cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gg1839b
title: Data from: An androgenic endocrine disruptor alters male mating behaviour in the guppy (Poecilia reticulata)

description: Hormonally active chemical pollution threatens human and wildlife
 populations globally. However, despite the well-established capacity of
 endocrine-disrupting chemicals (EDCs) to alter reproductive traits,
 relatively few studies have examined the impacts of EDCs on mechanisms of
 sexual selection. This study investigated the effects of short-term
 exposure to an environmentally realistic level of 17β-trenbolone—a potent
 anabolic steroid used in livestock production worldwide—on male mate
 preference, reproductive behaviour and morphology in the guppy (Poecilia
 reticulata). Male guppies prefer to mate with larger females because such
 females are generally more fecund. Hence, males gain direct fitness
 benefits by being choosy. Here, we found no significant effect of
 17β-trenbolone exposure on male courting behaviour, with both unexposed
 and exposed males courting larger females more often. However, exposure to
 17β-trenbolone significantly altered the amount of coercive copulatory
 behaviour (‘sneak’ matings) performed. Specifically, while both unexposed
 and exposed males demonstrated a preference for larger females by
 conducting more sneaking attempts towards these females, exposed males
 carried out a greater number of sneaks towards large females than did
 unexposed males. Further, exposure resulted in increased male condition
 index (i.e., mass relative to length). Together, our results show for the
 first time that 17β-trenbolone can alter reproductive behaviour and
 morphology in male fish at concentrations as low as 4 ng/L, highlighting
 the potential for disruption of reproductive processes in wildlife exposed
 to this potent agricultural contaminant.
description: Bertram 2018 - Behav
 Ecol
DOI: 10.5061/dryad.ph02r
title: Data from: Reduced mycorrhizal responsiveness leads to increased competitive tolerance in an invasive exotic plant

description: Arbuscular mycorrhizal (AM) fungi can exert a powerful influence on the
 outcome of plant–plant competition. Since some exotic plants interact
 differently with soil biota such as AM fungi in their new range,
 range-based shifts in AM responsiveness could shift competitive
 interactions between exotic and resident plants, although this remains
 poorly studied. We explored whether genotypes of the annual exotic
 Centaurea solstitialis (yellow starthistle), collected from populations
 across the native and non-native ranges, differed in responsiveness to AM
 fungi in the introduced range and whether range-based differences in
 mycorrhizal responsiveness affected how strongly C. solstitialis tolerated
 competition with the North American native bunchgrass, Stipa pulchra.
 Grown alone, C. solstitialis from both ranges derived only weak benefits
 from AM fungi. However, association with AM fungi was costly to plants
 when grown in competition with S. pulchra. The magnitude of the
 suppressive effect of AM fungi was greater for genotypes from native
 versus introduced populations. Synthesis. Many exotic invasive species are
 known to associate weakly with AM fungi, which may be beneficial in
 disturbed habitats where competition for resources is low. Our results
 indicate that reduced mycorrhizal associations may also benefit invaders
 in a competitive environment. Centaurea solstitialis were more strongly
 suppressed by established S. pulchra plants in the presence versus absence
 of AM fungi, but exotic genotypes were less suppressed than native
 genotypes. This suggests that AM fungi may contribute to invasion
 resistance in established native communities, but range-based shifts in
 the way exotic genotypes respond to AM fungal partners may counter such
 biotic resistance.
description: Biomass and root to
 shoot ratiosBiomass (g) and root to
 shoot ratios of Centaurea solstitialis plants originating from North
 America and EuropeBIOMASS.xlsx
DOI: 10.5061/dryad.hr3s0
title: Data from: Indices of immune function used by ecologists are mostly unaffected by repeated freeze-thaw cycles and methodological deviations

description: Background: Over the past couple of decades, measuring immunological
 parameters has become widespread in studies of ecology and evolution. A
 combination of different immunological indices is useful for quantifying
 different parts of the immune system and comprehensively assessing immune
 function. Running multiple immune assays usually requires samples to be
 repeatedly thawed and re-frozen. There is some evidence that repeated
 freezing and thawing can affect assay results, but this has never been
 comprehensively studied in some common ecological immunology assays. We
 tested the effect of multiple (1, 2, 3, 4, 5, 10) freeze-thaw cycles on
 the results of four commonly used immunological assays:
 haemolysis-haemagglutination titres, haptoglobin concentration, bacterial
 killing capacity and total immunoglobulins (IgY). We tested five different
 bird species from four different bird orders (Passeriformes,
 Columbiformes, Charadriiformes and Galliformes), and we included both
 captive and free-living individuals. In addition, we tested for
 haptoglobin concentrations and the haemolysis-haemagglutination assay if
 re-analysing samples 1 year apart led to different results. For the
 haemolysis-haemagglutination assay we also tested two different sources of
 rabbit blood, and we compared untreated microtitre plates with plates that
 were “blocked” to prevent nonspecific interactions between the plate and
 assay reagents. Results: Repeated freezing and thawing of plasma had no
 effect on lysis titres, haptoglobin concentrations, bacterial killing
 capacity, or total immunoglobulin levels. Agglutination titres were
 unaffected by up to five cycles but were lower after ten freeze-thaw
 cycles. For the haemolysis-haemagglutination assay and haptoglobin
 concentrations, re-analysing samples 1 year apart yielded highly
 correlated data. For the haemolysis haemagglutination
 assay,thesourceofrabbit blood did not influence the results, and the
 untreated vs. blocked plates differed slightly overall, but at the
 individual level assay results were highly correlated. Using different
 rabbit blood sources or different types of microtitre plates yielded
 highly correlated data.Conclusions: Our data suggest that repeated
 freeze-thaw cycles do not impair assay results to the point of influencing
 ecological or evolutionary conclusions. Plasma samples can be safely
 stored in one tube and thawed repeatedly for different assays.
 Nevertheless, we recommend consistent treatment of samples in terms of
 freeze-thaw cycles or other laboratory treatments to minimize the
 potential for introducing a systematic bias.
description: data Hegemann et al 2017
 FrontZoolAll data for the
 publication "Hegemann A, Pardal S & Matson KD: Indices of immune
 function used by ecologists are mostly unaffected by repeated freeze-thaw
 cycles and methodological deviations. Frontiers in Zoology 14:43"
 divided over 4 different sheets
DOI: 10.5061/dryad.0157d
title: Data from: Plant genetics and interspecific competitive interactions determine ectomycorrhizal fungal community responses to climate change

description: Although the importance of plant-associated microbes is increasingly
 recognized, little is known about the biotic and abiotic factors that
 determine the composition of that microbiome. We examined the influence of
 plant genetic variation, and two stressors, one biotic and one abiotic, on
 the ectomycorrhizal (EM) fungal community of a dominant tree species,
 Pinus edulis. During three periods across 16 years that varied in drought
 severity, we sampled the EM fungal communities of a wild stand of P.
 edulis in which genetically based resistance and susceptibility to insect
 herbivory was linked with drought tolerance and the abundance of competing
 shrubs. We found that the EM fungal communities of insect-susceptible
 trees remained relatively constant as climate dried, while those of
 insect-resistant trees shifted significantly, providing evidence of a
 genotype by environment interaction. Shrub removal altered the EM fungal
 communities of insect-resistant trees, but not insect-susceptible trees,
 also a genotype by environment interaction. The change in the EM fungal
 community of insect-resistant trees following shrub removal was associated
 with greater shoot growth, evidence of competitive release. However, shrub
 removal had a 7-fold greater positive effect on the shoot growth of
 insect-susceptible trees than insect-resistant trees when shrub density
 was taken into account. Insect-susceptible trees had higher growth than
 insect-resistant trees, consistent with the hypothesis that the EM fungi
 associated with susceptible trees were superior mutualists. These complex,
 genetic-based interactions among species (tree-shrub-herbivore-fungus)
 argue that the ultimate impacts of climate change are both ecological and
 evolutionary.
description: Hypothesis 2 dryad data
 1data
 on shoot length, shoot mortality and cone production used to test
 hypothesis 2.Hypothesis 1 ascomycota
 and spp richness dryad bData on the percentage
 of fungi from the division ascomycota and ectomycorrhizal fungal species
 richness used to test hypothesis 1. This file includes GenBank accession
 numbers and species identity information for the species richness
 data.Hypothesis 2 dryad data
 2bData on the relative
 abundance of ectomycorrhizal fungi used to test hypothesis 2. This file
 includes species names and GenBank accession numbers.
DOI: 10.5061/dryad.6mv5372
title: Data from: Landscape composition, configuration, and trophic interactions shape arthropod communities in rice agroecosystems

description: 1. Increasing landscape heterogeneity of agroecosystems can enhance
 natural enemy populations and promote biological control. However, little
 is known about the multi-scale effects of landscape heterogeneity on
 arthropod communities in rice agroecosystems, especially in combination
 with trophic interactions. 2. We examined for the first time how landscape
 heterogeneity, measured by four independent metrics of landscape
 composition and configuration at three spatial scales, affected species
 abundance and species richness of rice arthropods within four functional
 groups and the abundance of the most common species at 28 sites in the
 Philippines. We additionally examined the influence of trophic
 interactions among these functional groups. 3. We found that both the
 compositional and configurational landscape heterogeneity in combination
 with trophic interactions determine the structure of rice-arthropod
 communities. Herbivore abundance decreased with increasing landscape
 diversity. The abundance of parasitoids and species richness of both
 parasitoids and predators increased with the structural connectivity of
 rice bunds. Fragmentation of the rice landscape had a clear negative
 effect on most arthropod groups, with the exception of highly mobile
 predatory arthropods. Abundance of common predators and detritivore
 species decreased with increasing complexity in the shape of rice patches.
 4. Trophic interactions, measured as the abundance of prey, outweighed the
 importance of landscape heterogeneity for predators. In contrast,
 parasitoids responded positively to configurational landscape
 heterogeneity but were unaffected by prey abundance. 5. Synthesis and
 applications. Landscape heterogeneity and trophic interactions had
 different effects on different functional groups. While predator abundance
 was solely driven by the availability of prey, all other functional groups
 in the rice-arthropod community were significantly affected by the
 composition and configuration of surrounding landscape features. Landscape
 management aiming to improve biodiversity and biological pest control in
 rice agroecosystems should promote a diversity of land uses and habitat
 types within 100–300 m radii to reduce the presence of pests. Management
 practices should also focus on maintaining smaller rice patches and the
 structural connectivity of rice bunds to enhance populations of the
 natural enemies of rice pests. Future research should focus on the
 temporal and spatial manipulation of rice fields to maximize the effects
 of biological control.
description: Effects of landscape
 heterogeneity on the abundance of rice arthropods Data were collected in
 three regions of the Philippines. Data contain the abundance of all
 functional groups and the abundance of the most common species as well as
 environmental data and landscape metrics. Metadata is provided within the
 excel file. Dominik-JAPPL-2018-00200.xlsx
DOI: 10.5061/dryad.pb282
title: Data from: Toxoplasma gondii infection reduces predator aversion in rats through epigenetic modulation in the host medial amygdala

description: Male rats (Rattus novergicus) infected with protozoan Toxoplasma gondii
 relinquish their innate aversion to the cat odors. This behavioral change
 is postulated to increase transmission of the parasite to its definitive
 felid hosts. Here, we show that the Toxoplasma gondii infection institutes
 an epigenetic change in the DNA methylation of the arginine vasopressin
 promoter in the medial amygdala of male rats. Infected animals exhibit
 hypomethylation of arginine vasopressin promoter, leading to greater
 expression of this nonapeptide. The infection also results in the greater
 activation of the vasopressinergic neurons after exposure to the cat odor.
 Furthermore, we show that loss of fear in the infected animals can be
 rescued by the systemic hypermethylation, and recapitulated by directed
 hypomethylation in the medial amygdala. These results demonstrate an
 epigenetic proximate mechanism underlying the extended phenotype in the
 Rattus novergicus – Toxoplasma gondii association.
description: Raw
 dataraw data used to create
 figures in the manuscript.Dryad Dass
 Vyas.xlsx
DOI: 10.5061/dryad.01vm510
title: Data from: Internal acoustic structuring in pied babbler recruitment cries specifies the form of recruitment

description: Language is inherently combinatorial, and parallels of this combinatorial
 capacity are found in nonhuman systems, with animals combining sounds and
 calls into larger meaningful structures. However, further analogue
 examples are central in unveiling the diversity, distribution, and
 evolutionary drivers of combinatoriality. Here, we provide evidence for
 internal “meaning-refining” acoustic variation within a larger stereotyped
 signal in pied babblers (Turdoides bicolor). Using acoustic analyses, we
 demonstrate that males produce 2 long, raucous, “cry-like” structures,
 both starting with a wind-up segment grading into repetitions of
 A/single-note or AB/double-note motifs. Behavioral observations indicated
 that, consistent with similarities in their larger stereotyped structure,
 both variants function overall in recruiting group members during
 locomotion, but the internal A or AB substructure specifies the “precise”
 form of recruitment, from approaching the caller’s announced location to
 following it over longer distances. Playing back cries from a stationary
 loudspeaker further supported that the 2 variants elicit different
 responses, with more individuals approaching the loudspeaker in response
 to single-note compared with double-note cries. Additionally, despite
 similarities in overall distance travelled, group movement was only
 directional for single-note, but undefined for double-note cries. We
 suggest that the overall structure of the 2 cry variants conveys the same
 general meaning, with embedded variation refining this meaning. These
 results further illustrate the variability of generative mechanisms
 outside of human language and lend support to the hypothesis that
 combinatorial structuring may have emerged in species with limited or
 fixed vocal repertoires in order to enhance communicative output.
description: Engesser et al
 2018_Supporting datasetEngesser_et_al_Pied-RecruitmentCries_Dataset.xlsx
DOI: 10.5061/dryad.8jm70
title: Data from: Geometric models to explore mechanisms of dynamic shape change in skeletal muscle

description: Skeletal muscle bulges when it contracts. These 3-dimensional (3D) dynamic
 shape changes play an important role in muscle performance by altering the
 range of fascicle velocities over which a muscle operates. However
 traditional muscle models are 1D and cannot fully explain in vivo shape
 changes. In this study we compared medial gastrocnemius behaviour during
 human cycling (fascicle length changes and rotations) predicted by a
 traditional 1D Hill-type model and by models that incorporate 2D and 3D
 geometric constraints to in vivo measurements from B-mode ultrasound
 during a range of mechanical conditions ranging from 14-44 N m and 80-140
 rpm. We found that a 1D model predicted fascicle lengths and pennation
 angles similar to a 2D model that allowed the aponeurosis to stretch, and
 to a 3D model that allowed for aponeurosis stretch and variable shape
 changes to occur. This suggests that if the intent of a model is to
 predict fascicle behaviour alone, then the traditional 1D Hill-type model
 may be sufficient. Yet, we also caution that 1D models are limited in
 their ability to infer the mechanisms by which shape changes influence
 muscle mechanics. To elucidate the mechanisms governing muscle shape
 change, future efforts should aim to develop imaging techniques able to
 characterize whole muscle 3D geometry in vivo during active contractions.
description: Suppl data_Dick and
 Wakeling OpenSci geometric modelsdata contains two
 spreadsheets with individual subject muscle parameters as compared to
 model predictions and means with standard errors for 3
 models
DOI: 10.5061/dryad.fs6hq7b
title: Data from: Rapid assessment of conformational preferences in biaryl and aryl carbonyl fragments

description: The ability to rapidly assess the preferred conformation of key fragments
 in a structure "by visual inspection" is a very useful starting
 point in the process of drug design. With the ability to do so, one could
 address questions like: "How could we avoid planarity in a
 molecule?", "Will a molecule change its conformational
 preference if we make it more or less basic?" or "How does this
 electronic repulsion affect the conformational preference in the
 system?" in timely fashion. In this paper, we describe how the
 conformational energy profile (CEP, plot of energy as a function of
 dihedral bond angle) of a fragment can be interpreted through the
 understanding the interplay between resonance stabilization, steric
 effects and electrostatic interactions. Fifty-nine biaryl and aryl
 carbonyl fragments present in oral drugs or which are close derivatives
 thereof were selected. Calculation of their CEPs using ab initio
 methodology allowed us to conclude the relative importance of these
 factors in the conformational preference of these fragments as follows:
 steric repulsion &gt; lone pair - lone pair repulsion &gt; lone
 pair - fluorine repulsion &gt; resonance stabilization and, to
 formulate "rules of thumb" that the practicing medicinal/organic
 chemist can apply when analysing molecules that contain these fragments.
description: S1_TableDFT energy value in each studied dihedral angle using 6-31g* or lacvp*for each fragment. Tabulated data to build up the Conformational Energy Profiles for biaryl (1-44) and aryl carbonyl fragments (45-59) 4-pyrimidin-4-ylpyrimidine data was added at the end of the tableS2_TableDFT energy value in each studied dihedral angle using cc-pvtz(-f) for biaryl (1, 4, 5-7, 15, 23-25, 31, 32, 42, 44) and aryl carbonyl fragments (45-47, 50) and cc-pvtz-pp(-f) for 26. Tabulated data to build up the Conformational Energy Profiles for biaryl fragments (1, 4, 5-7, 15, 23-25, 26, 31, 32, 42, 44) and acetophenone 45-47, 49, 50 with a more complex basis sets.Conquest_statistcsStatistical Analysis of extracted data from Cambridge Crystallographic Databases (CSD): Collected data from ConQuest and calculation of True positive, True negative, False positive and False NegativeRelibase_statistcsStatistical Analysis of extracted data from Cambridge Crystallographic Databases (CSD): Collected data from Relibase and calculation of True positive, True negative, False positive and False Negative
DOI: 10.5061/dryad.2k80f
title: Data from: Simultaneous synergist, antagonistic, and additive interactions between multiple local stressors all degrade algal turf communities on coral reefs

description: 1.Ecological communities are subjected to multiple anthropogenic stressors
 at both global and local scales that are increasing in number and
 magnitude. Stressors can interact in complex ways, and are classified as
 additive, synergistic, or antagonistic; the nature of the interaction is
 key to predicting changes and understanding community resilience. Coral
 reefs are among the most impacted communities and have shifted from coral-
 to algal-dominated states, and overfishing, nutrient enrichment, and
 sedimentation are local stressors that often co-occur and may support
 degraded algal states. Short algal turfs are abundant benthic
 space-holders on healthy reefs that may be pushed by local stressors to
 long algal turfs, a more degraded state that may prevent recovery to coral
 dominance. 2. We conducted a fully crossed 3-factor field experiment on
 short algal turf communities manipulating herbivory pressure (+/-cages),
 nutrients (+/-fertilizer), and sediments (natural accumulation/removal).
 We applied stressors for 16 days, removed them, and monitored turf height
 during and after manipulations. 3.We found significant pair-wise
 interactions between all stressors pushed the community toward a degraded
 state with longer algal turfs. All three types of interactions (additive,
 synergistic, and antagonistic) were common and occurred in equal
 frequency, suggesting more investigations into all types are needed to
 accurately predict community responses to multiple stressors. For example,
 when herbivores were present nutrients and sediments interacted additively
 while in the absence of herbivores, nutrients and sediments interacted
 synergistically. All interactions broke down following termination of
 experimental manipulations and all effects were undetectable after 49
 days, indicating this reef may be resilient, at least when stressors are
 applied on a short time scale. 4.Synthesis. Because management of local
 stressors is often more tractable than global stressors, local management
 has been proposed as a means to offset global stressors. However,
 ecological communities often experience multiple local stressors
 simultaneously, and interactions between stressors, including synergisms
 and antagonisms, may be the source of non-linear shifts in communities or
 ‘ecological surprises’. The majority of interactions in our study were
 both strong and non-linear and we suggest that, if pervasive across
 systems, non-linear interactions may drive the recent global increase in
 ‘ecological surprises’.
description: JoE Data for
 DryadTurf and Sediment
 average heights over time