for serial CT imaging in those with low pCA,
 52% (n = 13) were managed more aggressively with PET imaging or biopsy;
 12% (n = 3) underwent biopsy procedures for benign disease. Alternatively,
 in the high-risk category, the majority (n = 103 [75%]) were managed more
 conservatively. Stratified by diagnosis, 92% (n = 22) with benign disease
 underwent more conservative management with CT imaging (20%), PET scanning
 (15%), or biopsy (8%), although three had surgery (8%). CONCLUSIONS:
 Physician assessment as a means for predicting malignancy in pulmonary
 nodules is more accurate than previously validated nodule prediction
 calculators. Despite the accuracy of clinical intuition, physicians did
 not follow guideline-based recommendations when selecting the next
 diagnostic test. To provide optimal patient care, focus in the areas of
 guideline refinement, implementation, and dissemination is needed.
description: chest_pca_data_v1This data file contains the source data for the associated publication.
DOI: 10.5061/dryad.k20ng
title: Data from: Rodent-avoidance, topography and forest structure shape territory selection of a forest bird

description: Background - Understanding the factors underlying habitat selection is
 important in ecological and evolutionary contexts, and crucial for
 developing targeted conservation action in threatened species. However,
 the key factors associated to habitat selection often remain poorly known.
 We evaluated hypotheses related to abiotic and biotic factors thought to
 affect territory selection of the wood warbler Phylloscopus sibilatrix, a
 passerine living in an unpredictable environment owing to irregular rodent
 outbreaks and showing long-term declines particularly in Western Europe.
 Results - Comparing breeding territories to unoccupied areas located
 close-by revealed that territory occupancy in north-western Switzerland
 was positively related to slope steepness (topographic hypothesis
 supported) as well as to numbers of tussocks and trees, respectively,
 while it showed a unimodal relationship to cover of herb layer (forest
 structure hypothesis supported). Furthermore, a strong negative
 correlation between breeding territory occupancy and rodent numbers was
 found, suggesting that wood warblers avoid areas with high rodent
 densities (rodent-avoidance hypothesis supported). Comparing breeding
 territories to abandoned territories showed that breeding territories were
 located on steeper slopes (topography hypothesis supported), at larger
 distance from the forest edge (anthropogenic disturbance hypothesis
 supported) and harboured more trees (forest structure hypothesis
 supported) than abandoned territories. Conclusions - Aside from structural
 and topographic features of the habitat, wood warblers are affected by
 rodent numbers when settling, making habitat selection unpredictable from
 year to year. Forestry practices promoting relatively high tree densities,
 few bushes and an intermediate low-growing ground vegetation cover would
 enhance habitat quality for this declining passerine. In contrast,
 forestry practices aiming at increasing light in forests (selective
 thinning, group-felling) or keeping forest stands permanently covered with
 shrubs, bushes and trees of various sizes (continuous cover forestry) do
 not benefit the wood warbler.
description: occ_contrData used to analyse occupied territories versus nearby control areas (not occupied by wood warblers)occ_abandData used to analyse occupied territories vs. abandoned territories. The readme file is the same as for the data set on occupied territories vs control areas.