cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7wm37pvsd
title: Trans-ovo permethrin exposure in quail (Cortunix japonica)

description: Permethrin is a commonly used, highly effective pesticide in poultry
 agriculture, and has recently been trialed in conservation efforts to
 protect Galá​pagos finch hatchlings from an invasive ectoparasite.
 Although permethrin is considered safe for adults, pesticides can have
 health consequences when animals are exposed during early life stages. The
 few studies that have examined permethrin’s effects in embryonic chicks
 and rats have shown hydrocephaly, anencephaly, reduced cellular energy
 conversion, and disruption of developing heart muscle. To test
 whether trans-ovo exposure of permethrin affects early
 development in birds, we exposed Japanese quail (Coturnix japonica) eggs
 to cotton treated with 1% permethrin that was incorporated into nests in
 two amounts (0.2, 0.8 g), each with a paired untreated cotton control
 group. When measured on incubation day 15, we found permethrin-treated
 developing birds were smaller and showed signs of microcephaly, although
 mortality rates were the same. Despite no difference in heart mass,
 ventricular tissue was less compact, cardiac arteries were reduced and
 heart rates were slower in permethrin-treated birds. Differences in heart
 development were also observed at 5 days of incubation, indicating that
 abnormalities are present from early in cardiac development. Future
 studies are needed to examine permethrin’s effects on developmental
 pathways and to determine if these effects persist after hatching to
 affect offspring health. This study provides evidence that permethrin can
 cross the eggshell to cause non-lethal but adverse effects on embryonic
 development, and studies should look beyond hatching when monitoring the
 efficacy of permethrin on wild bird populations. 
description: Data was collected on experimental animals at the time of
 euthanasi and after buffered formalin fixation. Data was transferred from
 hand-written tables into Excel then saved as .csv comma-deliminted files
 so they can be imported into a variety of data analysis tools.
DOI: 10.5061/dryad.47d7wm3cp
title: Predators override rainfall effects on tropical food webs

description: Predators alter ecological communities by inducing changes in prey
 abundance and phenotypes, including elemental and isotopic composition.
 Climatic factors are known to often moderate predator effects on prey
 abundance, but few studies consider the combined effects of climate and
 predators on prey phenotype. We examined how altered precipitation
 moderates the effects of predators on the abundance and the chemical
 composition of prey, as well as the indirect effects on the basal
 resource: leaf litter coated in biofilm. Using an experiment with an
 invertebrate food web module from tank bromeliads, we manipulated the
 presence of an odonate predator under scenarios of 10-fold decreased,
 ambient, and 3-fold increased precipitation and measured responses of prey
 and their basal resource. Predators reduced prey abundance while
 precipitation did not. Both precipitation and predators, either singly or
 interactively, affected the elemental composition of prey. Predators
 increased C:N ratios of detritivorous beetles under high precipitation,
 but reduced the C:N ratio of the basal resource. Precipitation reduced the
 N content of filter feeding mosquitoes. The observed changes in chemical
 composition may reflect physiological or developmental responses to stress
 imposed by both predators and drought. This study demonstrates that the
 impact of predators and precipitation can vary substantially across a food
 web, including additive and synergistic effects, and numerical and
 phenotypic responses.
DOI: 10.15468/dl.kc52nc
title: Occurrence Download

description: A dataset containing 453206 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-120.0",
 "HasCoordinate is True",
 "HasGeospatialIssue is False",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "GadmGid is USA.39_1",
 "Year 2015-2025"
 ]
}

 The dataset includes 453206 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002821-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1zcrjdfrg
title: On the Identification of Power-Law Creep Parameters from Conical Indentation

description: Load and hold conical indentation responses calculated for materials
 having creep stress exponents of 1.15, 3.59 and 6.60 are regarded as input
 “experimental” responses. The creep parameters are identified using the
 Bayesian-type statistical approach of Zhang et al. [1] for noise-free and
 noise-contaminated data. A database for the Bayesian-type analysis is
 created using finite element calculations for a relatively coarse set of
 parameter values with interpolation used to create the refined database
 used for parameter identification. The uniaxial creep and stress
 relaxation responses using the identified creep parameters provide a very
 good approximation to those of the “experimental” materials with stress
 exponents of 1.15 and 3.59. The sensitivity to noise increases with
 increasing stress exponent. The uniaxial creep response is more sensitive
 to the accuracy of the predictions than is the uniaxial stress relaxation
 response. Good agreement with the indentation response does not guarantee
 good agreement with the uniaxial response. If the noise level is
 sufficiently small, the model of Bower et al. [2] provides a good fit to
 the “experimental” data for the three values of creep stress exponent
 considered, while the model of Ginder et al. [3] provides a good fit for a
 creep stress exponent of 1.15.
DOI: 10.5061/dryad.612jm6436
title: Manganese limitations and the enhanced soil carbon sequestration of temperate rainforests

description: Manganese (Mn) has been identified as a regulatory bottleneck in the
 accumulation of humus because of its role as an enzymatic co-factor in the
 breakdown of recalcitrant C by Mn-peroxidase (MnP). We tested this abiotic
 limit on decay via contrasting soils along a podzolization gradient of
 coastal British Columbia, where an inverse exponential relationship
 between soil organic carbon (SOC) and exchangeable Mn had been observed.
 Moderately weathered soils (Brunisols) had an average 3.6-fold increase in
 MnP activity within the upper soil profile in comparison to highly
 weathered Podzols. An ordination of the Agaricomycete fungal community,
 which are responsible for MnP production in soils, confirmed significant
 differences in assemblages across soil types for saprotrophic fungi,
 particularly species within the Agaricales, Trechisporales and
 Auriculariales. Ectomycorrhizal fungi of Pseudotsuga menziesii were
 equally aligned with soil type and select taxa more abundant on Brunisols
 may have supplemented MnP activity. A laboratory incubation with an Mn
 amendment produced significant interactions in MnP activity by soil type.
 Surprisingly, MnP activity of both Brunisol substrates declined
 substantially with an amendment (-56% and -40% for forest floor and
 mineral soil, respectively), in contrast to Podzols (-30% and +26%,
 respectively). This inhibitory response was linked to considerable uptake
 of the amendment, and underscores how Mn2+ operates directly on fungi as a
 regulator of mnp transcription for MnP production. Our study highlights a
 new perspective concerning the abiotic drivers underpinning the large,
 expansive soil C stocks across perhumid temperate rainforests of the
 Pacific Northwest.
DOI: 10.5061/dryad.f7m0cfxvs
title: Life history and environment predict variation in testosterone across vertebrates

description: Endocrine systems act as key intermediaries between organisms and their
 environments. This interaction leads to high variability in hormone
 levels, but we know little about the ecological factors that influence
 this variation within and across major vertebrate groups. We study this
 topic by assessing how various social and environmental dynamics influence
 testosterone levels across the entire vertebrate tree of life. Our
 analyses show that breeding season length and mating system are the
 strongest predictors of average testosterone concentrations, whereas
 breeding season length, environmental temperature, and variability in
 precipitation are the strongest predictors of within-population variation
 in testosterone. Principles from small-scale comparative studies that
 stress the importance of mating opportunity and competition on the
 evolution of species differences in testosterone levels therefore likely
 apply to the entire vertebrate lineage. Meanwhile, climatic factors
 associated with rainfall and ambient temperature appear to influence
 variability in plasma testosterone, within a given species. These results
 therefore reveal how unique suites of ecological factors differentially
 explain scales of variation in circulating testosterone across mammals,
 birds, reptiles, amphibians, and fishes.
description: It was aggregated from the Climatic Research Unit Time-Series
 Data.
description: It corresponds to hormone data archived at HormoneBase.org.
DOI: 10.5061/dryad.zcrjdfnb7
title: Field data and microsatellite genotypes of Cercidiphyllum japonicum

description: Field data and genotypes at five microsatellite loci of 281 Cercidiphyllum
 japonicum adults of a population distributed over a ca. 80 ha along a
 stream and 755 C. japonicum current-year seedlings sampled
 at approximate center of the populatoin. The population is
 located in Iwanazawa Forest Reserve (43°13′N, 142°34′E), University of
 Tokyo Hokkaido Forest, in central Hokkaido, Japan.
DOI: 10.5061/dryad.6m905qfzt
title: Western Australian distribution of Acacia saligna

description: Comments were presented on an article published in October 2020 in Ecology
 and Evolution (“Predictive ability of a process-based versus a correlative
 species distribution model”) by Higgins et al. This analyzed natural
 distributions of Australian eucalypt and acacia species and assessed the
 adventive range of selected species outside Australia. Unfortunately,
 inappropriate variables were used with the example MaxEnt species
 distribution model of Acacia saligna when applied outside Australia, so
 that large climatically suitable areas in the Mediterranean area of the
 Northern Hemisphere were not identified. To illustrate the problem, data
 from the natural distribution of A. saligna in Western Australia were
 accessed using the spatial portal of the Atlas of Living Australia (ALA,
 spatial.ala.org.au). The MaxEnt analysis method available in the ALA was
 used to show that large areas of the  Mediterranean Basin are
 climatically suitable for A. saligna.
description: See Ecology and Evolution paper for details.
description: The archived data describe
 the natural distribution of <i>Acacia saligna</i> in Western
 Australia. They were generated by the Atlas of Living Australia (ALA).
 Only the latitude and longitude occurrence data (columns G and H) were
 used in the MaxEnt analysis. Column
 A – Record
 ID – as used by ALA B – Institution –
 Parent organization of collecting agency C – Collection ID
 – identification code for collection D – Collection
 agency  within parent organization F – Locality of
 occurrence G –
 Latitude H –
 Longitude I – Coordinate
 uncertainty in metres J – Collecting
 individual K – Year of
 collection L – Month of
 collection M – Day of
 collection
DOI: 10.5061/dryad.6t1g1jwz6
title: Behavioural response to songs between genetically diverged allopatric populations of Darwin’s small tree finch in the Galápagos

description: Empirical data that identify contemporary mechanisms of divergence shed
 light on how species could multiply. In this study, we measured population
 genetic structure, song syllable diversity, and response to simulated
 intruder song in Darwin’s small tree finch (Camarhynchus parvulus) on
 Santa Cruz and Floreana Islands, Galápagos archipelago. Our aim was to
 test whether the magnitude of contemporary behavioural response in
 resident birds was consistent with patterns of genetic or cultural
 differences between populations. We analysed genetic structure and the
 occurrence of song syllable types, and experimentally measured the
 response of resident birds to intruder bird song from different
 geographical origin (i.e., island) or syllable type. We discovered a weak
 signal of population genetic structure between Santa Cruz and Floreana
 Islands. While some song syllables occurred on both islands, others were
 unique to each island; Santa Cruz Island males used more unique syllables
 than Floreana Island males. Both Santa Cruz and Floreana resident males
 discriminated their response towards a simulated intruder song based on
 the geographical origin of the intruder song, but not on the syllable type
 sung by the intruder. We conclude that the populations are diverging in
 genetic and cultural traits and identified a signal of contemporary
 behavioural response that could maintain divergence upon secondary
 contact.
DOI: 10.5061/dryad.2280gb5rb
title: Negative frequency dependent selection maintains shell banding polymorphisms in two marine snails (Littorina fabalis and L. saxatilis)

description: The presence of shell bands is common in gastropods. The marine snails,
 Littorina fabalis and L. saxatilis, are both polymorphic for this trait.
 Such polymorphism would be expected to be lost by the action of genetic
 drift or directional selection, but it appears to be widespread at
 relatively constant frequencies. This suggests it is maintained by
 balancing selection on the trait or on a genetically linked trait. Using
 long time-series of empirical data, we compared potential effects of
 genetic drift and negative frequency-dependent selection, in the two
 species. The contribution of genetic drift to changes in the frequency of
 bands in L. fabalis was estimated using the effective population size
 estimated from microsatellite data, while the effect of genetic drift in
 L. saxatilis were derived from previously published study.
 Frequency-dependent selection was assessed comparing the cross-product
 estimator of fitness with the frequency of the polymorphism across years
 using a regression analysis. Both studied species showed patterns of
 negative frequency-dependent selection. In addition, in L. fabalis,
 contributions from genetic drift could explain some of the changes in
 banding frequency. Overdominance and heterogeneous selection did not fit
 well to our data. The possible biological explanations resulting on the
 maintenance of the banding polymorphism are discussed.
DOI: 10.5061/dryad.d2547d82c
title: A matter of time: Recovery of plant species diversity in wild plant communities at declining nitrogen deposition

description: Aim: High levels of nitrogen deposition have been responsible for
 important losses of plant species diversity. It is often assumed that
 reduction of ammonia and nitrogen oxide emissions will result in the
 recovery of the former biodiversity. In Western Europe N deposition peaked
 between 1980 and 1988 and declined thereafter. In a 60-year experiment in
 hay meadows we tested the hypothesis that increasing and declining
 nitrogen deposition had negative, respectively, positive effects on plant
 species diversity. Location: Wageningen, The Netherlands Method:
 Duplicated plots received different fertilization treatments from 1958
 onwards (control, Ca, K, P, PK, N, NPK). Productivity, soil pH and species
 composition were measured at regular intervals. In the control plots the
 correlations between N deposition, diversity, production and soil
 acidification were analysed. Subsequently, we tested whether the treatment
 effects (e.g., N addition and liming) confirmed the hypothesized
 interactions. Results: In the control plots soil pH, species diversity and
 the abundance of legumes and short forbs declined between 1958 and 1987
 when atmospheric N deposition was high but recovered after 1987 when N
 deposition decreased. However, also in the N addition plots species
 diversity recovered partly after 1987, although the soil pH of the
 acidified soils in these plots did not. In addition, also in the limed
 plots diversity decreased rapidly during the first 30 years while in this
 treatment soil acidification was more than compensated. Main conclusions:
 We conclude that declining N deposition resulted in the recovery of plant
 species diversity, but not in recovery of the former species composition.
 Time appears to be an additional, but crucial factor for the recovery of
 diverse, flowering meadows. Species not adapted to the new management
 conditions created at the start of the experiment disappeared during the
 first decades, while species fit for the new environment needed many years
 to establish.  
description: See README.pdf
DOI: 10.5281/zenodo.18394491
title: T_tildes_artifact
DOI: 10.5281/zenodo.18173490
title: T_tildes_artifact
DOI: 10.5061/dryad.95x69p8k3
title: Data from: There is only one winner: the negative impact of red deer density on roe deer numbers and distribution in the Słowiński National Park and its vicinity

description: Red and roe deer are the most numerous cervids in Europe and they occur in
 sympatry in most regions. Roe deer were considered to be an inferior
 competitor in studies in which they co-occurred with fallow deer or
 muntjac. Despite the remarkable overlap of their ranges, there are few
 studies on the competition between the red and roe deer. Since
 interspecific interactions among ungulates are often related to their
 mutual densities, the current study focused on the effects of high red
 deer density on the roe deer numbers and spatial distribution in the
 unhunted Słowiński National Park (SNP) in northern Poland and forest
 districts open to hunting bordering the park. Using fecal pellet
 group counts, it was found that in the forest districts (where
 red deer densities were 2-3 times lower than in the SNP), roe deer
 densities were significantly higher than in the park. The red-to-roe deer
 density ratio was 10.8 and 2.7, in the SNP and the surrounding forest
 districts, respectively. Moreover, in the SNP, the roe deer distribution
 was negatively affected by the red deer habitat use, while in the hunting
 areas, such an effect was not recorded. The negative influence of the red
 deer on the roe deer population in the park was most probably due to the
 red deer impact on food availability. The biomass of the plant groups
 forming the staple food of the roe deer (Rubus spp., forbs, dwarf shrubs)
 was significantly higher in the fenced plots than in the unfenced ones.
 Lack of hunting in the protected areas may benefit only some species in
 ungulate assemblages which, in turn, may contradict one of their
 objectives - to maintain viable and ecologically functional populations.
DOI: 10.5061/dryad.gxd2547kt
title: Scale-dependent signatures of local adaptation in a widespread foundation tree species

description: Understanding local adaptation is critical for conservation management
 under rapidly changing environmental conditions. Local adaptation inferred
 from genotype-environment associations may show different genomic patterns
 depending on the spatial scale of sampling, due to differences in the
 slope of environmental gradients and the level of gene flow. We compared
 signatures of local adaptation across the genome of mountain ash
 (Eucalyptus regnans) at two spatial scales: a species-wide dataset and a
 topographically-complex sub-regional dataset. We genotyped 367 individual
 trees at over 3700 single-nucleotide polymorphisms (SNPs), quantified
 patterns of spatial genetic structure among populations, and used two
 analytical methods to identify loci associated with at least one of three
 environmental variables at each spatial scale. Together, the analyses
 identified 549 potentially adaptive SNPs at the sub-region scale, and 435
 SNPs at the range-wide scale. Thirty-nine genic or near-genic SNPs,
 associated with 28 genes, were identified at both spatial scales, although
 no SNP was identified by both methods at both scales. We observed that
 non-genic regions had significantly higher homozygote excess than genic
 regions, possibly due to selective elimination of inbred genotypes during
 stand development. Our results suggest that strong environmental selection
 occurs in mountain ash, and that the identification of putatively adaptive
 loci can differ substantially depending on the spatial scale of analyses.
 We also highlight the importance of multiple adaptive genetic
 architectures for understanding patterns of local adaptation across large
 heterogenous landscapes, with comparison of putatively adaptive loci among
 spatial scales providing crucial insights into the process of adaptation.
description: We used next-generation sequencing data of mountain ash
 (<em>Eucalyptus regnans</em>) to compare patterns of putative
 local adaptation at two spatial scales of sampling. Detailed methods are
 provided in the published manuscript. All bioinformatic
 and R scripts used in the analysis are provided as part of
 this dataset. ANGSD output, scripts, and GDM data are provided in separate
 folders, with separate metadata spreadsheets and unfiltered genotypes
 (filtering steps provided in the main R script).
description: See README file for all details. All sequence
 data in BAM file format has been uploaded to the NCBI Sequence Read
 Archive (PRJNA560448).
DOI: 10.5061/dryad.0rxwdbrzz
title: More than just noise: chance, mating success, and sexual selection

description: Chance plays a critical but under-appreciated role in determining mating
 success. In many cases, we tend to think of chance as background noise
 that can be ignored in studies of mating dynamics. When the influence of
 chance is consistent across contexts, chance can be thought of as
 background noise; in other cases, however, the impact of chance on mating
 success can influence our understanding of how mates are acquired and how
 sexual selection operates. In particular, when the importance of chance
 co-varies with biological or ecological factors in a systematic manner—
 that is when chance becomes consistently more or less important under
 certain conditions– then chance is important to consider if we want to
 fully understand the operation of mate acquisition and sexual selection.
 Here, we present a model that explores how chance co-varies with factors
 such as sex ratio, adult population size, and mating regime in determining
 variation in mating success. We find that in some cases, chance co-varies
 with adult population size and OSR to create variation in mating success.
 We discuss how chance can influence our more general understanding of the
 operation of mating dynamics and sexual selection.
description: See Klug & Stone for the details of the model used to
 generate the datasets.