cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sn314pt
title: Data from: How do morphological sharpness measures relate to puncture performance in viperid snake fangs?

description: It makes intuitive sense that you need a sharp tool to puncture through a
 tough material. The typical approach to evaluating sharpness in biological
 puncturing tools is to treat morphological measurements as a proxy for
 puncture ability. However there are multiple approaches to measuring
 sharpness, and the relative influence of morphology on function remains
 unclear. Our goal is to determine what aspects of tip morphology have the
 greatest impact on puncture ability, using a) viper fangs and b)
 engineered punches to isolate the effects of different sharpness measures.
 Our results indicate that tip included angle is the strongest predictor of
 puncture performance in both viper fangs and engineered punches. For
 puncture tools with small included angles, sharpness index (based on
 radius of curvature) also affects puncture ability. Finally, we found that
 punches serve as good predictors of fang performance at small angles and
 sharpness index values.
description: Fang Sharpness
 DataSpecimen morphology and
 FI data for first set of fang tests, second set of fang tests, and punch
 tests
DOI: 10.5061/dryad.6g8qr82
title: Data from: Does body size predict the buzz-pollination frequencies used by bees?

description: Body size is an important trait linking pollinators and plants.
 Morphological matching between pollinators and plants is thought to
 reinforce pollinator fidelity, as the correct fit ensures that both
 parties benefit from the interaction. We investigated the influence of
 body size in a specialized pollination system (buzz‐pollination) where
 bees vibrate flowers to release pollen concealed within poricidal stamens.
 Specifically, we explored how body size influences the frequency of
 buzz‐pollination vibrations. Body size is expected to affect frequency as
 a result of the physical constraints it places on the indirect flight
 muscles that control the production of floral vibrations. Larger insects
 beat their wings less rapidly than smaller‐bodied insects when flying, but
 whether similar scaling relationships exist with floral vibrations has not
 been widely explored. This is important because the amount of pollen
 ejected is determined by the frequency of the vibration and the
 displacement of a bee's thorax. We conducted a field study in three
 ecogeographic regions (alpine, desert, grassland) and recorded flight and
 floral vibrations from freely foraging bees from 27 species across four
 families. We found that floral vibration frequencies were significantly
 higher than flight frequencies, but never exceeded 400 Hz. Also, only
 flight frequencies were negatively correlated with body size. As a
 bee's size increased, its buzz ratio (floral frequency/flight
 frequency) increased such that only the largest bees were capable of
 generating floral vibration frequencies that exceeded double that of their
 flight vibrations. These results indicate size affects the capacity of
 bees to raise floral vibration frequencies substantially above flight
 frequencies. This may put smaller bees at a competitive disadvantage
 because even at the maximum floral vibration frequency of 400 Hz, their
 inability to achieve comparable thoracic displacements as larger bees
 would result in generating vibrations with lower amplitudes, and thus less
 total pollen ejected for the same foraging effort.
description: Bee averages for buzz
 parametersThis data file provides
 the individual bee averages for the various buzz parameters we measured.
 Please see the README text for more information.cbp_20181126.csvIndividual flight and floral vibration measurementsThis data file provides the individual buzz measurements for each floral and flight vibration. Please see the README text for more information.cdat_20181126.csv
DOI: 10.5061/dryad.99k4n5s
title: Data from: Phenotype-environment matching predicts both positive and negative effects of intraspecific variation

description: Natural populations can vary considerably in their genotypic and/or
 phenotypic diversity. Differences in this intraspecific diversity can have
 important consequences for contemporary ecological dynamics, but the
 direction and magnitude of these effects appear inconsistent across
 studies and systems. Here we proposed and tested the hypothesis that
 context-dependent ecological effects of altering phenotypic variance are
 predictable and arise from the relationship between a population’s mean
 phenotype and the local environmental optimum. By factorially manipulating
 the mean and variance of a key host trait in environments with and without
 a lethal parasite, we demonstrate that increasing phenotypic variance can
 have beneficial effects for host populations (e.g. smaller disease
 epidemics), but only when the population’s initial phenotype was
 poorly-matched to the local environment. When phenotypes were initially
 well-suited to environmental conditions, in contrast, greater phenotypic
 variance led to larger disease epidemics. Significant reductions in
 individual susceptibility occurred in both contexts over time, but the
 mechanisms leading to those reductions differed; strong selection was
 caused by either a ‘suboptimal’ trait mean and insufficient trait
 variance, or a ‘near-optimal’ trait mean and too much trait variance.
 Increasing intraspecific variation is clearly not always beneficial for
 populations, instead producing predictable ecological and evolutionary
 effects that depend on environmental context and biological interactions.
description: Life table
 AssayThis is a life table
 assay to quantify individual variation in life history traits of Daphnia.
 Method details are in corresponding mansucriptlifetableEuler.csvData fro variance-mean experimentThis includes data on population dynamics of host and parasite described in the variance-mean treatment in the manuscript.meanvardata.csvPost epidemic infection essayThis essay tested for selection in infection susceptibility of Daphnia hosts after the mean-variance treatment.infectionassay.csv
DOI: 10.5061/dryad.8004512
title: Data from: Cost-efficient high throughput capture of museum arthropod specimen DNA using PCR-generated baits

description: Gathering genetic data for rare species is one of the biggest remaining
 obstacles in modern phylogenetics, particularly for megadiverse groups
 such as arthropods. Next generation sequencing techniques allow for
 sequencing of short DNA fragments contained in preserved specimens
 &gt;20 years old, but approaches such as whole genome sequencing are
 often too expensive for projects including many taxa. Several methods of
 reduced representation sequencing have been proposed that lower the cost
 of sequencing per specimen, but many remain costly because they involve
 synthesizing nucleotide probes and target hundreds of loci. These datasets
 are also frequently unique for each project and thus generally
 incompatible with other similar datasets. Here, we explore utilization of
 in‐house generated DNA baits to capture commonly utilized mitochondrial
 and ribosomal DNA loci from insect museum specimens of various age and
 preservation types without the a priori need to know the sequence of the
 target loci. Both within species and cross‐species capture are explored,
 on preserved specimens ranging in age from one to 54 years old. We found
 most samples produced sufficient amounts of data to assemble the nuclear
 ribosomal rRNA genes and near complete mitochondrial genomes and produce
 well‐resolved phylogenies in line with expected results. The dataset
 obtained can be straightforwardly combined with the large cache of
 existing Sanger‐sequencing‐generated data built up over the past 30 years
 and targeted loci can be easily modified to those commonly used in
 different taxa. Furthermore, the protocol we describe allows for
 inexpensive data generation (as low as ~$35/sample), of at least 20
 kilobases per specimen, for specimens at least as old as ~1965, and can be
 easily conducted in most laboratories. If widely applied, this technique
 will accelerate the accurate resolution of the Tree of Life especially on
 non‐model organisms with limited existing genomic resources.
description: Data matrix for ingroup
 analysisData matrix for ingroup
 analysis, representing concatenated nuclear ribosomal and mitochondrial
 genes and comprising 60 taxa and 18543 positionsin022218-1.phyPartitioning scheme for ingroup analysisPartitioning scheme optimized by PartitionFinder 2.1.1in022218-1-pf2.txtData matrix for outgroup analysisData matrix for outgroup analysis, representing concatenated nuclear ribosomal and 2 mitochondrial genes and comprising 198 taxa and 6051 positionsout022318-1.phyPartitioning scheme for outgroup analysisPartitioning scheme for outgroup analysisout022318-1.txt
DOI: 10.5061/dryad.5757d42
title: Data from: Evidence for contemporary and historical gene flow between guppy populations in different watersheds, with a test for associations with adaptive traits

description: In dendritic river systems, gene flow is expected to occur primarily
 within watersheds. Yet, rare cross‐watershed transfers can also occur,
 whether mediated by (often historical) geological events or (often
 contemporary) human activities. We explored these events and their
 potential evolutionary consequences by analyzing patterns of neutral
 genetic variation (microsatellites) and adaptive phenotypic variation
 (male color) in wild guppies (Poecilia reticulata) distributed across two
 watersheds in northern Trinidad. We found the expected signatures of
 within‐watershed gene flow; yet we also inferred at least two instances of
 cross‐watershed gene flow—one in the upstream reaches and one further
 downstream. The upstream cross‐watershed event appears to be very recent
 (41 ± 13 years), suggesting dispersal via recent flooding or undocumented
 human‐mediated transport. The downstream cross‐watershed event appears to
 be considerably older (577 ± 265 years), suggesting a role for rare
 geological or climatological events. Alongside these strong signatures of
 both contemporary and historical gene flow, we found little evidence of
 impacts on presumably adaptive phenotypic differentiation, except perhaps
 in the one instance of very recent cross‐watershed gene flow. Selection in
 this system seems to overpower gene flow—at least on the spatiotemporal
 scales investigated here.
description: Genotypic and phenotypic
 dataThis excel file contains
 phenotypic data (male color) and microsatellite genotypes (two datasets)
 from guppies located in the Marianne and Paria rivers,
 Trinidad.MS-gene-flow-data-dryad.xlsx
DOI: 10.5061/dryad.617n11q
title: Data from: An integrated iterative annotation technique for easing neural network training in medical image analysis

description: Neural networks promise to bring robust, quantitative analysis to medical
 fields. However, their adoption is limited by the technicalities of
 training these networks and the required volume and quality of
 human-generated annotations. To address this gap in the field of
 pathology, we have created an intuitive interface for data annotation and
 the display of neural network predictions within a commonly used digital
 pathology whole-slide viewer. This strategy used a ‘human-in-the-loop’ to
 reduce the annotation burden. We demonstrate that segmentation of human
 and mouse renal micro compartments is repeatedly improved when humans
 interact with automatically generated annotations throughout the training
 process. Finally, to show the adaptability of this technique to other
 medical imaging fields, we demonstrate its ability to iteratively segment
 human prostate glands from radiology imaging data.
description: Raw_DatasetThis dataset is comprised of T2-weighted magnetic resonance images from 39 patients along with prostate masks that identify where the prostate is on each image. The data format is .tif. Included are 1235 total images. This folder contains the T2 images and masks.Data sorted for analysisThis dataset is comprised of T2-weighted magnetic resonance images from 39 patients along with prostate masks that identify where the prostate is on each image. The data format is .tif. Included are 1235 total images. This is the dataset from the paper analysis sorted into groups.data.zip
DOI: 10.5061/dryad.4dh535d
title: Data from: The evolution of eye size in response to increased fish predation in Daphnia

description: Variation in eye size is ubiquitous across taxa. Increased eye size is
 correlated with improved vision and increased fitness via shifts in
 behavior. Tests of the drivers of eye size evolution have focused on
 macroevolutionary studies evaluating the importance of light availability.
 Predator-induced mortality has recently been identified as a potential
 driver of eye size variation. Here we tested the influence of increased
 predation by the fish predator, the alewife (Alosa pseudoharengus) on eye
 size evolution in waterfleas (Daphnia ambigua) from lakes in Connecticut.
 We quantified the relative eye size of Daphnia from lakes with and without
 alewife using wild-caught and third generation laboratory reared
 specimens. This includes comparisons between lakes where alewife are
 present seasonally (anadromous) or permanently (landlocked). Wild-caught
 specimens did not differ in eye size across all lakes. However, third
 generation lab reared Daphnia from lakes with alewife, irrespective of the
 form of alewife predation, exhibited significantly larger eyes than
 Daphnia from lakes without alewife. This genetically based increase in eye
 size may enhance the ability of Daphnia to detect predators.
 Alternatively, such shifts in eye size may be an indirect response to
 Daphnia aggregating at the bottom of lakes. To test these mechanisms, we
 collected Daphnia as a function of depth and found that eye size differed
 in Daphnia found at the surface versus the bottom of the water column
 between anadromous alewife and no alewife lakes. However, we found no
 evidence of Daphnia aggregating at the bottom of lakes. Such results
 indicate that the evolution of a larger eye may be explained by a
 connection between eyes and enhanced survival. We discuss the cause of the
 lack of concordance in eye size variation between our phenotypic and
 genetic specimens and the ultimate drivers of eye size.
description: Data for densities,
 wild-caught eye size, and lab eye size of DaphniaDaphnia_Eye_MS_Evol_AllData.xlsx
DOI: 10.5061/dryad.s4rr2vf
title: Data from: Clonal diversity impacts coral cover in Acropora cervicornis thickets: potential relationships between density, growth and polymorphisms

description: As coral reefs decline, cryptic sources of resistance and resilience to
 stress may be increasingly important for the persistence of these
 communities. Among these sources, inter‐ and intraspecific diversity
 remain understudied on coral reefs but extensively impact a variety of
 traits in other ecosystems. We use a combination of field and sequencing
 data at two sites in Florida and two in the Dominican Republic to examine
 clonal diversity and genetic differentiation of high‐ and low‐density
 aggregations of the threatened coral Acropora cervicornisin the Caribbean.
 We find that high‐density aggregations called thickets are composed of up
 to 30 genotypes at a single site, but 47% of genotypes are also found as
 isolated, discrete colonies outside these aggregations. Genet–ramet ratios
 are comparable for thickets (0.636) and isolated colonies after
 rarefaction (0.569), suggesting the composition of each aggregation is not
 substantially different and highlighting interactions between colonies as
 a potential influence on structure. There are no differences in growth
 rate, but a significant positive correlation between genotypic diversity
 and coral cover, which may be due to the influence of interactions between
 colonies on survivorship or fragment retention during asexual
 reproduction. Many polymorphisms distinguish isolated colonies from
 thickets despite the shared genotypes found here, including putative
 nonsynonymous mutations that change amino acid sequence in 25 loci. These
 results highlight intraspecific diversity as a density‐dependent factor
 that may impact traits important for the structure and function of coral
 reefs.
description: Mosaic
 ArchiveAll completed mosaics of
 Florida sites, including 1 from Cheetos reef and 4 from Sunny Isles.
 Collected June 2014.Archive.zip
DOI: 10.5061/dryad.rg57q6m
title: Data from: Patterned frequency-modulated oral stimulation in preterm infants: a multicenter randomized controlled trial

description: Objective To evaluate the effect of patterned, frequency-modulated
 oro-somatosensory stimulation on time to full oral feeds in preterm
 infants born 26 - 30 weeks gestation. Study Design This is a multicenter
 randomized controlled trial. The experimental group (n = 109) received
 patterned, frequency-modulated oral stimulation via the NTrainer system
 through a pulsatile pacifier and the control group (n = 101) received a
 non-pulsatile pacifier. Intent-to-treat analysis (n = 210) was performed
 to compare the experimental and control groups and the outcomes were
 analyzed using generalized estimating equations. Time-to-event analyses
 for time to reach full oral feeds and length of hospital stay were
 conducted using Cox proportional hazards models. Results The experimental
 group had reduction in time to full oral feeds compared to the control
 group (-4.1 days, HR 1.37 (1.03, 1.82) p = 0.03). In the 29-30 weeks
 subgroup, infants in the experimental group had a significant reduction in
 time to discharge (-10 days, HR 1.87 (1.23, 2.84) p &lt; 0.01). This
 difference was not observed in the 26-28 weeks subgroup. There was no
 difference in growth, mortality or morbidities between the two groups.
 Conclusions Patterned, frequency-modulated oro-somatosensory stimulation
 improves feeding development in premature infants and reduces their length
 of hospitalization.
description: Data from: Patterned
 Frequency-Modulated Oral Stimulation in Preterm Infants:A Multicenter
 Randomized Controlled TrialSong_ntrainerdeidentified_datadryad_2.13.19.csv
DOI: 10.5061/dryad.766m402
title: Data from: Genetic diversity of Chamaecrista fasciculata (Fabaceae) from the USDA germplasm collection

description: Objective: Chamaecrista fasciculata is a widespread annual legume across
 Eastern North America, with potential as a restoration planting, biofuel
 crop, and genetic model for non-papillinoid legumes. As a non-Papilinoid,
 C. fasciculata, belongs to the Caesalpiniod group in which nodulation
 likely arose independently of the nodulation in Papilinoid and Mimosoid
 legumes. Thus, C. fasciculata is an attractive model system for legume
 evolution. In this study, we describe population structure and genetic
 diversity among 32 USDA germplasm accessions of C. fasciculata using 317
 AFLP markers developed from 12 primer pairs, to assess where
 geographically there is the most genetic variation. Results: We found that
 the C. fasciculata germplasm collection fall into four clusters with
 admixture among them. After correcting for outliers, our analysis shows
 two primary groups across Eastern and Central North America. To better
 understand the population biology of this species, further sampling of the
 full range of this widespread species is needed across North America, as
 well as the development of a larger set of markers providing denser
 coverage of the genome. Further sampling will help clarify geographical
 relationships in this widespread temperate species.
description: data_check_TED_structure_groupsRaw AFLP scoring data
DOI: 10.5061/dryad.20vd145
title: Data from: Homophily around specialized foraging underlies dolphin social preferences

description: Individuals often associate socially with those who behave the same way.
 This principle, homophily, could structure populations into distinct
 social groups. We tested this hypothesis in a bottlenose dolphin
 population that appeared to be clustered around a specialized foraging
 tactic involving cooperation with net-casting fishermen, but in which
 other potential drivers of such social structure have never been assessed.
 We measured and controlled for the contribution of sex, age, genetic
 relatedness, home range, and foraging tactics on social associations to
 test for homophily effects. Dolphins tended to group with others having
 similar home ranges and frequency of using the specialized foraging
 tactic, but not other traits. Such social preferences were particularly
 clear when dolphins were not foraging, showing that homophily extends
 beyond simply participating in a specific tactic. Combined, these findings
 highlight the need to account multiple drivers of group formation across
 behavioural contexts to determine true social affiliations. We suggest
 that homophily around behavioural specialization can be a major driver of
 social patterns, with implications for other social processes. If
 homophily based on specialized tactics underlies animal social structures
 more widely, then it may be important in modulating opportunities for
 social learning, and therefore influence patterns of cultural
 transmission.
description: 01_Dryad_DJ12_groupsThis file contains five variables of 503 groups (rows). date contains information of the sampling period; calf is the presence or absence of calves in the group; behavior contains information of the behavioural state (D = travelling; DP = travelling and foraging; DS = travelling and socializing; P = foraging; S = socializing); coop contains information about the cooperative foraging behaviour, where S refer to groups engaged in cooperative foraging and N to groups that were foraging independently from fishermen. IDs contains the identity of all individuals observed in the groups.03_Dryad_DJ12_id_covThis file contains nine covariables of 52 photo-identified individuals. Id contains the identity of all 52 photo-identified individuals; Freq_Int contains the relative frequency of participation (fp), ranging from 0 to 100%; SEX contains the sex of each individual, where M refer to male individuals, F to femeales and I for those individuals that we were unable to determine the sex; age contains the age class for each individual, classified as adult or senior (individuals observed in the area for more than 30 years); HR is the home range area in km², estimated via fixed kernel methods with a 95% probability contour for each individual04_Dryad_DJ12_relatedness_QThis file contains the pairwise genetic relatedness (Queller and Goodnight index) among 13 individuals.02_Dryad_DJ12_homerangeThis file contains a 35x35 matrix with home range overlap values, ranging from 0 (no overlap) to 1 (completely overlapped).