cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1m056
title: Data from: Ovarian fluid allows directional cryptic female choice despite external fertilization

description: In species with internal fertilization, females can favour certain males
 over others, not only before mating but also within the female’s
 reproductive tract after mating. Here, we ask whether such directional
 post-mating (that is, cryptic) female mate choice can also occur in
 species with external fertilization. Using an in vitro sperm competition
 experiment, we demonstrate that female ovarian fluid (ovarian fluid)
 changes the outcome of sperm competition by decreasing the importance of
 sperm number thereby increasing the relative importance of sperm velocity.
 We further show that ovarian fluid does not differentially affect sperm
 from alternative male phenotypes, but generally enhances sperm velocity,
 motility, straightness and chemoattraction. Under natural conditions,
 female ovarian fluid likely increases the paternity of the preferred
 parental male phenotype, as these males release fewer but faster sperm.
 These results imply females have greater control over fertilization and
 potential to exert selection on males in species with external
 fertilization than previously thought possible.
description: Alonzo_et_al_Nature_Comm_2016_Expt1This file contains the data from Experiment 1 (the “in vitro” sperm competition experiments. These data are represented in Figures 1 and 2 and Tables 1 and 2.Alonzo_et_al_Nature_Comm_2016_Expt2This file contains the data from Experiment 2 (the experiment examining the effect of ovarian fluid on sperm characteristics). These data are represented in Figure 3.Alonzo_et_al_Nature_Comm_2016_Expt3This file contains the data from Experiment 3 (the experiment examining the effect of ovarian fluid on sperm chemoattraction). These data are represented in Figure 4.
DOI: 10.5061/dryad.pc053
title: Data from: Spatial genetic structure in American black bears (Ursus americanus): female philopatry is variable and related to population history

description: Previously, American black bears (Ursus americanus) were thought to follow
 the pattern of female philopatry and male-biased dispersal. However,
 recent studies have identified deviations from this pattern. Such
 flexibility in dispersal patterns can allow individuals greater ability to
 acclimate to changing environments. We explored dispersal and spatial
 genetic relatedness patterns across ten black bear populations—including
 long established (historic), with known reproduction &gt;50 years ago,
 and newly established (recent) populations, with reproduction recorded
 &lt;50 years ago—in the Interior Highlands and Southern Appalachian
 Mountains, United States. We used spatially-explicit, individual-based
 genetic simulations to model gene flow under scenarios with varying levels
 of population density, genetic diversity, and female philopatry. Using
 measures of genetic distance and spatial autocorrelation, we compared
 metrics between sexes, between population types (historic and recent), and
 among simulated scenarios which varied in density, genetic diversity, and
 sex-biased philopatry. In empirical populations, females in recent
 populations exhibited stronger patterns of isolation-by-distance (IBD)
 than females and males in historic populations. In simulated populations,
 low density populations had a stronger indication of IBD than medium to
 high density populations; however, this effect varied in empirical
 populations. Condition dependent dispersal strategies may permit species
 to cope with novel conditions and rapidly expand populations.
 Pattern-process modelling can provide qualitative and quantitative means
 to explore variable dispersal patterns, and could be employed in other
 species, particularly to anticipate range shifts in response to changing
 climate and habitat conditions.
description: Code for regression of
 slopeWe generated a linear
 regression of genetic distance (Dps) on Euclidean distance for each dyad
 type, then recorded the slope of the linear model. This file provides code
 for one scenario, which included each of the ten simulated
 replicates.SubsamplingRegression_10_01_17.rGenotypes for bears from the Appalachian MountainsFile contains 20-loci genotypes for bears from population sin the Appalachian Mountains. Genotyped by Wildlife Genetics International. Each allele is coded for with three digits.genotypes_appalachian.csvInput for CDPOP simulationsWe used CDPOP v1.2.30 (Landguth and Cushman, 2010) for our simulations. The headers in this file correspond to those required for input into this program. Each line lists one of the individual simulations we ran.cdpop_inputfiles_dryad.csv
DOI: 10.5061/dryad.1f7sk
title: Data from: Linking host traits, interactions with competitors, and disease: mechanistic foundations for disease dilution

description: 1.The size of disease epidemics remains difficult to predict, especially
 when parasites interact with multiple species. Traits of focal hosts like
 susceptibility could directly predict epidemic size, while other traits
 including competitive ability might shape it indirectly in communities
 with a ‘dilution effect’. 2.In a dilution effect, diluter taxa can reduce
 disease by regulating (lowering) the density of focal hosts (i.e., through
 competition), or by reducing encounters between focal hosts and parasites.
 However, these dilution mechanisms are rarely grounded in focal host
 traits, and the relative importance of host regulation vs. encounter
 reduction remains understudied. 3.Here, we map focal host traits to
 disease—via these dilution mechanisms—in communities with diluters. We
 measured two traits (competitive ability and susceptibility) for eight
 genotypes of a focal host (Daphnia), tracked the densities of each
 genotype in experimental mesocosms (+/- Ceriodaphnia competitor/diluters),
 and monitored their infections with a virulent fungal parasite
 (Metschnikowia) over 6-8 host generations. We disentangled the impacts of
 both traits on the density of infected hosts and partitioned dilution
 mechanisms using path models. 4.Higher susceptibility directly fueled
 larger epidemics. Simultaneously, weaker competitive ability indirectly
 suppressed epidemics by enabling higher densities of diluters. These
 higher densities of diluters reduced the density of infected hosts
 indirectly via host regulation. In contrast, encounter reduction was much
 weaker. 5.Our experiment strengthens the dilution effect paradigm with a
 predictable, traits-oriented framework. Similar traits—susceptibility,
 competitive ability, and their covariance—could help predict epidemic
 severity in a variety of other systems. Partitioning the direct and
 indirect effects of diluters could also delineate how they impact disease.
 Such trait-based insights could help broadly predict the size of epidemics
 in diverse communities.
description: time series data for
 mesocosm experimentFC.traits.time.data.csvtraits datatraits.csvR script for linear and path modelsFC.Traits.Traits.R
DOI: 10.5061/dryad.83dv5j7
title: Data from: Large and fast human pyramidal neurons associate with intelligence

description: It is generally assumed that human intelligence relies on efficient
 processing by neurons in our brain. Although gray matter thickness and
 activity of temporal and frontal cortical areas correlate with IQ scores,
 no direct evidence exists that links structural and physiological
 properties of neurons to human intelligence. Here, we find that high IQ
 scores and large temporal cortical thickness associate with larger, more
 complex dendrites of human pyramidal neurons. We show in silico that
 larger dendritic trees enable pyramidal neurons to track activity of
 synaptic inputs with higher temporal precision, due to fast action
 potential kinetics. Indeed, we find that human pyramidal neurons of
 individuals with higher IQ scores sustain fast action potential kinetics
 during repeated firing. These findings provide the first evidence that
 human intelligence is associated with neuronal complexity, action
 potential kinetics and efficient information transfer from input s to
 output within cortical neurons.
description: Numerical data
 tableNumerical data from
 figures 1-5. The table contains cellular data for morphology, physiology
 and modelling used in the article.DataTable_Dryad.xlsx
DOI: 10.5061/dryad.nc66n
title: Data from: Rapid divergence of nesting depth and digging appendages among tunneling dung beetle populations and species

description: Many dung beetle communities are characterized by species that share very
 similar morphological, ecological, and behavioral traits and requirements
 yet appear to be stably maintained. Here, we document that the
 morphologically nearly indistinguishable, sympatric, and syntopic
 tunneling sister species Onthophagus taurus and Onthophagus illyricus may
 be avoiding competitive exclusion by nesting at remarkably different soil
 depths. Intriguingly, we also find rapid divergence in preferred nesting
 depth across native and recently established O. taurus populations.
 Furthermore, geometric morphometric analyses reveal that both inter- and
 intraspecific divergences in nesting depth are paralleled by similar
 changes in the shape of the primary digging appendages, the fore tibiae.
 Collectively, our results identify preferred nesting depth and tibial
 shape as surprisingly evolutionarily labile and with the potential to ease
 interspecific competition and/or to facilitate adaptation to local
 climatic conditions.
description: F0 brood ball
 massBrood ball (BB) mass
 produced by the parental generation across layers of soil in native O.
 illyricus and O. taurus (Italy)F0 BB
 weight.csvF1 body
 sizePronotum width (=body
 size) of emerging offspring across layers of soil in native O. illyricus
 and O. taurus (Italy)Brood ball
 depthBrood balls (BBs)
 harvested from three layers of soil (bottom, center, top) in breeding
 containers (BCs). The dataset includes the date each BC was set up and
 taken down, and the number of females and males used in each. Four
 populations: O. taurus (IT, IN, WA); O. illyricus
 (ILLY).BB
 depth.csvTibia centroid
 sizePronotum width (=body
 size) and tibia centroid size (CS) of 12 randomly selected females per
 population analyzed: O. taurus (IT, IN, WA); O. illyricus
 (ILLY).F0
 tibia CS.csvTibia
 landmarksCoordinates of landmarks
 placed on each tibia specimen [12 randomly selected females per population
 analyzed: O. taurus (IT, IN, WA); O. illyricus (ILLY)]. Images available
 upon request.tibia.tps
DOI: 10.5061/dryad.md0vg
title: Data from: Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli

description: The intestinal microbiota is vital for shaping the local intestinal
 environment as well as host immunity and metabolism. At the same time,
 epidemiological and experimental evidence suggest an important role for
 parasitic worm infections in maintaining the inflammatory and regulatory
 balance of the immune system. In line with this, the prevalence of
 persistent worm infections is inversely correlated with the incidence of
 immune-associated diseases, prompting the use of controlled parasite
 infections for therapeutic purposes. Despite this, the impact of parasite
 infection on the intestinal microbiota, as well as potential downstream
 effects on the immune system, remain largely unknown. We have assessed the
 influence of chronic infection with the large-intestinal nematode
 Trichuris muris, a close relative of the human pathogen Trichuris
 trichiura, on the composition of the murine intestinal microbiota by 16S
 ribosomal-RNA gene-based sequencing. Our results demonstrate that
 persistent T. muris infection dramatically affects the large-intestinal
 microbiota, most notably with a drop in the diversity of bacterial
 communities, as well as a marked increase in the relative abundance of the
 Lactobacillus genus. In parallel, chronic T. muris infection resulted in a
 significant shift in the balance between regulatory and inflammatory T
 cells in the intestinal adaptive immune system, in favour of inflammatory
 cells. Together, these data demonstrate that chronic parasite infection
 strongly influences the intestinal microbiota and the adaptive immune
 system. Our results illustrate the complex interactions between these
 factors in the intestinal tract, and contribute to furthering the
 understanding of this interplay, which is of crucial importance
 considering that 500 million people globally are suffering from these
 infections and their potential use for therapeutic purposes.
description: Immune raw
 data
DOI: 10.5061/dryad.37jg4
title: Data from: What can we learn about beat perception by comparing brain signals and stimulus envelopes?

description: Entrainment of neural oscillations on multiple time scales is important
 for the perception of speech. Musical rhythms, and in particular the
 perception of a regular beat in musical rhythms, is also likely to rely on
 entrainment of neural oscillations. One recently proposed approach to
 studying beat perception in the context of neural entrainment and
 resonance (the “frequency-tagging” approach) has received an enthusiastic
 response from the scientific community. A specific version of the approach
 involves comparing frequency-domain representations of acoustic rhythm
 stimuli to the frequency-domain representations of neural responses to
 those rhythms (measured by electroencephalography, EEG). The relative
 amplitudes at specific EEG frequencies are compared to the relative
 amplitudes at the same stimulus frequencies, and enhancements at
 beat-related frequencies in the EEG signal are interpreted as reflecting
 an internal representation of the beat. Here, we show that
 frequency-domain representations of rhythms are sensitive to the acoustic
 features of the tones making up the rhythms (tone duration, onset/offset
 ramp duration); in fact, relative amplitudes at beat-related frequencies
 can be completely reversed by manipulating tone acoustics. Crucially, we
 show that changes to these acoustic tone features, and in turn changes to
 the frequency-domain representations of rhythms, do not affect beat
 perception. Instead, beat perception depends on the pattern of onsets
 (i.e., whether a rhythm has a simple or complex metrical structure).
 Moreover, we show that beat perception can differ for rhythms that have
 numerically identical frequency-domain representations. Thus,
 frequency-domain representations of rhythms are dissociable from beat
 perception. For this reason, we suggest caution in interpreting direct
 comparisons of rhythms and brain signals in the frequency domain. Instead,
 we suggest that combining EEG measurements of neural signals with creative
 behavioral paradigms is of more benefit to our understanding of beat
 perception.
description: single participant
 behavioral data files.mat files for single
 participants. README.txt file in each zipped folder describes
 columnsdryad_data.zip
DOI: 10.5061/dryad.hp1ct
title: Data from: Restoration and management for plant diversity enhances the rate of belowground ecosystem recovery

description: The positive relationship between plant diversity and ecosystem
 functioning has been criticized for its applicability at large scales and
 in less controlled environments that are relevant to land management. To
 inform this gap between ecological theory and application, we compared
 recovery rates of belowground properties using two chronosequences
 consisting of continuously cultivated and independently restored fields
 with contrasting diversity management strategies: grasslands restored with
 high plant richness and managed for diversity with frequent burning (n=20)
 and grasslands restored with fewer species that were infrequently burned
 (n=15). Restoration and management for plant diversity resulted in 250%
 higher plant richness. Greater recovery of roots and more predictable
 recovery of the active microbial biomass across the high diversity
 management strategy chronosequence corresponded with faster recovery of
 soil structure. The high diversity grasslands also had greater nutrient
 conservation indicated by lower available inorganic nitrogen. Thus, mesic
 grasslands restored with more species and managed for high plant diversity
 with frequent burning enhances the rate of belowground ecosystem recovery
 from long-term disturbance at a scale relevant to conservation practices
 on the landscape.
description: Klopf et al. Ecological
 Applications DataKlopf et al Ecological
 Applications Data.xlsxKlopf et al Ecological
 Applications Dryad README.docx
DOI: 10.5061/dryad.r00n0
title: Data from: Costs and benefits of group living in primates: an energetic perspective

description: Group size is a fundamental component of sociality, and has important
 consequences for an individual's fitness as well as the collective
 and cooperative behaviours of the group as a whole. This review focuses on
 how the costs and benefits of group living vary in female primates as a
 function of group size, with a particular emphasis on how competition
 within and between groups affects an individual's energetic balance.
 Because the repercussions of chronic energetic stress can lower an
 animal's fitness, identifying the predictors of energetic stress has
 important implications for understanding variation in survivorship and
 reproductive success within and between populations. Notably, we extend
 previous literature on this topic by discussing three physiological
 measures of energetic balance—glucocorticoids, c-peptides and thyroid
 hormones. Because these hormones can provide clear signals of metabolic
 states and processes, they present an important complement to field
 studies of spatial and temporal changes in food availability. We
 anticipate that their further application will play a crucial role in
 elucidating the adaptive significance of group size in different social
 and ecological contexts.
description: Raw for
 AnalysesTotal number of
 individuals, biomass (kg), and energetic demand (kg3/4) for 14 baboon
 social groups from 1990-2014 hydrological years (Nov-Oct). Analyses
 included only group-hydrological years in which the focal group was
 censused every calendar month during the hydrological year. Data provided
 by ABRP.Raw for Figure
 2Percent contribution by
 age-sex class to group’s total number of individuals, biomass (kg), and
 energetic demand (kg3/4) for 14 baboon social groups from 1990-2014
 hydrological years (Nov-Oct). Analyses included only group-hydrological
 years in which the focal group was censused every calendar month during
 the hydrological year. Data provided by ABRP.
DOI: 10.5061/dryad.ms750
title: Data from: Enhanced in vitro biocompatibility and osteogenesis of titanium immobilized with dopamine-assisted superparamagnetic Fe3O4 nanoparticles for hBMSCs

description: Titanium(Ti) is an ideal bone substitute due to its superior
 bio-compatibilities and remarkable corrosion resistance properties.
 However, in order to improve the osteoconduction and osteoinduction
 capacity in clinic applications, different kinds of surface modifications
 were usually applied for the Ti alloys. In this study, we fabricated a
 tightly attached PDA-assisted Fe3O4 nanoparticles coating on Ti with
 magnetic properties, aiming to improve the osteogenesis of the Ti
 substrates. The PDA-assisted Fe3O4 nanoparticles coatings were
 characterized by utilizing scanning electron microscopy(SEM), energy
 dispersive spectroscopy(EDS), atom force microscope(AFM), water contact
 angle measurement. Cell attachment and proliferation rate of the hBMSCs on
 the Ti surface were significantly improved with the Fe3O4/PDA coating when
 compared to the pure Ti without coatings. Furthermore, the results of in
 vitro ALP activity at 7, 14 days and ARS staining at 14 days both showed
 that Fe3O4/PDA coating on Ti promoted the osteogenic differentiation of
 hBMSCs. Moreover, hBMSCs co-cultured with the Fe3O4/PDA-coated Ti for
 about 14 days also exhibited significantly higher mRNA expression level of
 alkaline phosphatase(ALP), osteocalcin(OCN) and runt-related transcription
 factor-2(RUNX-2). Our in vitro results revealed that the present
 PDA-assisted Fe3O4 nanoparticles surface coating would be an innovative
 method for Ti surface modification and showed great potential for clinical
 application.
description: raw
 datathe raw data of
 statistics-graphoriginal source of statistical
 graph .zip
DOI: 10.5061/dryad.154
title: Data from: The Beagle collections of Darwin's finches (Geospizinae)

description: [No abstract entered]
description: Morphological
 Measurements of Galapagos FinchesSulloway's
 measurements of the finches collected during Darwin's journey on the
 Beagle.morphSulloway.TABmorphSulloway.xls
DOI: 10.5061/dryad.734c8
title: Data from: Evolution of drug-tolerant nematode populations in response to density reduction

description: Resistance to xenobiotics remains a pressing issue in parasite treatment
 and global agriculture. Multiple factors may affect the evolution of
 resistance, including interactions between life-history traits and the
 strength of selection imposed by different drug-doses. We experimentally
 created replicate selection lines of free-living Caenorhabditis remanei
 exposed to Ivermectin at high and low doses to assess whether survivorship
 of lines selected in drug-treated environments increased, and if this
 varied with dose. Additionally, we maintained lines where mortality was
 imposed randomly to control for differences in density between
 drug-treatments and to distinguish between the evolutionary consequences
 of drug-treatment vs ecological processes due to changes in
 density-dependent feedback. After 10 generations we exposed all of the
 selected lines to high-dose, low-dose and drug-free environments to
 evaluate evolutionary changes in survivorship as well as any costs to
 adaptation. Both adult and juvenile survival was measured to explore
 relationships between life-history stage, selection regime and survival.
 Intriguingly, both drug-selected and random-mortality lines showed an
 increase in survivorship when challenged with Ivermectin; the magnitude of
 this increase varied with the intensity of selection and life-history
 stage. Our results suggest that interactions between density-dependent
 processes and life-history may mediate evolved changes in susceptibility
 to control measures.
description: Selection experiment
 dataThis file contains adult
 survival data and juvenile population counts during the course of the
 selection experiment described in the associated publication. The
 proportion of surviving adults and juveniles numbers are given for
 replicate populations within each treatment.Selection_exp_data.txtResistance bioassay dataThis file contains survival data for the resistance bioassays conducted in the associated publication. The initial number of worms alive and dead is given for each developmental stage (adults and juveniles) and for replicate populations within each treatment from generations 0, 5 and 10 of the selection experiment. In addition, bioassays were conducted at zero, high and low doses of Ivermectin signified in the data set by dose.bioassay.txt