cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nj2mg77
title: Data from: A demonstration of unsupervised machine learning in species delimitation

description: One major challenge to delimiting species with genetic data is
 successfully differentiating population structure from species-level
 divergence, an issue exacerbated in taxa inhabiting naturally fragmented
 habitats. Many fields of science are now using machine learning, and in
 evolutionary biology supervised machine learning has recently been used to
 infer species boundaries. These supervised methods require training data
 with associated labels. Conversely, unsupervised machine learning (UML)
 uses inherent data structure and does not require user-specified training
 labels, potentially providing more objectivity in species delimitation.
 Here we demonstrate the utility of three UML approaches (random forests,
 variational autoencoders, t-distributed stochastic neighbor embedding) for
 species delimitation in an arachnid taxon with high population genetic
 structure (Opiliones, Laniatores, Metanonychus). We find that UML
 approaches successfully cluster samples according to species-level
 divergences and not high levels of population structure, while model-based
 validation methods severely over-split putative species. UML offers
 intuitive data visualization in two-dimensional space, the ability to
 accommodate various data types, and has potential in many areas of
 systematic and evolutionary biology. We argue that machine learning
 methods are ideally suited for species delimitation and may perform well
 in many natural systems and across taxa with diverse biological
 characteristics.
description: Input
 MatricesData Input matrices used
 for all analyses conducted in this study (COI, UCE, and SNP
 data).Metanonychus_Input_Matrices.zipUCE alignments 50% taxon coverageIndividual UCE locus alignments included in the 50% taxon coverage datasetMetanonychus_UCEalignments_50percent.zipUCE alignments 70% taxon coverageIndividual UCE locus alignments included in the 70% taxon coverage datasetMetanonychus_UCEalignments_70percent.zipPhylogeniesResulting tree files for the COI and UCE 70% taxon coverage analyses.
DOI: 10.5061/dryad.25pp406
title: Data from: Engineered action at a distance: blood-meal-inducible paralysis in Aedes aegypti

description: Background: Population suppression through mass-release of Aedes aegypti
 males carrying dominant-lethal transgenes has been demonstrated in the
 field. Where population dynamics show negative density-dependence,
 suppression can be enhanced if lethality occurs after the
 density-dependent (i.e. larval) stage. Existing molecular tools have
 limited current examples of such Genetic Pest Management (GPM) systems to
 achieving this through engineering ‘cell-autonomous effectors’ i.e. where
 the expressed deleterious protein is restricted to the cells in which it
 is expressed – usually under the control of the regulatory elements (e.g.
 promoter regions) used to build the system. This limits the flexibility of
 these technologies as regulatory regions with useful spatial, temporal or
 sex-specific expression patterns may only be employed if the cells they
 direct expression in are simultaneously sensitive to existing effectors,
 and also precludes the targeting of extracellular regions such as
 cell-surface receptors. Expanding the toolset to ‘non-cell autonomous’
 effectors would significantly reduce these limitations.
 Methodology/Principal Findings: We sought to engineer female-specific,
 late-acting lethality through employing the Ae. aegypti VitellogeninA1
 promoter to drive blood-meal-inducible, fat-body specific expression of
 tTAV. Initial attempts using pro-apoptotic effectors gave no evident
 phenotype, potentially due to the lower sensitivity of
 terminally-differentiated fat-body cells to programmed-death signals.
 Subsequently, we dissociated the temporal and spatial expression of this
 system by engineering a novel synthetic effector (Scorpion neurotoxin –
 TetO-gp67.AaHIT) designed to be secreted out of the tissue in which it was
 expressed (fat-body) and then affect cells elsewhere (neuro-muscular
 junctions). This resulted in a striking, temporary-paralysis phenotype
 after blood-feeding. Conclusions/Significance: These results are
 significant in demonstrating for the first time an engineered ‘action at a
 distance’ phenotype in a non-model pest insect. The potential to
 dissociate temporal and spatial expression patterns of useful endogenous
 regulatory elements will extend to a variety of other pest insects and
 effectors.
description: Knockdown
 datasetObservational data of
 two knockdown events as well as oviposition events following these
 knockdownsScorpion
 toxin.xlsx
DOI: 10.5061/dryad.7g6gc67
title: Data from: How differing modes of non-genetic inheritance affect population viability in fluctuating environments

description: Different modes of non-genetic inheritance are expected to affect
 population persistence in fluctuating environments. We here analyze
 Caenorhabiditis elegans density-independent per capita growth rate time
 series on 36 populations experiencing 6 controlled sequences of
 challenging oxygen level fluctuations across 60 generations, and
 parameterize competing models of non-genetic inheritance in order to
 explain observed dynamics. Our analysis shows that phenotypic plasticity
 and anticipatory maternal effects are sufficient to explain growth rate
 dynamics, but that a carryover model where ``epigenetic" memory is
 imperfectly transmitted and might be reset at each generation is a better
 fit to the data. We further find that this epigenetic memory is asymmetric
 since it is kept for longer when populations are exposed to the more
 challenging environment. Our analysis suggests that population persistence
 in fluctuating environments depends on the non-genetic inheritance of
 phenotypes whose expression is regulated across multiple generations.
description: Additive Maternal Effect
 Model CodeRmarkdown file for
 running only the "additive" model of the maternal effects
 model.AdditiveModel.RmdAdditive maternal effects model stan fileAdditive maternal effects model stan fileAdditiveTGP_logscale.stanMaternal Effects stan fileMaternal Effects stan fileAME.stanPhenotypic carryover stan fileCarryover stan file which includes generated quantities that can be used for additional statistical analysis. Output using this stan file is quite largeCarryover_generatedQuant.stanPhenotypic carryover stan fileCarryover stan file which does not include generated quantities. Output using this stan file is smaller.Carryover.stanSimulation code for population genetic dataForward stochastic simulation of population genetic process to generate null model time-series dataCreatePopGenSim.nbGrowth rate time series dataset rmdPopulation growth rate time series data in R formatGrowthData-normoxia_anoxia.rdsPopulation growth rate time series datasetPopulation growth rate time series dataset in csv format.GrowthRateTimeSeries.csvMain analysis fileThis is the main R file for running the analysis. It includes descriptive plots of the time series data, Bayesian fitting for the alternative models, and comparison of LOO values.MainStats.RmdGenerate plots of phenotype dynamicsRmarkdown to generate the figures that show the dynamics of the hidden S phenotype.PhenotypePlots.RmdGenerate posterior predictive plotsRmarkdown to perform posterior predictive fit analysis. This requires the model fitting ourput from MainStats to already be complete.PosteriorPredictiveFits.RmdFit models to simulated data.Rmarkdown to fit the alternative models to a set of simulated data.RunStanSimData.Rmdsimulated data from population genetic modelSimulated time-series data from forward popualtion genetic model.simdata.csv
DOI: 10.5061/dryad.gr91p44
title: Data from: Multi-year stigmatic pollen-load sampling reveals temporal stability in interspecific pollination of flowers in a subalpine meadow

description: Co-flowering plants may commonly experience interspecific pollination. It
 remains unknown, however, whether interspecific pollination is a largely
 stochastic process or consistent enough over years to exert selection for
 traits that can reduce interspecific pollination or ameliorate its
 deleterious effects on reproduction. To assess the likelihood of this
 precondition being met, stigmatic pollen loads on 17 to 34
 insect-pollinated plant species over 3 consecutive years were scored in a
 subalpine meadow in southwestern China. Plant species varied significantly
 in the amount and proportion of heterospecific pollen (HP) on stigmas.
 Both the number of HP species and the proportion of the pollen load that
 was HP for each recipient species correlated positively between years
 (reflected in pairwise correlations for all year-by-year combinations).
 Although inter-annual variation was smaller for conspecific pollen (CP)
 than for HP loads, species tended to experience either consistently high
 or consistently low HP proportions across years. We found that species
 with higher stigmatic HP proportions generally experienced lower
 proportional variation in stigmatic HP, an unexpected result if high HP
 loads are the result of rare stochastic events. The novel finding of
 between-year consistency in stigmatic loads of heterospecific pollen
 suggests that adaption to stigmatic loads of HP is possible, and two
 divergent strategies may have evolved: HP avoidance and HP tolerance. The
 observation of temporally consistent differences among species in levels
 of HP supports the idea that natural selection may be operating either to
 increase tolerance or to minimize arrival of heterospecific pollen on
 stigmas in co-flowering plants. Such adaptations may be important for the
 maintenance of high levels of local plant diversity in biodiversity
 hotspots such as our study area.
description: Raw data for MS
 OIK-06447.R3 Qiang FangAn Excel file contains
 two tables presenting raw data for MS OIK-06447.R3 coauthored by Qiang
 Fang et al.
DOI: 10.5061/dryad.55s9h5r
title: Data from: Extreme heat events and the vulnerability of endemic montane fishes to climate change

description: Identifying how close species live to their physiological thermal maxima
 is essential to understand historical warm-edge elevational limits of
 montane faunas and forecast upslope shifts caused by future climate
 change. We used laboratory experiments to quantify the thermal tolerance
 and acclimation potential of four fishes (Notropis leuciodus, N.
 rubricroceus, Etheostoma rufilineatum, E. chlorobranchium) that are
 endemic to the southern Appalachian Mountains (USA), exhibit different
 historical elevational limits, and represent the two most species-rich
 families in the region. All-subsets selection of linear regression models
 using AICc indicated that species, acclimation temperature, collection
 location and month, and the interaction between species and acclimation
 temperature were important predictors of thermal maxima (Tmax), which
 ranged from 28.5 to 37.2°C. Next, we implemented water temperature models
 and stochastic weather generation to characterize the magnitude and
 frequency of extreme heat events (Textreme) under historical and future
 climate scenarios across 25,379 stream reaches in the upper Tennessee
 River system. Lastly, we used environmental niche models to compare
 warming tolerances (acclimation-corrected Tmax minus Textreme) between
 historically occupied versus unoccupied reaches. Historical warming
 tolerances, ranging from +2.2 to +10.9°C, increased from low to high
 elevation and were positive for all species, suggesting that Tmax does not
 drive warm-edge (low elevation) range limits. Future warming tolerances
 were lower (-1.2 to +9.3°C) but remained positive for all species under
 the direst warming scenario except for a small proportion of reaches
 historically occupied by E. rufilineatum, indicating that Tmax and
 acclimation potentials of southern Appalachian minnows and darters are
 adequate to survive future heat waves. We caution concluding that these
 species are invulnerable to 21st century warming because sublethal thermal
 physiology remains poorly understood. Integrating physiological
 sensitivity and warming exposure demonstrates a general and fine-grained
 approach to assess climate change vulnerability for freshwater organisms
 across physiographically diverse riverscapes.
description: temp_parametersCSV file containing modeled temperature parameters. See README file for variable definitions. All modeled variables are associated with National Hydrography Dataset flowlines ComIDs.ENM_hab_suitCSV file containing modeled ENM habitat suitability values for four fish species. See README file for variable definitions. All modeled variables are associated with National Hydrography Dataset flowlines ComIDs.laboratory_CTMCSV file containing thermal maximum (Tmax) measurements from laboratory assays for four fish species.
DOI: 10.5061/dryad.5p3q298
title: Data from: Genetic inheritance and environment determine endocrine plasticity to urban living

description: As urban areas continue to expand globally, understanding how and why
 species respond to novel habitats becomes increasingly important.
 Knowledge of the mechanisms behind observed phenotypic changes in urban
 animals will enable us to better evaluate the impact of urbanization on
 current and future generations of wildlife. Physiological changes, such as
 those involved in the endocrine stress response, may allow individuals to
 inhabit and thrive in urbanized areas, but it is currently unknown how
 these changes arise in natural populations. In this study, we performed a
 4-way crossfoster experiment in free-living house wren chicks, Troglodytes
 aedon, to disentangle whether differences in baseline corticosterone
 between urban and rural individuals is a result of genetic and/or plastic
 mechanisms during development. We found that urban chicks already had
 higher corticosterone levels than their rural counterparts on the day they
 hatched, which suggests a possible genetic component to the corticosterone
 phenotype. However, rural offspring that were moved to an urban
 environment significantly increased their corticosterone levels, mimicking
 those of urban offspring. Our findings suggest that, although differences
 in baseline corticosterone concentrations between urban and rural
 individuals may have a genetic component, plasticity plays a pivotal role
 and can modify the corticosterone phenotype in response to the environment
 experienced in the first two weeks of life.
description: Data for GC house wren
 crossfosterRaw data
 file2018-8-10 howr
 dryad.csv
DOI: 10.5061/dryad.8h07878
title: Data from: Broodmate aggression and life history variation in accipitrid birds of prey

description: Aggressive sibling competition for parental food resources is relatively
 infrequent in animals but highly prevalent and extreme among certain bird
 families, particularly accipitrid raptors (Accipitriformes). Intense
 broodmate aggression within this group is associated with a suite of
 traits including a large adult size, small broods, low provisioning rates,
 and slow development. In this study, we apply phylogenetic comparative
 analyses to assess the relative importance of several behavioral,
 morphological, life history, and ecological variables as predictors of the
 intensity of broodmate aggression in 65 species of accipitrid raptors. We
 show that intensity of aggression increases in species with lower parental
 effort (small clutch size and low provisioning rates), while size effects
 (adult body mass and length of nestling period) are unimportant. Intense
 aggression is more closely related to a slow life history pace (high adult
 survival coupled with a restrained parental effort), rather than a
 by‐product of allometry or food limitation. Consideration of several
 ecological variables affecting prey abundance and availability reveals
 that certain lifestyles (e.g., breeding in aseasonal habitats or hunting
 for more agile prey) may slow a species’ life history pace and favor the
 evolution of intense broodmate aggression.
description: Broodmate aggression in
 accipitrid raptors data: including behavioural, life-history and
 ecological predictorsThe archive file
 contains the raw data file (Broodmate_aggression_raptors_database.txt),
 sources and references (Readme_Database_Sources_and_references.docx),
 variable description (Readme_Database_Variable_description.txt) and
 additional tables for the main article (CIC table for candidate model set
 (Path Analysis).docx, AIC table for candidate model set (life history plus
 ecological predictors).docx).Redondo_etal_EcolEvol_broodmate_aggression_raptors_Dataset.zip
DOI: 10.5061/dryad.nh0fp1b
title: Data from: Human foveal cone photoreceptor topography and its dependence on eye length

description: We provide the first measures of foveal cone density as a function of
 axial length in living eyes and discuss the physical and visual
 implications of our findings. We used a new generation Adaptive Optics
 Scanning Laser Ophthalmoscope to image cones at and near the fovea in 28
 eyes of 16 subjects. Cone density and other metrics were computed in units
 of visual angle and linear retinal units. The foveal cone mosaic in longer
 eyes is expanded at the fovea, but not in proportion to eye length.
 Despite retinal stretching (decrease in cones/mm2), myopes generally have
 a higher angular sampling density (increase in cones/deg2) in and around
 the fovea compared to emmetropes, offering the potential for better visual
 acuity. Reports of deficits in best-corrected foveal vision in myopes
 compared to emmetropes cannot be explained by increased spacing between
 photoreceptors caused by retinal stretching during myopic progression.
description: HUMAN_FOVEAL_CONESThis dataset contains high resolution images of the foveal region of 28 eyes of 16 subjects. The images are accompanied by text files listing all cone locations in pixels. There is a Matlab script that can be used to plot the cone locations on the corresponding image. There is a *.csv file listing the subject code, eye, retinal magnification factor (microns/degree) and image scale (pixels per degree).
DOI: 10.5061/dryad.2hj1404
title: Data from: Assessing the influence of biotic, abiotic, and social factors on the physiological stress of a large Neotropical primate in Atlantic Forest fragments

description: Wildlife physiological responses to environmental and human-related
 stressors provide useful clues on animal welfare. Non-invasive biomarkers,
 such as fecal glucocorticoid metabolites (fGCM), allow researchers to
 assess whether variations in habitat quality, behavior, and climate
 influence the animals' physiological stress. We examined the role of
 fragment size, ambient temperature, ripe fruit availability and
 consumption, percentage of records moving, sex, female reproductive state,
 and group composition as predictors of the level of fGCM in adult brown
 howler monkeys (Alouatta guariba clamitans) inhabiting three small
 (&lt;10 ha) and three large (&gt;90 ha) Atlantic Forest fragments
 in southern Brazil. We collected bimonthly behavioral data and fecal
 samples from adult individuals over three years, and used a multimodel
 inference framework to identify the main predictors of fGCM. We found that
 the mean (±SD) fGCM in the study groups ranged from 57 ± 49 ng/g to
 93 ± 58 ng/g, which were within the known range for howler monkeys. We
 found 10 best models including five of the 17 tested variables. Sex and
 reproductive state were the only variables included in all these models.
 We found that fGCM was higher in nursing females
 (mean ± SD = 104 ± 73 ng/g) than in non-nursing females (64 ± 55 ng/g) and
 males (53 ± 40 ng/g, P &lt; 0.05) and that it decreased with
 increasing ripe fruit consumption and minimum temperature. However,
 fragment size did not predict fGCM concentration (groups in small
 fragments = 71 ± 58 ng/g vs. groups in large fragments = 63 ± 54 ng/g,
 P &gt; 0.05). We conclude that factors related to the energetic
 balance of individuals play major roles in modulating the physiological
 stress of brown howler monkeys. Future studies should investigate the
 consequences of higher levels of stress hormones on howler monkey health
 and demography.
description: Dataset on fGCM drivers
 in brown howlersDatasets used to run the
 linear mixed models (LMM) assessing the influence of 17 predictor
 variables on fecal glucocorticoid metabolites (fGCM) in six groups of
 brown howlers (Alouatta guariba clamitans) in southern Brazil (see full
 details on each predictor variable in Table 3).Dataset_fGCM_drivers_in_brown_howlers.xlsxRarified dataset used to compare fGCM between sex/reproductive statesThis dataset was used to run the linear mixed model (LMM) comparing the fGCM between sex/reproductive states in six groups of brown howlers (Alouatta guariba clamitans) in southern Brazil (N=212 fecal samples). The number of fecal samples used in this analysis was rarified for males and females in each fragmentDataset_fGCM_rep.state_comparison_rarified.xlsx
DOI: 10.5061/dryad.qf6gk58
title: Data from: Human overexploitation and extinction risk correlates of Chinese snakes

description: China is one of the countries with the richest snake biodiversity in the
 world. However, about one-third of all 236 species are now considered
 threatened, partially due to the intense human overexploitation. Despite
 that, to date, no study has explicitly investigated the patterns and
 processes of extinction and threats of Chinese snakes, or between human
 exploited and unexploited snake subgroups. We addressed the following
 three questions: (1) which snake families proportionally include more
 human exploited species than expected by chance? (2) which species traits
 and extrinsic factors are correlated with their extinction risk? (3) are
 there differences between human exploited and unexploited species in terms
 of patterns and processes of extinction? We found that the family Elapidae
 contained a significantly higher number of exploited species. Considering
 eight species traits and four extrinsic factors, we performed phylogenetic
 correlation tests, finding that small geographic range size, large body
 length, oviparous reproduction, diurnal activity, and high human
 exploitation were important in determining the extinction risk of all
 Chinese snakes. Moreover, human exploited snakes had a higher percentage
 of threatened species and large-bodied species than unexploited snakes.
 Extinction risk of human exploited species was related to body length,
 reproduction mode and activity period, whereas that of human unexploited
 species were associated with geographic range size, microhabitat, and
 annual temperature. Overall, we highlight the phylogenetic non-random
 exploitation of snakes, and different factors underlying species response
 to human overexploitation. We suggest that conservation priority should be
 given to exploitation-prone families and species with extinction-prone
 traits, as identified in this study. Moreover, human exploited and
 unexploited species should be managed considering different strategies
 since their extinction risk was associated with different ecological
 traits. Conservation actions should also focus on preventing human
 threats, such as overexploitation, for the effective preservation of
 Chinese snakes.
description: Dryad
 DataDetailed data for
 Chinese snakes