cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tn3vp
title: Data from: Past tree influence and prescribed fire mediate biotic interactions and community reassembly in a grassland-restoration experiment

description: Woody plant encroachment of grasslands is occurring globally, with
 profound ecological consequences. Attempts to restore herbaceous dominance
 may fail if the woody state is resilient or if intervention leads to an
 alternate, undesirable state. Restoration outcomes often hinge on biotic
 interactions – particularly on priority effects that inhibit or promote
 community reassembly. Following experimental tree removal from
 conifer-invaded grasslands, we documented substantial variation in
 community reassembly associated with the changing abundance of the native
 clonal sedge Carex inops L.H. Bailey subsp. inops. We explored possible
 mechanisms for this variation, focusing on the nature and timing of
 interactions between the meadow community and Carex and on how past tree
 influence and prescribed fire mediate the outcomes of these interactions.
 Meadow species increased after tree removal, but less so in burned than in
 unburned plots. Carex expanded dramatically after fire, particularly where
 past tree influence had been greater. Meadow species and Carex developed
 an increasingly negative association over time; pre-emption was
 reciprocal, but offset in time and space. Meadow species inhibited Carex
 through vegetative recovery in areas of limited or recent tree influence,
 irrespective of fire. Carex inhibited meadow reassembly in areas of
 greater tree influence, but only with burning. Synthesis and applications.
 Tree removal and fire imposed across a range of altered meadow states
 yielded varying outcomes, reflecting biotic interactions and species'
 regenerative traits that inhibited or promoted reassembly. Fire tended to
 destabilize the remnant meadow community and, in areas more degraded by
 encroachment, stimulated release of Carex, which inhibited reassembly.
 Knowledge of the context dependence of biotic interactions can enhance the
 effectiveness of restoration by establishing the bounds within which
 treatments produce desirable or undesirable outcomes.
description: Cover and richness in
 the experimental subplotsSee
 Readme.docExp_subplots.csvCover and richness in the reference meadow transectsSee Readme.docRef_meadows.csvBurn severity in the burned suplotsSee Readme.docBurn_severity.csvList of species and their classification by habitat affinitySee Readme.docSpecies.csv
DOI: 10.5061/dryad.4gg07
title: Data from: New evidence from linguistic phylogenetics identifies limits to punctuational change

description: Since the early 1970s, biologists have debated whether evolution is
 punctuated by speciation events with bursts of cladogenetic changes, or
 whether evolution tends to be of a more gradual, anagenetic nature. A
 similar discussion among linguists has barely begun, but the present
 results suggest that there is also room for controversy over this issue in
 linguistics. The only previous study correlated the number of nodes in
 linguistic phylogenies with branch lengths and found support for
 punctuated equilibrium. We replicate this result for branch lengths, but
 find no support for punctuated equilibrium using a different, automated
 measure of linguistic divergence and a much larger data set. With the
 automated measure, segments of trees containing more nodes show no greater
 divergence from an outgroup than segments containing fewer nodes.
description: Holman&Wichmann
 Appendix 1Proof of algorithm to
 maximize number of independent testsHolman&Wichmann
 Appendix 2Data sources and
 outgroup test results by language familyHolman&Wichmann
 Appendix 3Simulation
 methodsHolman&Wichmann
 Folder 1Program to produce
 simulated language familiesHolman&Wichmann
 Folder 2Program to run outgroup
 tests on simulated language families
DOI: 10.5061/dryad.j03q3
title: Data from: A five gene phylogenetic study of Fuireneae (Cyperaceae) with a revision of Isolepis humillima

description: Cyperaceae tribe Fuireneae consists of six genera (Actinoscirpus,
 Pseudoschoenus, Fuirena, Bolboschoenus, Schoenoplectus, and
 Schoenoplectiella) and approximately 155 species distributed widely across
 all continents except Antarctica. Recent molecular analyses suggest that
 Fuireneae is paraphyletic with respect to Cypereae, but limited taxonomic
 sampling and low branch support have resulted in unresolved relationships
 among key genera. To address the potential paraphyly of Fuireneae as well
 as intratribal and intertribal relationships, thirty taxa representing
 major lineages from the six Fuireneae genera within Cypereae were
 sequenced for five coding and non-coding regions from the nuclear
 (internal transcribed spacer, ITS) and chloroplast (trnL intron/trnL-trnF
 spacer; partial ndhF, rbcL and matK genes) genomes. Maximum parsimony,
 maximum likelihood and Bayesian analyses of the dataset strongly support
 Fuireneae as a grade of three clades: (1) Fuirena, (2) Bolboschoenus and
 (3) a group composed of Cypereae and the four remaining Fuireneae genera
 (Schoenoplectus, Schoenoplectiella, Actinoscirpus, and Pseudoschoenus).
 Individual and combined gene trees consistently position Isolepis
 humillima within a well supported clade consisting of species in
 Schoenoplectiella sect. Schoenoplectiella. Based on molecular evidence, we
 transfer Isolepis humillima to Schoenoplectiella humillima , and suggest
 that a large-scale revision of tribal limits is required to reflect the
 natural relationships of the genera currently treated in Fuireneae.
description: Alignment_ITS_4.11Alignment of ITS regionAlignment_trnL_trnLF_4.11Alignment of trnL and trnL-FAlignment_ndhF_4.11Alignment of ndhFAlignment_rbcL_4.11Alignment of rbcLAlignment_matK_4.11Alignment of matK
DOI: 10.5061/dryad.43508
title: Data from: Antipsychotic dose mediates the association between polypharmacy and corrected QT interval

description: Antipsychotic (AP) drugs have the potential to cause prolongation of the
 QT interval corrected for heart rate (QTc). As this risk is
 dose-dependent, it may be associated with the number of AP drugs
 concurrently prescribed, which is known to be associated with increased
 cumulative equivalent AP dosage. This study analysed whether AP dose
 mediates the relationship between polypharmacy and QTc interval. We used
 data from a cross-sectional survey that investigated the prevalence of QTc
 lengthening among people with psychiatric illnesses in Italy. AP
 polypharmacy was tested for evidence of association with AP dose and QTc
 interval using the Baron and Kenny mediational model. A total of 725
 patients were included in this analysis. Of these, 186 (26%) were treated
 with two or more AP drugs (AP polypharmacy). The mean cumulative AP dose
 was significantly higher in those receiving AP polypharmacy (prescribed
 daily dose/defined daily dose = 2.93, standard deviation 1.31) than
 monotherapy (prescribed daily dose/defined daily dose = 0.82, standard
 deviation 0.77) (z = −12.62, p &lt; 0.001). Similarly, the mean QTc
 interval was significantly longer in those receiving AP polypharmacy (mean
 = 420.86 milliseconds, standard deviation 27.16) than monotherapy (mean =
 413.42 milliseconds, standard deviation 31.54) (z = −2.70, p = 0.006). The
 Baron and Kenny mediational analysis showed that, after adjustment for
 confounding variables, AP dose mediates the association between
 polypharmacy and QTc interval. The present study found that AP
 polypharmacy is associated with QTc interval, and this effect is mediated
 by AP dose. Given the high prevalence of AP polypharmacy in real-world
 clinical practice, clinicians should consider not only the myriad risk
 factors for QTc prolongation in their patients, but also that adding a
 second AP drug may further increase risk as compared with monotherapy.
description: qtc_database to
 share
DOI: 10.5061/dryad.4rb0r
title: Data from: Assessing the potential information content of multicomponent visual signals: a machine learning approach

description: Careful investigation of the form of animal signals can offer novel
 insights into their function. Here, we deconstruct the face patterns of a
 tribe of primates, the guenons (Cercopithecini), and examine the
 information that is potentially available in the perceptual dimensions of
 their multicomponent displays. Using standardized colour-calibrated images
 of guenon faces, we measure variation in appearance both within and
 between species. Overall face pattern was quantified using the computer
 vision ‘eigenface’ technique, and eyebrow and nose-spot focal traits were
 described using computational image segmentation and shape analysis.
 Discriminant function analyses established whether these perceptual
 dimensions could be used to reliably classify species identity, individual
 identity, age and sex, and, if so, identify the dimensions that carry this
 information. Across the 12 species studied, we found that both overall
 face pattern and focal trait differences could be used to categorize
 species and individuals reliably, whereas correct classification of age
 category and sex was not possible. This pattern makes sense, as guenons
 often form mixed-species groups in which familiar conspecifics develop
 complex differentiated social relationships but where the presence of
 heterospecifics creates hybridization risk. Our approach should be broadly
 applicable to the investigation of visual signal function across the
 animal kingdom.
description: Guenon face pattern
 classification dataThree Excel spreadsheets
 containing the data used for classification analyses based on 1.)
 eigenfaces, 2.) nose-spots and 3.) eyebrow patches.guenon_face_pattern_classification_data_WA&JH_11_12_14.xlsx
DOI: 10.5061/dryad.n4m40vm
title: Data from: Seasonal dynamics and changing sea level as determinants of the community and trophic structure of oribatid mites in a salt marsh of the Wadden Sea

description: Global change processes affect seasonal dynamics of salt marshes and
 thereby their plant and animal communities. However, these changes have
 been little investigated for microarthropod communities. We studied the
 effect of seasonality and changes in sea level on oribatid mites in the
 natural salt marsh and on artificial islands in the back-barrier
 environment of the island Spiekeroog (Wadden Sea, Germany). Three zones of
 the artificial islands were filled with transplanted sods from the lower
 salt marsh zone and thereby exposed to three different inundation
 frequencies. We hypothesized that oribatid mite communities will differ
 along the natural salt marsh vegetation zones [upper salt marsh (USM),
 lower salt marsh (LSM), pioneer zone (PZ)], which are influenced by
 different tidal regimes. Accordingly, total oribatid mite densities
 declined from the USM and LSM to the PZ. Similarly, oribatid mite species
 compositions changed along the salt marsh transect and also responded to
 variations in inundation frequency in LSM on artificial islands with
 typical species of the USM, LSM and PZ being Multioppia neglecta (USM),
 Hermannia pulchella (LSM), Zachvatkinibates quadrivertex (LSM, PZ) and
 Ameronothrus schneideri (LSM, PZ). Oribatid mite density in the salt marsh
 and on the artificial islands was at a maximum in winter and spring; this
 was due in part to high density of juveniles, pointing to two reproductive
 periods. We hypothesized that oribatid mite trophic structure changes due
 to variations in abiotic (e.g., tidal dynamics, temperature) and biotic
 conditions (e.g., resource availability). Stable isotope (15N, 13C) and
 neutral lipid fatty acid analyses indicated that oribatid mite species
 have different diets with e.g., Z. quadrivertex feeding on macroalgae and
 fungi, A. schneideri feeding on microalgae and bacteria, and Scheloribates
 laevigatus and M. neglecta feeding on dead organic matter, bacteria and
 fungi. Overall, the results indicate that oribatid mite species in salt
 marshes are affected by changes in environmental factors such as
 inundation intensity, with the effects being most pronounced in species
 with narrow trophic niches and limited niche plasticity. The results also
 indicate that oribatid communities of the LSM respond little to short-term
 (one year) changes in inundation frequency.
description: fatty_acid_oribatid_mitesFatty acid data (NLFAs) of oribatid mites from Spiekeroog, GermanyMeanDensity_oribatid_mites_artificial_islandsMeanDensity_oribatid_mites_salt_marshstable_isotopes_oribatid_mites
DOI: 10.5061/dryad.t530ps6
title: Data from: Dolphins simplify their vocal calls in response to increased ambient noise

description: Ocean noise varies spatially and temporally and is driven by natural and
 anthropogenic processes. Increased ambient noise levels can cause signal
 masking and communication impairment, affecting fitness and recruitment
 success. However, the effects of increasing ambient noise levels on marine
 species, such as marine mammals that primarily rely on sound for
 communication, are not well understood. We investigated the effects of
 concurrent ambient noise levels on social whistle calls produced by
 bottlenose dolphins (Tursiops truncatus) in the Western North Atlantic.
 Elevated ambient noise levels were mainly caused by ship noise. Increases
 in ship noise, both within and below the dolphins’ call bandwidth,
 resulted in higher dolphin whistle frequencies and a reduction in whistle
 contour complexity, an acoustic feature associated with individual
 identification. Consequently, the noise-induced simplification of dolphin
 whistles may reduce the information content in these acoustic signals and
 decrease effective communication, parent-offspring proximity or group
 cohesion.
description: Dolphin whistle
 characteristics and associated ambient noise levelsCharacteristics of
 dolphin whistles recorded off Ocean City, Maryland, U.S.A., and the
 associated ambient noise levels in various frequency
 bands.Supplement_Data.xlsx
DOI: 10.15468/dl.fc6rbw
title: Occurrence Download

description: A dataset containing 202 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Nerodia rhombifer",
 "Year 1960-2026"
 ]
}

 The dataset includes 202 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000715-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tnwxq3
title: Occurrence Download

description: A dataset containing 355217 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paris"
 ]
}

 The dataset includes 355217 records from 1297 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000689-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.27p4s
title: Data from: Protein structure determination using metagenome sequence data

description: Despite decades of work by structural biologists, there are still ~5200
 protein families with unknown structure outside the range of comparative
 modeling. We show that Rosetta structure prediction guided by
 residue-residue contacts inferred from evolutionary information can
 accurately model proteins that belong to large families and that
 metagenome sequence data more than triple the number of protein families
 with sufficient sequences for accurate modeling. We then integrate
 metagenome data, contact-based structure matching, and Rosetta structure
 calculations to generate models for 614 protein families with currently
 unknown structures; 206 are membrane proteins and 137 have folds not
 represented in the Protein Data Bank. This approach provides the
 representative models for large protein families originally envisioned as
 the goal of the Protein Structure Initiative at a fraction of the cost.
description: Starting
 modelsStarting models for the
 iterative hybrid protocol. Based on the prefix you can determine where the
 models are coming from. (ab_v01) top10 denovo models using sigmoid only
 restraints. (ab_v02) top10 denovo models using bounded+sigmoid restraints
 during centroid, and sigmoid only during full atom stage. (mp) top10
 map-align models from one round of hybrid.aah4043_starting.zipInitial modelsTop models from initial experiments where only the (ab_v01+ab_v02) OR mp models are iteratively hybridizedaah4043_initial.zipTop 30 modelsTop 30 models across 30 iterations of hybrid of ab_v01+ab_v02 + map-align models.aah4043_top_30.zipFinal modelsSingle model for each target.aah4043_final.zip
DOI: 10.5061/dryad.589g3
title: Data from: Phylogeny of Morella rubra and its relatives (Myricaceae) and genetic resources of Chinese bayberry using RAD sequencing

description: Phylogenetic relationships among Chinese species of Morella (Myricaceae)
 are unresolved. Here, we use restriction site-associated DNA sequencing
 (RAD-seq) to identify candidate loci that will help in determining
 phylogenetic relationships among Morella rubra, M. adenophora, M. nana and
 M. esculenta. Three methods for inferring phylogeny, maximum parsimony
 (MP), maximum likelihood (ML) and Bayesian concordance, were applied to
 data sets including as many as 4253 RAD loci with 8360 parsimony
 informative variable sites. All three methods significantly favored the
 topology of (((M. rubra, M. adenophora), M. nana), M. esculenta). Two
 species from North America (M. cerifera and M. pensylvanica) were placed
 as sister to the four Chinese species. According to BEAST analysis, we
 deduced speciation of M. rubra to be at about the Miocene-Pliocene
 boundary (5.28 Ma). Intraspecific divergence in M. rubra occurred in the
 late Pliocene (3.39 Ma). From pooled data, we assembled 29378, 21902 and
 23552 de novo contigs with an average length of 229, 234 and 234 bp for M.
 rubra, M. nana and M. esculenta respectively. The contigs were used to
 investigate functional classification of RAD tags in a BLASTX search.
 Additionally, we identified 3808 unlinked SNP sites across the four
 populations of M. rubra and discovered genes associated with fruit
 ripening and senescence, fruit quality and disease/defense metabolism
 based on KEGG database.
description: The raw data for
 MorellaThese files including
 contig assemblies in fasta format (Morella esculenta-Contigs.fa, Morella
 esculenta-Contigs.fa and Morella rubra-Contigs.fa), matrix used to infer
 phlogenetic trees (Morella phlogeney.phy), shared SNP loci between four
 different populations (4Morella rubra shared.loci) and the raw RAD
 dataThe_raw_data_for_Morella.zip
DOI: 10.5061/dryad.2t8r1
title: Data from: Queen signalling in social wasps

description: Social Hymenoptera are characterized by a reproductive division of labour,
 whereby queens perform most of the reproduction and workers help to raise
 her offspring. A long-lasting debate is whether queens maintain this
 reproductive dominance by manipulating their daughter workers into
 remaining sterile (queen control), or if instead queens honestly signal
 their fertility and workers reproduce according to their own evolutionary
 incentives (queen signalling). Here we test these competing hypotheses
 using data from Vespine wasps. We show that in natural colonies of the
 Saxon wasp, Dolichovespula saxonica, queens emit reliable chemical cues of
 their true fertility and that these putative queen signals decrease as the
 colony develops and worker reproduction increases. Moreover, these
 putative pheromones of D. saxonica show significant conservation with
 those of Vespula vulgaris and other Vespinae, thereby arguing against fast
 evolution of signals as a result of a queen-worker arms race ensuing from
 queen control. Lastly, levels of worker reproduction in these species
 correspond well with their average colony kin structures, as predicted by
 the queen signalling hypothesis but not the queen control hypothesis.
 Altogether, this correlative yet comprehensive analysis provides
 compelling evidence that honest signalling explains levels of reproductive
 division of labour in social wasps.
description: Individual
 dataFor each sampled
 Dolichovespula saxonica indvidual (queens and workers), its colony
 affiliation, level of ovary development, classification of reproductive
 caste, and CHC raw peak areas.Raw data to be uploaded to
 DataDryad 1.xlsxData for linear
 regression modelsFor each reproductive
 individual (queens and workers), its colony affiliation (Colony), its
 repoductive caste (Caste), its score on the first principal component of
 CHC data (PC1), the percentage of worker-produced males in its colony
 (WPM), the percentage of reproductive workers in its colony (RW), its
 ovary development (OvaryScore), and the level of development of its colony
 (ColonyStage).Raw data to be uploaded to
 DataDryad 2.xlsx
DOI: 10.5061/dryad.g88r7
title: Data from: Seasonal variation in behavioral thermoregulation and predator avoidance in a small mammal

description: Understanding behavioral responses of animals to the thermal environment
 is of increasing importance under changing climate regimes.
 Thermoregulatory behaviors, such as exploitation of thermal refugia or
 temporal partitioning of activity, can buffer organisms against hot and
 cold thermal extremes but may conflict with other life history needs. Our
 objective was to evaluate strategies for behavioral thermoregulation by a
 small-bodied endotherm to test hypotheses about tradeoffs between thermal
 and security needs across seasons. We quantified the influence of both
 thermal and security properties of habitat on selection of rest sites by
 pygmy rabbits (Brachylagus idahoensis), and we identified environmental
 and endogenous factors affecting levels of activity during summer and
 winter. Behavioral strategies varied seasonally in response to both
 thermal challenges and risk of predation. During summer, rabbits selected
 rest sites with high concealment and low shortwave radiation, but activity
 levels were independent of ambient temperature. During winter, however,
 security, but not thermal properties, influenced selection of rest sites,
 and activity was positively correlated with ambient temperature during the
 most thermally stressful periods of the day (dawn, dusk, and night). The
 types of nuanced behavioral plasticity that we documented in response to
 the thermal environment is likely to be overlooked in evaluations of
 species tolerance to changing climates. Understanding the potential for
 behavior to buffer individuals as well as the limits of behavior to shield
 populations from consequences of climate change is critical for effective
 conservation of vulnerable species.
description: ActivityContains activity (as sum of motion counts) and predictors used in this study. Data can be subset by season and activity interval as necessary. Metadata can be found in the README.txt file.Milling_etal_activity.csvRest site selectionContains levels of thermal and security resources at rest sites used by pygmy rabbits and associated available sites. Data can be subset by season as necessary. Metadata can be found in the README.txt file.Milling_etal_restsite.csv