cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3b568
title: Data from: Limited scope for latitudinal extension of reef corals

description: An analysis of present-day global depth distributions of reef-building
 corals and underlying environmental drivers contradicts a commonly held
 belief that ocean warming will promote tropical coral expansion into
 temperate latitudes. Using a global data set of a major group of reef
 corals, we found that corals were confined to shallower depths at higher
 latitudes (up to 0.6 meters of predicted shallowing per additional degree
 of latitude). Latitudinal attenuation of the most important driver of this
 phenomenon—the dose of photosynthetically available radiation over
 winter—would severely constrain latitudinal coral range extension in
 response to ocean warming. Latitudinal gradients in species richness for
 the group also suggest that higher winter irradiance at depth in low
 latitudes allowed a deep-water fauna that was not viable at higher
 latitudes.
description: lat_by_depth_by_spData used in quantile regression modelling.Mean temperature environmental surfaceMTMP.csvMean aragonite environmental surfaceMARG.csvMean salinity environmental surfaceMSAL.csvMean daily photosynthetically available radiationMDPAR.csvMean winter daily photosynthetically available radiationWDPAR.csvMean autumn daily photosynthetically available radiationADPAR.csvMean summer daily photosynthetically available radiationSuDPAR.csvMean spring daily photosynthetically available radiationSpDPAR.csvValid species numbers
DOI: 10.5061/dryad.5dh5f
title: Data from: QTL mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

description: The wild North American sunflowers Helianthus annuus and H. debilis are
 participants in one of the earliest identified examples of adaptive trait
 introgression, and the exchange is hypothesized to have triggered a range
 expansion in H. annuus. However, the genetic basis of the adaptive
 exchange has not been examined. Here, we combine quantitative trait locus
 (QTL) mapping with field measurements of fitness to identify candidate H.
 debilis QTL alleles likely to have introgressed into H. annuus to form the
 natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping
 populations were grown in central Texas, genotyped for 384 single
 nucleotide polymorphism (SNP) markers and then phenotyped in the field for
 two fitness and 22 herbivore resistance, ecophysiological, phenological
 and architectural traits. We identified a total of 110 QTL, including at
 least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at
 least one H. debilis QTL allele that would shift the trait in the
 direction of the wild hybrid H. a. texanus. We identified three
 chromosomal regions where H. debilis alleles increased both female and
 male components of fitness; these regions are expected to be strongly
 favoured in the wild. QTL for a number of other ecophysiological,
 phenological and architectural traits colocalized with these three regions
 and are candidates for the actual traits driving adaptive shifts. G × E
 interactions played a modest role, with 17% of the QTL showing potentially
 divergent phenotypic effects between the two field sites. The candidate
 adaptive chromosomal regions identified here serve as explicit hypotheses
 for how the genetic architecture of the hybrid lineage came into
 existence.
description: Phenotype and SNP
 Genotype DataThis Excel file contains
 information on 906 field-grown backcross1 sunflower plants. Field site is
 identified in column Z. Plants are identified by the number in column AA.
 Columns A-Y contain field-measured trait data. Trait names correspond to
 the abbreviations in Table 1 of the associated manuscript. Columns AH - HO
 contain SNP genotype data; A = H. a. annuus allele; D = H. debilis
 allele.Whitney phenotype genotype
 data.xlsxLinkage
 MapThis Excel file contains
 the estimated linkage map for the H. a. annuus x H. debilis backcross1
 mapping populations. The position of each marker on the linkage group is
 given in centiMorgans (cM).Whitney linkage
 map.xlsx
DOI: 10.5061/dryad.4jv6312
title: Data from: Grafting or pruning in the animal tree: lateral gene transfer and gene loss?

description: Background: Lateral gene transfer (LGT), also known as horizontal gene
 transfer, into multicellular eukaryotes with differentiated tissues,
 particularly gonads, continues to be met with skepticism by many prominent
 evolutionary and genomic biologists. A detailed examination of 26 animal
 genomes identified putative LGTs in invertebrate and vertebrate genomes,
 concluding that there are fewer predicted LGTs in vertebrates/chordates
 than invertebrates, but there is still evidence of LGT into chordates,
 including humans. More recently, a reanalysis of a subset of these
 putative LGTs into vertebrates concluded that there is not horizontal gene
 transfer in the human genome. One of the genes in dispute is an
 N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which
 encodes ACY3. This gene was initially identified as a putative
 bacteria-chordate LGT but was later debunked as it has a significant BLAST
 match to a more recently deposited genome of Saccoglossus kowalevskii, a
 flatworm, Metazoan, and hemichordate. Results: Using BLAST searches, HMM
 searches, and phylogenetics to assess the evidence for LGT, gene loss, and
 rate variation in ACY3/ASPA homologues, the most parsimonious explanation
 for the distribution of ACY3/ASPA genes in eukaryotes involves both gene
 loss and bacteria-animal LGT, albeit LGT that occurred hundreds of
 millions of years ago prior to the divergence of gnathostomes.
 Conclusions: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these
 time scales in the ancestors of humans are not unexpected given the many
 known, well-characterized, and adaptive LGTs from bacteria to insects and
 nematodes.
description: ACY3_ASPA Dryad
 submissionZip archive of RAxML
 outputs for ACY3/ASPA phylogeny, along with a single output that was
 amended with the taxonomy.
DOI: 10.5061/dryad.0j6s6
title: Data from: The structure and distribution of benthic communities on a shallow seamount (Cobb Seamount, Northeast Pacific Ocean)

description: Partially owing to their isolation and remote distribution, research on
 seamounts is still in its infancy, with few comprehensive datasets and
 empirical evidence supporting or refuting prevailing ecological paradigms.
 As anthropogenic activity in the high seas increases, so does the need for
 better understanding of seamount ecosystems and factors that influence the
 distribution of sensitive benthic communities. This study used
 quantitative community analyses to detail the structure, diversity, and
 distribution of benthic mega-epifauna communities on Cobb Seamount, a
 shallow seamount in the Northeast Pacific Ocean. Underwater vehicles were
 used to visually survey the benthos and seafloor in ~1600 images (~5 m2 in
 size) between 34 and 1154 m depth. The analyses of 74 taxa from 11 phyla
 resulted in the identification of nine communities. Each community was
 typified by taxa considered to provide biological structure and/or be a
 primary producer. The majority of the community-defining taxa were either
 cold-water corals, sponges, or algae. Communities were generally
 distributed as bands encircling the seamount, and depth was consistently
 shown to be the strongest environmental proxy of the community-structuring
 processes. The remaining variability in community structure was partially
 explained by substrate type, rugosity, and slope. The study used
 environmental metrics, derived from ship-based multibeam bathymetry, to
 model the distribution of communities on the seamount. This model was
 successfully applied to map the distribution of communities on a 220 km2
 region of Cobb Seamount. The results of the study support the paradigms
 that seamounts are diversity 'hotspots', that the majority of
 seamount communities are at risk to disturbance from bottom fishing, and
 that seamounts are refugia for biota, while refuting the idea that
 seamounts have high endemism.
description: Faunal
 dataThe presence (1) or
 absence (0) of the 74 benthic taxa.faunal_data.txtSubstrate dataThe category of substrate type; where the ten categories are defined by the presence and percent-cover of sediment and debris.substrate_data.txtEnvironmental dataThe quantitative value of four seafloor characteristics at the location of the image (i.e., depth, slope, and small- and large-scale rugosity).environmental_data.txtLocation dataThe coordinates of each image in UTM (WGS_1984_UTM_zone_9N).location_data.txt
DOI: 10.5061/dryad.5s2h3
title: Data from: Shared decision-making as a cost-containment strategy: US physician reactions from a cross-sectional survey

description: Objective: To assess US physicians’ attitudes towards using shared
 decision-making (SDM) to achieve cost containment. Design: Cross-sectional
 mailed survey. Setting: US medical practice. Participants: 3897 physicians
 were randomly selected from the AMA Physician Masterfile. Of these, 2556
 completed the survey. Main outcome measures: Level of enthusiasm for
 “Promoting better conversations with patients as a means of lowering
 healthcare costs”; degree of agreement with “Decision support tools that
 show costs would be helpful in my practice” and agreement with “should
 promoting SDM be legislated to control overall healthcare costs”. Results:
 Of 2556 respondents (response rate (RR) 65%), two-thirds (67%) were ‘very
 enthusiastic’ about promoting SDM as a means of reducing healthcare costs.
 Most (70%) agreed decision support tools that show costs would be helpful
 in their practice, but only 24% agreed with legislating SDM to control
 costs. Compared with physicians with billing-only compensation,
 respondents with salary compensation were more likely to strongly agree
 that decision support tools showing costs would be helpful (OR 1.4; 95% CI
 1.1 to 1.7). Primary care physicians (vs surgeons, OR 1.4; 95% CI 1.0 to
 1.6) expressed more enthusiasm for SDM being legislated as a means to
 address healthcare costs. Conclusions: Most US physicians express
 enthusiasm about using SDM to help contain costs. They believe decision
 support tools that show costs would be useful. Few agree that SDM should
 be legislated as a means to control healthcare costs.
description: Raw Respondent Survey
 DataComplete dataset for
 2556 physician respondents.TilburtJC_USPhysicianSurveyData.csvData dictionarydata dictionary.xlsxSurvey InstrumentTilburt survey.pdf
DOI: 10.5061/dryad.55c3d
title: Data from: Walk before you jump: new insights on early frog locomotion from the oldest known salientian

description: Understanding the evolution of a Bauplan starts with discriminating
 phylogenetic signal from adaptation and the latter from exaptation in the
 observed biodiversity. Whether traits have predated, accompanied, or
 followed evolution of particular functions is the basic inference to
 establish the type of explanations required to determine morphological
 evolution. To accomplish this, we focus in a particular group of
 vertebrates, the anurans. Frogs and toads have a unique Bauplan among
 vertebrates, with a set of postcranial features that have been considered
 adaptations to jumping locomotion since their evolutionary origin. This
 interpretation is frequently stated but rarely tested in scientific
 literature. We test this assumption reconstructing the locomotor
 capabilities of the earliest known salientian, Triadobatrachus massinoti.
 This extinct taxon exhibits a mosaic of features that have traditionally
 been considered as representing an intermediate stage in the evolution of
 the anuran Bauplan, some of which were also linked to jumping skills. We
 considered T. massinoti in an explicit evolutionary framework by means of
 multivariate analyses and comparative phylogenetic methods. We used length
 measurements of major limb bones of 188 extant limbed amphibians (frogs
 and salamanders) and lizards as a morphological proxy of observed
 locomotor behavior. Our findings show that limb data correlate with
 locomotion, regardless of phylogenetic relatedness, and indicate that
 salamander-like lateral undulatory movements were the main mode of
 locomotion of T. massinoti. These results contrast with recent hypotheses
 and indicate that derived postcranial features that T. massinoti shared
 with anurans might have been later co-opted as exaptations in jumping
 frogs.
description: Appendix
 S1_R1Appendix S1 Species,
 collection numbers, locomotor modes and morphometric
 data.Appendix
 S2Appendix S2 Linear
 regressions. Epiphyses removal correction; data type.Appendix
 S3_R1Appendix 3
 Classification of cases in the DFA with their a posteriori probabilities.
 Misclassifications are marked with an asterisk (*).LIRESetal_Fig
 S1
DOI: 10.5061/dryad.df6qd5n
title: Data from: Cannabis analgesia in chronic neuropathic pain is associated with altered brain connectivity

description: Objective: The purpose of this study was to characterize the functional
 brain changes involved in THC modulation of chronic neuropathic pain.
 Methods: Fifteen patients with chronic radicular neuropathic pain
 participated in a randomized, double-blind, placebo-controlled trial
 employing a counterbalanced, within-subjects design. Pain assessments and
 functional resting state brain scans were performed at baseline and after
 sublingual THC administration. We examined functional connectivity of the
 anterior cingulate cortex (ACC) and pain related network dynamics using
 graph theory measures. Results: THC significantly reduced patients’ pain
 compared to placebo. THC-induced analgesia was correlated with a reduction
 in functional connectivity between the anterior cingulate cortex (ACC) and
 the sensorimotor cortex. Moreover, the degree of reduction was predictive
 of the response to THC. Graph theory analyses of local measures
 demonstrated reduction in network connectivity in areas involved in pain
 processing, and specifically in the dorsolateral prefrontal cortex
 (DLPFC), which were correlated with individual pain reduction.
 Conclusions: These results suggest that the ACC and DLPFC, two major
 cognitive-emotional modulation areas, and their connections to
 somatosensory areas, are functionally involved in the analgesic effect of
 THC in chronic pain. This effect may therefore be mediated through
 induction of functional disconnection between regulatory high-order
 affective regions and the sensorimotor cortex. Moreover, baseline
 functional connectivity between these brain areas may serve as a predictor
 for the extent of pain relief induced by THC.
description: AppendixTable.1a. Patient’s Demographic and Clinical Characteristics. Table.1b. Screening Criteria. Fig.1. CONSORT Flow Diagram. Fig.2. ROIs Constructing The Chronic Pain Matrix Used For Graph Theory Analysis. Fig.3. Adjacency Matrix Threshold
DOI: 10.5061/dryad.28n72
title: Data from: Interaction intensity and pollinator-mediated selection

description: In animal-pollinated plants, the opportunity for selection and the
 strength of pollinator-mediated selection are expected to increase with
 the degree of pollen limitation. However, whether differences in pollen
 limitation can explain variation in pollinator-mediated and net selection
 among animal-pollinated species is poorly understood. In the present
 study, we quantified pollen limitation, variance in relative fitness and
 pollinator-mediated selection on five traits important for pollinator
 attraction (flowering start, plant height, flower number, flower size) and
 pollination efficiency (spur length) in natural populations of 12 orchid
 species. Pollinator-mediated selection was quantified by subtracting
 estimates of selection gradients for plants receiving supplemental
 hand-pollination from estimates obtained for open-pollinated control
 plants. Mean pollen limitation ranged from zero to 0.96. Opportunity for
 selection, pollinator-mediated selection and net selection were all
 positively related to pollen limitation, whereas nonpollinator-mediated
 selection was not. Opportunity for selection varied five-fold, strength of
 pollinator-mediated selection varied three-fold and net selection varied
 1.5-fold among species. Supplemental hand-pollination reduced both
 opportunity for selection and selection on floral traits. The results show
 that the intensity of biotic interactions is an important determinant of
 the selection regime, and indicate that the potential for
 pollinator-mediated selection and divergence in floral traits is
 particularly high in species that are strongly pollen-limited.
description: Trunschke et
 al._NewPhytologist_2017_strength of selection_DRYAD_raw
 dataThe data file provides
 row data collect in summer 2013 (Mai-August) on five phenotypic traits
 (flowering start, plant height, flower number, flower size, spur length)
 and measurements of female reproductive success (number of fruits, fruit
 mass) for one population of each of twelve different orchid species
 (Anacamptis morio (L.) R.M.Bateman, Pridgeon & M.W.Chase, Dactylorhiza
 incarnata (L.) Soó, D. sambucina (L.) Soó, Orchis mascula (L.) L., O.
 militaris (L.), and Neotinea ustulata (L.) R.M.Bateman, Pridgeon &
 M.W.Chase, and of the rewarding species Dactylorhiza viridis (L.)
 R.M.Bateman, Pridgeon & M.W.Chase, Epipactis palustris (L.) Crantz,
 Gymnadenia conopsea (L.) R.Br., Neottia ovata (L.) Bluff & Fingerh.,
 Platanthera bifolia (L.) Rich., and P. chlorantha (Custer) Rchb.). These
 data were used calculate mean±SE of phenotypic traits and female fitness.
 In addition, phenotypic traits are provided as standardized values to a
 mean of 0 and a variance of 1, and relative fitness as individual fitness
 divided by mean fitness. Standardisation is done by population and
 treatment. These data are used to calculate selection gradients by
 population and treatment, whose absolute values were then used for all
 higher-level analysis relating strength of selection and degree of pollen
 limitation.
DOI: 10.5061/dryad.vk070
title: Data from: Does mixed-species flocking influence how birds respond to a gradient of land-use intensity?

description: Conservation biology is increasingly concerned with preserving
 interactions among species such as mutualisms in landscapes facing
 anthropogenic change. We investigated how one kind of mutualism,
 mixed-species bird flocks, influences the way in which birds respond to
 different habitat types of varying land-use intensity. We use data from a
 well-replicated, large-scale study in Sri Lanka and the Western Ghats of
 India, in which flocks were observed inside forest reserves, in ‘buffer
 zones' of degraded forest or timber plantations, and in areas of
 intensive agriculture. We find flocks affected the responses of birds in
 three ways: (i) species with high propensity to flock were more sensitive
 to land use; (ii) different flock types, dominated by different flock
 leaders, varied in their sensitivity to land use and because following
 species have distinct preferences for leaders, this can have a cascading
 effect on followers' habitat selection; and (iii) those
 forest-interior species that remain outside of forests were found more
 inside flocks than would be expected by chance, as they may use flocks
 more in suboptimal habitat. We conclude that designing policies to protect
 flocks and their leading species may be an effective way to conserve
 multiple bird species in mixed forest and agricultural landscapes.
description: Species
 DatasetIncludes all the bird
 species identified during the project, organized by family, and the
 following data: their scientific and English names, their distribution
 (country), their habitat, diet and weight from the literature, what
 analyses they are included in for the article in review at the Proceedings
 of the Royal Society B: Biological Sciences, the total number of
 sightings, the percentage seen inside protected forest, and the species’
 detectability, as calculated by DISTANCE.Species data for Dryad
 submission, 9.2.14.xlsxFlock
 DatasetThis is a data table
 that includes the composition of all complete flocks (80-100% of
 individuals detected), and is organized by transects (see transect data).
 Note that mammals species are included in these records as well as bird
 species, and species are ordered by English name.Flock database for Dryad,
 9.2.14.xlsTransect
 databaseTransect dataset. This
 Excel document lists all transects, their location, how much they were
 walked, and the number of flocks seen on them. The number of flocks
 includes incomplete flocks and is divided into Orange-billed Babbler
 (OBBA) led flocks and all other flocks, which are DISTANCE-adjusted to
 determine flock density.
DOI: 10.5061/dryad.7rs2d
title: Data from: The architecture of river networks can drive the evolutionary dynamics of aquatic populations

description: It is widely recognized that physical landscapes can shape genetic
 variation within and between populations. However, it is not well
 understood how riverscapes, with their complex architectures, affect
 patterns of neutral genetic diversity. Using a spatially explicit
 agent-based modeling (ABM) approach, we evaluate the genetic consequences
 of dendritic river shapes on local population structure. We disentangle
 the relative contribution of specific river properties to observed
 patterns of genetic variation by evaluating how different branching
 architectures and downstream flow regimes affect the genetic structure of
 populations situated within river networks. Irrespective of the river
 length, our results illustrate that the extent of river branching,
 confluence position, and levels of asymmetric downstream migration dictate
 patterns of genetic variation in riverine populations. Indeed, comparisons
 between simple and highly branched rivers show a 20-fold increase in the
 overall genetic diversity and a 7-fold increase in the genetic
 differentiation between local populations. Given that most rivers have
 complex architectures, these results highlight the importance of
 incorporating riverscape information into evolutionary models of aquatic
 species and could help explain why riverine fishes represent a
 disproportionately large amount of global vertebrate diversity per unit of
 habitable area.
description: R scripts to test the
 effect of river networks on population genetic structureSpatial explicit
 forward-time agent-based model scripts in R to simulate multi-locus
 genotypes for all individuals from every local population based on
 informed river shapes. For any questions please contact the paper's
 authors.River_network_Rscript.zip