cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6f052
title: Data from: Geometric morphometric analyses of worn cheek teeth help identify extant and extinct gophers (Rodentia: Geomyidae)

description: Studies of the biostratigraphy and palaeoecology of fossil vertebrate
 assemblages require large samples of accurately identified specimens. Such
 analyses can be hampered by the inability to assign isolated and worn
 remains to specific taxa. Entoptychine gophers are a diverse group of
 burrowing rodents found in Oligo-Miocene deposits of the western United
 States. In both entoptychines and their extant relatives the geomyines,
 diagnostic characters of the occlusal surface of the teeth are modified
 with wear, making difficult the identification of many isolated fossil
 teeth. We use geometric morphometrics to test the hypothesis that tooth
 shape informs taxonomic affinities and expected levels of morphological
 variation across gopher taxa. We also incorporate data from microcomputer
 tomography to investigate changes in occlusal surface shape through wear
 within individuals. Our analyses demonstrate the usefulness of our
 approach in identifying extant geomyines to the genus, subgenus and
 species levels, and fossil entoptychines to the genus and, in some cases,
 the species level. Our results cast doubt on the validity of some species
 within Entoptychus and suggest future revisions to entoptychine taxonomy.
 The amounts of morphological divergence observed among fossil and extant
 genera are similar. Fossil species do not differ greatly from extant ones
 in that regard either. Further work evaluating the morphological variation
 within and across entoptychine species, including unworn teeth and
 osteological material, will allow revised analyses of the biostratigraphy
 and palaeoecology of important Oligo-Miocene mammalian assemblages of the
 western United States and help to infer the phylogenetic relationships and
 evolution of gophers.
description: Data1_ExtantM3DatasetList of extant geomyid specimens used in the analyses of M3 shape. See main manuscript for repository abbreviations.Data2_Extantp4DatasetList of extant geomyid specimens used in the analyses of p4 shape. See main manuscript for repository abbreviations.Data3_FossilM3DatasetList of fossil geomyid specimens used in the analyses of M3 shape. See main manuscript for repository abbreviations.Data4_Fossilp4DatasetList of fossil geomyid specimens used in the analyses of p4 shape. See main manuscript for repository abbreviations.Data5_M3AnalysesScoresResults of the geometric morphometric analyses of M3s.Data6_p4AnalysesScoresResults of the geometric morphometric analyses of p4s.Data7_DistancesPostHocDetails of the posthoc Nemenyi tests between gopher genera (M3 shape).
DOI: 10.5061/dryad.44pf8
title: Data from: Bayesian total-evidence dating reveals the recent crown radiation of penguins

description: The total-evidence approach to divergence time dating uses molecular and
 morphological data from extant and fossil species to infer phylogenetic
 relationships, species divergence times, and macroevolutionary parameters
 in a single coherent framework. Current model-based implementations of
 this approach lack an appropriate model for the tree describing the
 diversification and fossilization process and can produce estimates that
 lead to erroneous conclusions. We address this shortcoming by providing a
 total-evidence method implemented in a Bayesian framework. This approach
 uses a mechanistic tree prior to describe the underlying diversification
 process that generated the tree of extant and fossil taxa. Previous
 attempts to apply the total-evidence approach have used tree priors that
 do not account for the possibility that fossil samples may be direct
 ancestors of other samples, that is, ancestors of fossil or extant species
 or of clades. The fossilized birth–death (FBD) process explicitly models
 the diversification, fossilization, and sampling processes and naturally
 allows for sampled ancestors. This model was recently applied to estimate
 divergence times based on molecular data and fossil occurrence dates. We
 incorporate the FBD model and a model of morphological trait evolution
 into a Bayesian total-evidence approach to dating species phylogenies. We
 apply this method to extant and fossil penguins and show that the modern
 penguins radiated much more recently than has been previously estimated,
 with the basal divergence in the crown clade occurring at ∼12.7∼12.7 Ma
 and most splits leading to extant species occurring in the last 2 myr. Our
 results demonstrate that including stem-fossil diversity can greatly
 improve the estimates of the divergence times of crown taxa. The method is
 available in BEAST2 (version 2.4) software www.beast2.org with packages SA
 (version at least 1.1.4) and morph-models (version at least 1.0.4)
 installed.
description: Supporting
 informationSI.pdfXML files for all analysesxmls.zip
DOI: 10.5061/dryad.m9s45
title: Data from: A metacognitive illusion in monkeys

description: Like humans, monkeys can make accurate judgements about their own memory
 by reporting their confidence during cognitive tasks. Some have suggested
 that animals use associative learning to make accurate confidence
 judgements, while others have suggested animals directly access and
 estimate the strength of their memories. Here we test a third,
 non-exclusive possibility: perhaps monkeys, like humans, base
 metacognitive inferences on heuristic cues. Humans are known to use cues
 like perceptual fluency (e.g. how easy something is to see) when making
 metacognitive judgements. We tested monkeys using a match-to-sample task
 in which the perceptual fluency of the stimuli was manipulated. The
 monkeys made confidence wagers on their accuracy before or after each
 trial. We found that monkeys' wagers were affected by perceptual
 fluency even when their accuracy was not. This is novel evidence that
 animals are susceptible to metacognitive illusions similar to those
 experienced by humans.
description: A metacognitive illusion
 in monkeys - DataFerrigno_Kornell_Cantlon.csv
DOI: 10.5061/dryad.n572r
title: Data from: Population dynamics and threats to an apex predator outside protected areas: implications for carnivore management

description: Data on the population dynamics and threats to large carnivores are vital
 to conservation efforts, but these are hampered by a paucity of studies.
 For some species, such as the leopard (Panthera pardus), there is such
 uncertainty in population trends that leopard trophy hunting has been
 banned in South Africa since 2016 while further data on leopard abundance
 are collected. We present one of the first assessments of leopard
 population dynamics, and identify the key threats to a population of
 leopards outside of protected areas in South Africa. We conducted a
 long-term trap survey between 2012 and 2016 in the Soutpansberg Mountains,
 and drew on a previous estimate of leopard population density for the
 region from 2008. In 24 sampling periods, we estimated the population
 density and assessed population structure. We fitted eight leopards with
 GPS collars to assess threats to the population. Leopard population
 density declined by 66%, from 10.73 to 3.65 leopards per 100 km2 in 2008
 and 2016, respectively. Collared leopards had a high mortality rate, which
 appeared to be due to illegal human activity. While improving the
 management of trophy hunting is important, we suggest that mitigating
 human–wildlife conflict could have a bigger impact on carnivore
 conservation.
description: SPACECAP inputs
 usedZip archive containing
 SPACECAP input files for 24 surveys of leopard population density in the
 Soutpansberg Mountains, South Africa from 2012 to 2016. For each survey
 (for dates see article) the archive contains a - capture history file
 "capture_sXX.csv" - trap deployment file
 "deployment_sXX.csv" - potential home range centres file
 "HRC_s01.csv"ANIMAL_ID coding in
 capture fileDetails of coding used
 in SPACECAP input files. In input files ANIMAL_IDs must be represented as
 sequential numbers. This file shows which ANIMAL_IDs correspond to which
 individual animals.LOC_ID coding in
 deployment filesDetails of coding used
 in SPACECAP input files. In input files LOC_IDs must be represented as
 sequential numbers. This file shows which LOC_IDs correspond to which
 camera station numbers.densityInclExcl2008Camera trap data analysed using "cameraTrapAnalysis.R".leopardTenureCamera trap data analysed using "cameraTrapAnalysis.R".individualsCamera trap data analysed using "cameraTrapAnalysis.R".heatmapLeopardCamera trap data analysed using "cameraTrapAnalysis.R".cameraTrapAnalysisR code used to analyse the datacameraTrapAnalysis outputOutput of data analysisREADMEREADME file containing additional information about the files in this dataset
DOI: 10.5061/dryad.5vp20
title: Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)

description: The honeybee (Apis mellifera) has been threatened by multiple factors,
 including pests and pathogens, pesticides, and loss of locally adapted
 gene complexes due to replacement and introgression. In western Europe,
 the genetic integrity of the native A.m. mellifera (M-lineage) is
 endangered due to trading and intensive queen breeding with commercial
 subspecies of eastern European ancestry (C-lineage). Effective
 conservation actions require reliable molecular tools to identify purebred
 A.m. mellifera colonies. Microsatellites have been preferred for
 identification of A.m. mellifera stocks across conservation centers.
 However, owing to high-throughput, easy transferability between
 laboratories and low genotyping error, SNPs promise to become popular.
 Here, we compared the resolving power of a widely utilized microsatellite
 dataset to detect structure and introgression with that of different
 datasets that combine a variable number of SNPs selected for their
 information content and genomic proximity to the microsatellites. Contrary
 to every SNP dataset, microsatellites were unable to clearly separate the
 two European lineages in the PCA space. Mean introgression proportions
 were identical across the two marker types, although at the individual
 level microsatellites’ performance was relatively poor at the upper range
 of introgression, a result reflected by their lower precision. Although
 mean accuracy was relatively high across datasets (&gt;91%),
 microsatellites were the least accurate and the top-ranked informative 144
 SNPs were the most accurate. Comparisons amongst the SNP datasets showed
 that those combining SNPs flanking microsatellites performed worst. Our
 results suggest that SNPs are more powerful for identification of A.m.
 mellifera colonies, especially when they are selected by information
 content.
description: Genotypes for
 microsatellites and SNPsGenotypes for 11
 microsatellites, 55 and 110 closest SNPs, 48, 96 and 144 AIMs, and 1183
 SNPs for the 77 A. m. mellifera individuals sampled in western Europe
 (M-lineage) and for the 17 A. m. ligustica and 19 A. m. carnica
 individuals sampled in eastern Europe (C-lineage).Dryad_def_Muñoz et
 al.xlsx
DOI: 10.5061/dryad.6v4c0
title: Data from: Partner choice creates fairness in humans

description: Many studies demonstrate that partner choice has played an important role
 in the evolution of human cooperation, but little work has tested its
 impact on the evolution of human fairness. In experiments involving
 divisions of money, people become either over-generous or over-selfish
 when they are in competition to be chosen as cooperative partners. Hence,
 it is difficult to see how partner choice could result in the evolution of
 fair, equal divisions. Here, we show that this puzzle can be solved if we
 consider the outside options on which partner choice operates. We conduct
 a behavioural experiment, run agent-based simulations and analyse a
 game-theoretic model to understand how outside options affect partner
 choice and fairness. All support the conclusion that partner choice leads
 to fairness only when individuals have equal outside options. We discuss
 how this condition has been met in our evolutionary history, and the
 implications of these findings for our understanding of other aspects of
 fairness less specific than preferences for equal divisions of resources.
description: Simulation result files,
 ztree result files and mathematica notebooks for
 analysisData and analysis files
 for paper "Partner choice creates fairness in humans", published
 in Proceedings B, 2015, by Stéphane Debove, Jean-Baptiste André and
 Nicolas Baumard. Please read the README.txt files found in the folders for
 a description of the content of the folders. If more details are needed on
 the data or the analysis, please contact the first author of the
 publication (find contact on personal website at http://stephanedebove.net
 ). Netlogo code is available both within this zip file and as a separate
 download.data_Debove_2015_partner_choice_creates_fairness.zipNetlogo code for the agent-based simulationsThe file fairness_code.nlogo is also available in the zip archive data_Debove_2015_partner_choice_creates_fairness.zipfairness_code.nlogo
DOI: 10.5061/dryad.7v6q3
title: Data from: Vocal traits and diet explain avian sensitivities to anthropogenic noise

description: Global population growth has caused extensive human-induced environmental
 change, including a near-ubiquitous transformation of the acoustical
 environment due to the propagation of anthropogenic noise. Because the
 acoustical environment is a critical ecological dimension for countless
 species to obtain, interpret and respond to environmental cues, highly
 novel environmental acoustics have the potential to negatively impact
 organisms that use acoustics for a variety of functions, such as
 communication and predator/prey detection. Using a comparative approach
 with 308 populations of 183 bird species from 14 locations in Europe,
 North American and the Caribbean, I sought to reveal the intrinsic and
 extrinsic factors responsible for avian sensitivities to anthropogenic
 noise as measured by their habitat use in noisy versus adjacent quiet
 locations. Birds across all locations tended to avoid noisy areas, but
 trait-specific differences emerged. Vocal frequency, diet and foraging
 location predicted patterns of habitat use in response to anthropogenic
 noise, but body size, nest placement and type, other vocal features and
 the type of anthropogenic noise (chronic industrial vs. intermittent
 urban/traffic noise) failed to explain variation in habitat use. Strongly
 supported models also indicated the relationship between sensitivity to
 noise and predictive traits had little to no phylogenetic structure. In
 general, traits associated with hearing were strong predictors – species
 with low-frequency vocalizations, which experience greater spectral
 overlap with low-frequency anthropogenic noise tend to avoid noisy areas,
 whereas species with higher frequency vocalizations respond less severely.
 Additionally, omnivorous species and those with animal-based diets were
 more sensitive to noise than birds with plant-based diets, likely because
 noise may interfere with the use of audition in multimodal prey detection.
 Collectively, these results suggest that anthropogenic noise is a powerful
 sensory pollutant that can filter avian communities nonrandomly by
 interfering with birds' abilities to receive, respond to and dispatch
 acoustic cues and signals.
description: 100
 phylogeniesThe 100 trees used as
 phylogenetic hypotheses in this study were subsets of those developed by
 Jetz et al. (2012) and available through birdtree.org. Several species are
 represented by more than one record in this dataset, thus phylogeny tips
 for those taxa were transformed into multichotomies (i.e., polytomies) in
 each phylogeny. Here, 101 phylogenies are included. Models using the 74th
 phylogeny failed to converge so an additional phylogeny (i.e., phylogeny
 101) was added to complete a set of 100 for the analyses. For all
 phylogenies the tip labels are coded to match the "record_id"
 field code in the corresponding dataset.FrancisGCB2015_FinalTree.treData: responses to noise, species traits, study-specific informationFrancisGCB2015Data.csv
DOI: 10.5061/dryad.5pp17kd
title: Data from: Ergogenic effects of an epidural neuroprosthesis in one individual with spinal cord injury

description: N/A
description: Supplementary Figure
 e-1. Test day and exercise protocolThe participant arrived
 at the laboratory at ~13:00 following a 4 hr fast, having abstained from
 smoking, alcohol, and caffeine for the preceding 16 hrs. Routine bowel
 management was completed &gt;24 hrs prior to each trial. Upon arrival, the
 participant emptied his bladder and confirmed compliance with these
 pre-exercise requirements. The participant was fitted with surface
 electrodes to record EMG (Bagnoli; Delsys Inc) signals across multiple
 muscles, a 12 lead ECG (Cardio-card; Nasiff Associates Inc) and heart rate
 monitor (T1; Polar) prior to testing (A). We took three resting brachial
 blood pressure (BP) measurements (Dinamap Pro 300V2; General Electric)
 before an un-blinded clinician adjusted the neurostimulator (B, C), as per
 the trial allocation, while investigators left the room. We attached a
 facemask to an online metabolic cart (TrueOne 2400®; ParvoMedics) to
 capture breath-by-breath variables. Following a 5 min rest, whereby BP
 measurements were recorded every minute (D), the participant performed a
 two-minute warm-up with no resistance (0W) on an arm-crank ergometer
 (Angio; Lode). We increased power output by 10W/minute, until the
 participant reached volitional exhaustion (E). The participant cycled at
 50 revolutions per minute (rpm) throughout. During every minute of the
 test we recorded the participants global rating of perceived exertion
 (RPE) using a (Borg 6 -20) RPE scale. We defined peak oxygen uptake
 (V̇O2peak) and ventilation as the highest 15-breath rolling averages
 recorded during exercise. A schematic of the trial day is shown in panel
 (F).Supplementary Figure
 e-1.pdf
DOI: 10.5061/dryad.60c370d
title: Data from: Do zombie ant fungi turn their hosts into light seekers?

description: Specialized parasites can modify host behavior to benefit transmission and
 reproduction. Such behavior is considered an extended phenotype of the
 parasite. The interactions between certain ant species and fungi of the
 genus Ophiocordyceps form an evident example. Once infected by
 Ophiocordyceps camponoti-atricipis, Camponotus atriceps ants die, biting
 at specific sites where abiotic conditions are optimal for fungal
 development. For many species of free-living fungi, light is needed to
 induce growth of the reproductive stage. However, the role of light in
 Ophiocordyceps behavioral manipulation and fruiting body development is
 largely unknown. Here, we investigated the association between illuminance
 and the incidence of dead manipulated C. atriceps ants. We identified ant
 graveyards in the field and experimentally changed the incident
 illumination for half of each graveyard using shading screens. Such
 screens resulted in a clear reduction of incident light, as well as
 slightly higher, more stable humidity levels. We measured the appearance
 of recently died, infected ants, the height at which they were found and
 their fruiting body production. The presence of dead infected C. atriceps
 was strongly influenced by experimental light reduction. Shaded areas
 harbored fewer recently infected ants compared to naturally illuminated
 areas. In addition, in shaded areas, a smaller number of ants produced
 fruiting bodies and these ants also appeared to have climbed to higher
 elevations in comparison to control areas. Our findings indicate that
 light influences the place of the C.atriceps death, and fungal development
 by seemingly affecting fruiting body formation in O. camponoti-atricipis.
description: z_ant_lightSite of dead ants monitored by the studylight_sensor_z_antLight sensor collected by the studytemp_rel_humid_z_antRelative-Humidity sensor collected by the study
DOI: 10.5061/dryad.1854
title: Data from: Inbreeding depression increases with environmental stress: an experimental study and meta-analysis

description: Inbreeding-environment interactions occur when inbreeding leads to
 differential fitness loss in different environments. Inbred individuals
 are often more sensitive to environmental stress than are outbred
 individuals, presumably because stress increases the expression of
 deleterious recessive alleles or cellular safeguards against stress are
 pushed beyond the organism's physiological limits. We examined
 inbreeding-environment interactions, along two environmental axes
 (temperature and rearing host) that differ in the amount of developmental
 stress they impose, in the seed-feeding beetle Callosobruchus maculatus.
 We found that inbreeding depression (inbreeding load, L) increased with
 the stressfulness of the environment, with the magnitude of stress
 explaining as much as 66% of the variation in inbreeding depression. This
 relationship between L and developmental stress was not explainable by an
 increase in phenotypic variation in more stressful environments. To
 examine the generality of this experimental result, we conducted a
 meta-analysis of the available data from published studies looking at
 stress and inbreeding depression. The meta-analysis confirmed that the
 effect of the environment on inbreeding depression scales linearly with
 the magnitude of stress; a population suffers one additional lethal
 equivalent, on average, for each 33% reduction in fitness induced by the
 stressful environment.
description: FoxandReed-Larvalsurvival.xlsSurvival data for larvae from two populations (SI=South India and BF=Burkina Faso) of Callosobruchus maculatus reared at three temperature (l=17C, m=27C, h=37C) on two hosts (c=cowpea, m=mung bean). Data are presented as the stage at which larvae died (egg did not develop, egg developed but did not hatch, egg hatched but did not produce an adult, or an adult emerged) for each family. The first sheet presents data for each family. Families are grouped into blocks, with each block containing two inbred and two outbred families, as described in the paper. The additional sheets present summaries of the data, by blocks, or population/treatments. d = inbreeding depression, L = inbreeding load.