cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qg8vf45
title: Data from: Mitochondrial genome fragmentation unites the parasitic lice of eutherian mammals

description: Organelle genome fragmentation has been found in a wide range of
 eukaryotic lineages; however, its use in phylogenetic reconstruction has
 not been demonstrated. We explored the use of mitochondrial (mt) genome
 fragmentation in resolving the controversial suborder-level phylogeny of
 parasitic lice (order Phthiraptera). There are ~5,000 species of parasitic
 lice in four suborders (Amblycera, Ischnocera, Rhyncophthirina and
 Anoplura), which infest mammals and birds. The phylogenetic relationships
 among these suborders are unresolved despite decades of studies. We
 sequenced the mt genomes of eight species of parasitic lice and compared
 them with 17 other species of parasitic lice sequenced previously. We
 found that the typical single-chromosome mt genome is retained in the lice
 of birds but fragmented into many minichromosomes in the lice of eutherian
 mammals. The shared derived feature of mt genome fragmentation unites the
 eutherian mammal lice of Ischnocera (family Trichodectidae) with Anoplura
 and Rhyncophthirina to the exclusion of the bird lice of Ischnocera
 (family Philopteridae). This novel clade is also supported by phylogenetic
 analysis of mt genome and cox1 gene sequences. Our results demonstrate,
 for the first time, that organelle genome fragmentation is informative for
 resolving controversial high-level phylogenies.
description: AlignmentsThis is the nucleotide alignments used in Song et al. (in review) USYB-2018-080Supplementary Material-USYB-2018-080-R1This file include all Supplementary Tables S1-S3 and Supplementary Figures S1-S4
DOI: 10.15468/dl.b2dfua
title: Occurrence Download

description: A dataset containing 206 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is one of (Zero coordinate, Coordinate out of range, Coordinate invalid, Country mismatch, Country coordinate mismatch, Continent invalid, Continent coordinate mismatch, Taxon match fuzzy, Taxon match higher rank, The scientific name ID was not found in the checklist)",
 "TaxonKey is Crocodylus acutus"
 ]
}

 The dataset includes 206 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001740-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f77k3
title: Data from: Selection for mechanical advantage underlies multiple cranial optima in new world leaf-nosed bats

description: Selection for divergent performance optima has been proposed as a central
 mechanism underlying adaptive radiation. Uncovering multiple optima
 requires identifying forms associated with different adaptive zones and
 linking those forms to performance. However, testing and modeling the
 performance of complex morphologies like the cranium is challenging. We
 introduce a three-dimensional finite element (FE) model of the cranium
 that can be morphed into different shapes by varying simple parameters to
 investigate the relationship between two engineering-based measures of
 performance, mechanical advantage and von Mises stress, and four divergent
 adaptive zones occupied by New World leaf-nosed bats. To investigate these
 relationships,we tested the fit of Brownian motion and Ornstein-Uhlenbeck
 models of evolution in mechanical advantage and von Mises stress using
 dated multi-locus phylogenies. The analyses revealed three performance
 optima for mechanical advantage among species from three adaptive zones:
 bats that eat nectar; generalized insectivores omnivores and some
 frugivores; and bats that specialize on hard canopy fruits. Only two
 optima, one corresponding to nectar feeding, were consistently uncovered
 for von Mises stress. These results suggest that mechanical advantage
 played a larger role than von Mises stress in the radiation of New World
 leaf-nosed bats into divergent adaptive zones.
description: Dumont_etal2014_Evolution_engineering_model_outputDate from engineering model used as input in Brownian motion and Ornstein-Uhlenbeck models of trait evolution.Supplementary methodsSupplementary methods: engineering model, qualitative and quantitative validation, and phylogeneticssupplementary_methods20140108.docxSupplementary Tables and Figuressupplementary_tables_figures20161116.docx
DOI: 10.5061/dryad.3h9k4
title: Data from: Forty years of seagrass population stability and resilience in an urbanizing estuary

description: Coasts and estuaries contain among the most productive and ecologically
 important habitats in the world and face intense pressure from current and
 projected human activities, including coastal development. Seagrasses are
 a key habitat feature in many estuaries perceived to be in widespread
 decline owing to human actions. We use spatio-temporal models and a
 41-year time series from 100s of km of shoreline which includes over 160
 000 observations from Puget Sound, Washington, USA, to examine multiscale
 trends and drivers of eelgrass (Zostera spp.) change in an urbanizing
 estuary. At whole estuary scale (100s of km), we find a stable and
 resilient eelgrass population despite a more than doubling of human
 population density and multiple major climactic stressors (e.g. ENSO
 events) over the period. However, the aggregate trend is not reflected at
 the site scale (10s of km), where some sites persistently increase while
 others decline. Site trends were spatially asynchronous; adjacent sites
 sometimes exhibited opposite trends over the same period. Substantial
 change in eelgrass occurred at the subsite (0·1 km) scale, including both
 complete local loss and dramatic increase of eelgrass. Metrics of local
 human development including shoreline armouring, upland development
 (imperviousness) and human density provide no explanatory power for
 eelgrass population change at any spatial scale. Our results suggest that
 the appropriate scale for understanding eelgrass change is smaller than
 typically assumed (approximately 1- to 3-km scale) and contrasts strongly
 with previous work. Synthesis. Despite ongoing conservation concern over
 seagrasses world-wide, eelgrass in Puget Sound has been highly resilient
 to both anthropogenic and environmental change over four decades. Our work
 provides general methods that can be applied to understand spatial and
 temporal scales of change and can be used to assess hypothesized drivers
 of change.
description: GIS-Vegetation
 dataThis is a .zip file
 containing the raw observations of eelgrass occurrence at each location.
 Each are is included as a separate .csv file. Site abbreviations are
 present in each file title and are described fully in the main text of the
 paper. Included in the .zip file is a file titled "Shapefile
 attribute table descriptions.xlsx" which has a description of the
 fields and how they connect to other files.reorderd
 segmentsThis is a file with
 reordered segments for each of the eelgrass areas. See ReadMe file for
 details.shore_midpoints_with_attributes_utm_nad83_pat-pubShoreline attribute file for 100m segments of Puget Sound, WA shoreline. Description of the columns can be found in the readme file accompanying the GIS-Vegetation data.Example estimation code and control filesEstimating Code and Control file.zip
DOI: 10.5061/dryad.6052r
title: Data from: Populations of aspen (Populus tremuloides Michx.) with different evolutionary histories differ in their climate occupancy

description: Quaking aspens (Populus tremuloides Michx.) are found in diverse habitats
 throughout North America. While the biogeography of aspens'
 distribution has been documented, the drivers of the phenotypic diversity
 of aspen are still being explored. In our study, we examined differences
 in climate between northern and southwestern populations of aspen, finding
 large-scale differences between the populations. Our results suggest that
 northern and southwestern populations live in distinct climates and
 support the inclusion of genetic and phenotypic data with species
 distribution modeling for predicting aspens' distribution.
description: Aspen_Population_GISThis file contains ArcGIS GRID files that represent the predicted distributions of EP, NC, and SC.model_evaluation_and_variablesThis zip file contains the outputs from the models for the model evaluation scores, and the relative contributions of each variableInput DataThese data are the input data for modeling and niche overlap analysisAspen_GIS_inputs.zip
DOI: 10.5061/dryad.64048p0
title: Data from: Heaviside's dolphins (Cephalorhynchus heavisidii) relax acoustic crypsis to increase communication range

description: The costs of predation may exert significant pressure on the mode of
 communication used by an animal, and many species balance the benefits of
 communication (e.g. mate attraction) against the potential risk of
 predation. Four groups of toothed whales have independently evolved
 narrowband high-frequency (NBHF) echolocation signals. These signals help
 NBHF species avoid predation through acoustic crypsis by echolocating and
 communicating at frequencies inaudible to predators such as mammal-eating
 killer whales. Heaviside’s dolphins (Cephalorhynchus heavisidii) are
 thought to exclusively produce NBHF echolocation clicks with a centroid
 frequency around 125 kHz and little to no energy below 100 kHz. To test
 this, we recorded wild Heaviside’s dolphins in a sheltered bay in Namibia.
 We demonstrate that Heaviside’s dolphins produce a second type of click
 with lower frequency and broader bandwidth in a frequency range that is
 audible to killer whales. These clicks are used in burst-pulses and
 occasional click series but not foraging buzzes. We evaluate three
 different hypotheses and conclude that the most likely benefit of these
 clicks is to decrease transmission directivity and increase conspecific
 communication range. The expected increase in active space depends on
 background noise but ranges from 2.5 (Wenz Sea State 6) to 5 times (Wenz
 Sea State 1) the active space of NBHF signals. This dual click strategy
 therefore allows these social dolphins to maintain acoustic crypsis during
 navigation and foraging, and to selectively relax their crypsis to
 facilitate communication with conspecifics.
description: Martin et al. 2018
 Supplementary Data from Heaviside's dolphins (Cephalorhynchus
 heavisidii) relax acoustic crypsis to increase communication
 rangeThis .wav file includes
 an example of each pulsed signal type described for Heaviside's
 dolphins in Martin et al. 2018. The signal types are in the order: 1)
 broadband click train, 2) burst-pulse, 3) buzz and 4) NBHF click
 train.Martin et al. 2018
 Supplementary Data.wavMartin et al. 2018
 Supplementary Methods from Heaviside's dolphins (Cephalorhynchus
 heavisidii) relax acoustic crypsis to increase communication
 rangeSupplementary Methods
 contain details about the statistical analyses used to classify the pulsed
 signal types of Heaviside's dolphins. Also, methods include the steps
 and figures used to model the active space of a NBHF click compared to a
 click extracted from a lower-frequency burst-pulse
 signal.Martin et al 2018 Supplementary
 Methods.pdfMartin et al. 2018
 Appendix S1 from Heaviside’s dolphins (Cephalorhynchus heavisidii) relax
 acoustic crypsis to increase communication rangeAppendix S1 contains
 acoustic parameter measurements from pulsed signals measured from
 Heaviside's dolphinsMartin et al. 2018 Appendix
 S1.pdf
DOI: 10.15468/dl.s5s8bg
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scopellaria diversifolia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001743-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.47v3c
title: Data from: The global compendium of Aedes aegypti and Ae. albopictus occurrence

description: Aedes aegypti and Ae. albopictus are the main vectors transmitting dengue
 and chikungunya viruses. Despite being pathogens of global public health
 importance, knowledge of their vectors’ global distribution remains patchy
 and sparse. A global geographic database of known occurrences of Ae.
 aegypti and Ae. albopictus between 1960 and 2014 was compiled. Herein we
 present the database, which comprises occurrence data linked to point or
 polygon locations, derived from peer-reviewed literature and unpublished
 studies including national entomological surveys and expert networks. We
 describe all data collection processes, as well as geo-positioning
 methods, database management and quality-control procedures. This is the
 first comprehensive global database of Ae. aegypti and Ae. albopictus
 occurrence, consisting of 19,930 and 22,137 geo-positioned occurrence
 records respectively. Both datasets can be used for a variety of mapping
 and spatial analyses of the vectors and, by inference, the diseases they
 transmit.
description: # Data from: The global compendium of Aedes aegypti and Ae. albopictus
 occurrence Dataset DOI:
 [https://doi.org/10.5061/dryad.47v3c](https://doi.org/10.5061/dryad.47v3c)  Please note, these data are also referred to in another publication: [http://dx.doi.org/10.7554/eLife.08347](http://dx.doi.org/10.7554/eLife.08347) ## Description of the data and file structure Structure of the database for *Ae. aegypti and Ae. albopictus* occurrence: 1\. **VECTOR**: Identifying the species; *Ae. aegypti* or *Ae. albopictus* 2\. **OCCURRENCE_ID**: Unique identifier for each occurrence in the database after temporal and spatial standardisation. 3\. **SOURCE_TYPE**: Published literature or unpublished sources with reference ID that corresponds to the full list of references in the supplementary information. 4\. **LOCATION_TYPE:** Whether the record represents a point or a polygon location. 5\. **POLYGON_ADMIN:** Admin level or polygon size which the record represents when the location type is a polygon. -999 when the location type is a point (5 km x 5 km). 6\. **X**: The longitudinal coordinate of the point or polygon centroid (WGS1984 Datum). 7\. **Y:** The latitudinal coordinate of the point or polygon centroid (WGS1984 Datum). 8\. **YEAR:** The year of the occurrence. 9\. **COUNTRY**: The name of the country within which the occurrence lies. 10\. **COUNTRY_ID:** ISO alpha-3 country codes. 11\. **GAUL_AD0:** The country-level global administrative unit layer (GAUL) code (see [http://www.fao.org/geonetwork](http://www.fao.org/geonetwork)) which identifies the Admin-0 polygon within which any smaller polygons and points lie. 12\. **STATUS:** Established vs. transient populations.
DOI: 10.5061/dryad.3r4j45d2
title: Data from: Phylogenomic insights into the cambrian explosion, the colonization of land and the evolution of flight in arthropoda

description: The timing of the origin of arthropods in relation to the Cambrian
 explosion is still controversial, as are the timing of other arthropod
 macroevolutionary events such as the colonization of land and the
 evolution of flight. Here we assess the power of a phylogenomic approach
 to shed light on these major events in the evolutionary history of life on
 earth. Analyzing a large phylogenomic dataset (122 taxa, 62 genes) with a
 Bayesian-relaxed molecular clock, we simultaneously reconstructed the
 phylogenetic relationships and the absolute times of divergences among the
 arthropods. Simulations were used to test whether our analysis could
 distinguish between alternative Cambrian explosion scenarios with
 increasing levels of autocorrelated rate variation. Our analyses support
 previous phylogenomic hypotheses and simulations indicate a Precambrian
 origin of the arthropods. Our results provide insights into the 3
 independent colonizations of land by arthropods and suggest that evolution
 of insect wings happened much earlier than the fossil record indicates,
 with flight evolving during a period of increasing oxygen levels and
 impressively large forests. These and other findings provide a foundation
 for macroevolutionary and comparative genomic study of Arthropoda.
description: Insect8_no3rdTree FileTable S1 Sampled TaxaList of Sampled Taxa, their data and sourcesTable S2 Pairwise genomic agesTable S3 simulation resultsFigS1 v2Figure S1. Schematic of the ‘short fuse’ Cambrian explosion simulation analyses. Using all branch lengths &lt; 520 Ma identical to our Observed Tree (panel A) for a subset of taxa necessary to include all of our calibration points, branch lengths of basal lineages &gt; 520 Ma were modified to conform to a ‘short fuse’ Cambrian explosion event at 540 to 530 Ma (panel B). Branch lengths of this resulting tree were then modified at different levels of autocorrelated rate variation (panel C). For no rate variation among branches, the coefficient of variation (CoV) among branch rates is 0 (and there is only 1 tree). For each of the higher levels of rate variation, 10 different realizations of autocorrelated branch length manipulation were generated (with some examples shown in panel C). Each of these trees was then used as a template for generating simulated DNA datasets and then analyzed using BEAST and the same parameters as our observed data. Histograms of the distribution of posterior estimates for the age of the Arthropoda are show, for the three different levels of CoV shown in panel C, with posterior values pooled among replicates.
DOI: 10.5061/dryad.728b4
title: Data from: The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing

description: Next-generation sequencing (NGS) techniques are now key tools in the
 detection of population genomic and gene expression differences in a large
 array of organisms. However, so far few studies have utilized such data
 for phylogenetic estimations. Here, we use NGS data obtained from
 genome-wide restriction site-associated DNA (RAD) (∼66000 SNPs) to
 estimate the phylogenetic relationships among all 26 species of swordtail
 and platyfish (genus Xiphophorus) from Central America. Past studies, both
 sequence and morphology-based, have differed in their inferences of the
 evolutionary relationships within this genus, particularly at the
 species-level and among monophyletic groupings. We show that using a large
 number of markers throughout the genome, we are able to infer the
 phylogenetic relationships with unparalleled resolution for this genus.
 The relationships among all three major clades and species within each of
 them are highly resolved and consistent under maximum likelihood, Bayesian
 inference and maximum parsimony. However, we also highlight the current
 cautions with this data type and analyses. This genus exhibits a
 particularly interesting evolutionary history where at least two species
 may have arisen through hybridization events. Here, we are able to infer
 the paternal lineages of these putative hybrid species. Using the
 RAD-marker-based tree we reconstruct the evolutionary history of the
 sexually selected sword trait and show that it may have been present in
 the common ancestor of the genus. Together our results highlight the
 outstanding capacity that RAD sequencing data has for resolving previously
 problematic phylogenetic relationships, particularly among relatively
 closely related species.
description: m8_species_15SNP matrix file for species level analyses (maximum 8 mismatches allowed for hstacks processing and including a minimum number of 15 species).m8_species_20SNP matrix file for species level analyses (maximum 8 mismatches allowed for hstacks processing and including a minimum number of 20 species).m8_species_25SNP matrix file for species level analyses (maximum 8 mismatches allowed for hstacks processing and including a minimum number of 25 species).m5_species_15SNP matrix file for species level analyses (maximum 5 mismatches allowed for hstacks processing and including a minimum number of 15 species).m5_species_20SNP matrix file for species level analyses (maximum 5 mismatches allowed for hstacks processing and including a minimum number of 20 species).m5_species_25SNP matrix file for species level analyses (maximum 5 mismatches allowed for hstacks processing and including a minimum number of 25 species).m8_population_15SNP matrix - m8, 15 populationsm8_population_20SNP matrix - m8, 20 populationsm8_population_25SNP matrix - m8, 25 populationsm5_population_15SNP matrix - m5, 15 populationsm5_population_20SNP matrix - m5, 20 populationsm5_population_25SNP matrix - m5, 25 populations
DOI: 10.5061/dryad.2mg3t27
title: Data from: Age and sex differences in burnout, career satisfaction, and well-being in US neurologists

description: Objective: To examine age and sex differences in burnout, career
 satisfaction, and well-being in US neurologists. Methods: Quantitative and
 qualitative analyses of men’s (n = 1,091) and women’s (n = 580) responses
 to a 2016 survey of US neurologists. Results: Emotional exhaustion in
 neurologists initially increased with age, then started to decrease as
 neurologists got older. Depersonalization decreased as neurologists got
 older. Fatigue and overall quality of life in neurologists initially
 worsened with age, then started to improve as neurologists got older. More
 women (64.6%) than men (57.8%) met burnout criteria on univariate
 analysis. Women respondents were younger and more likely to work in
 academic and employed positions. Sex was not an independent predictive
 factor of burnout, fatigue, or overall quality of life after controlling
 for age. In both men and women, greater autonomy, meaning in work,
 reasonable amount of clerical tasks, and having effective support staff
 were associated with lower burnout risk. More hours worked, more nights on
 call, higher outpatient volume, and higher percent of time in clinical
 practice were associated with higher burnout risk. For women, greater
 number of weekends doing hospital rounds was associated with higher
 burnout risk. Women neurologists made proportionately more negative
 comments than men regarding workload, work–life balance, leadership and
 deterioration of professionalism, and demands of productivity eroding the
 academic mission. Conclusions: We identified differences in burnout,
 career satisfaction, and well-being in neurologists by age and sex. This
 may aid in developing strategies to prevent and mitigate burnout and
 promote professional fulfillment for different demographic subgroups of
 neurologists.
description: Supplement e-1: Survey
 Instrument with MBI redactedSupplement e-1: Survey
 Instrument with MBI redactedAge-Sex_Neurologist_Supplement_e-1-Survey_Instrument_with_MBI_redacted.pdfTables e-1 - e-7 and Figure e-1 and e-2 LegendsTables e-1 - e-7 and Figure e-1 and e-2 LegendsAge-Sex_Neurologist_e-Tables_and_e-Figure_Legends.pdfSupplement e-2: Representative Quotes from RespondentsSupplement e-2: Representative Quotes from RespondentsAge-Sex_Neurologist_Supplement_e-2_Representative_Quotes_from_Respondents.pdfFigure e-1Figure e-1. Age distribution of male and female neurologistsAge-Sex_Neurologist_Figure_e-1.jpgFigure e-2Figure e-2. Depersonalization, emotional exhaustion, and personal accomplishment by weekend responsibilities and sexAge-Sex_Neurologist_Figure_e-2.jpg
DOI: 10.17617/3.2joowa
title: Reference transcriptome of Cardamine chenopodiifolia for "Amphicarpic development in the emerging model organism Cardamine chenopodiifolia"

description: C.chenopodiifolia transcriptome associated with publication "Amphicarpic development in the emerging model organism Cardamine chenopodiifolia"