cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tr360
title: Data from: Drought-induced starvation of aardvarks in the Kalahari: an indirect effect of climate change

description: Aardvarks (Orycteropus afer) are elusive burrowing mammals, predominantly
 nocturnal and distributed widely throughout Africa except for arid
 deserts. Their survival may be threatened by climate change via direct and
 indirect effects of increasing heat and aridity. To measure their current
 physiological plasticity, we implanted biologgers into six adult aardvarks
 resident in the semi-arid Kalahari. Following a particularly dry and hot
 summer, five of the study aardvarks and 11 other aardvarks at the study
 site died. Body temperature records revealed homeothermy (35.4–37.2°C)
 initially, but heterothermy increased progressively through the summer,
 with declining troughs in the nychthemeral rhythm of body temperature
 reaching as low as 25°C before death, likely due to starvation. Activity
 patterns shifted from the normal nocturnal to a diurnal mode. Our results
 do not bode well for the future of aardvarks facing climate change.
 Extirpation of aardvarks, which play a key role as ecosystem engineers,
 may disrupt stability of African ecosystems.
description: Body temperature of
 Aardvarks in the Kalahari and meteorological dataThis file provides the
 body temperature of four aardvarks (Orycteropus afer) recorded in
 2012-2013 in the South African Kalahari (Tswalu Game Reserve) and black
 globe temperature measured on site. Data were recorded at a 30 min
 interval. Body temperature was recorded using miniaturized data logger
 implanted surgically. Three of the aardvarks died during the course of the
 study, one did survive the planned year.Tb_data_aardvark.xlsx
DOI: 10.5061/dryad.t8016
title: Data from: Species delimitation with gene flow

description: Species are commonly thought to be evolutionarily independent in a way
 that populations within a species are not. In recent years, studies that
 seek to identify evolutionarily independent lineages (i.e., to delimit
 species) using genetic data have typically adopted multispecies coalescent
 approaches that assume that evolutionary independence is formed by the
 differential sorting of ancestral alleles due to genetic drift. However,
 gene flow appears to be common among populations and nascent species, and
 while this process may inhibit lineage divergence (and thus independence),
 it is usually not explicitly considered when delimiting species. In this
 article, we apply Phylogeographic Inference using Approximate Likelihoods
 (PHRAPL), a recently described method for phylogeographic model selection,
 to species delimitation. We describe an approach to delimiting species
 using PHRAPL that attempts to account for both genetic drift and gene
 flow, and we compare the method’s performance to that of a popular
 delimitation approach (BPP) using both simulated and empirical datasets.
 PHRAPL generally infers the correct demographic-delimitation model when
 the generating model includes gene flow between taxa, given a sufficient
 amount of data. When the generating model includes only isolation in the
 recent past, PHRAPL will in some cases fail to differentiate between gene
 flow and divergence, leading to model misspecification. Nevertheless, the
 explicit consideration of gene flow by PHRAPL is an important complement
 to existing delimitation approaches, particularly in systems where gene
 flow is likely important.
description: Supplementary
 MaterialSupplementary Figures
 and TablesJackson.etal_SystBio_SupplementaryMaterials.pdfPHRAPL tutorialA tutorial for running PHRAPLJackson.etal_SystBio_SupplementaryMaterials_phrapl_vignette.htmlSequences for Homo sapiensSequences used from Homo sapiensHumans_sequences.zipScincella lateralis sequencesSequences used from Scincella lateralisScincella_sequences.zipSarracenia alata sequencesSequences used for Sarracenia alataSarracenia_sequences.zip
DOI: 10.5061/dryad.52m30
title: Data from: Do thermoregulatory costs limit altitude distributions of Andean forest birds?

description: Along tropical mountains, species often occupy narrow altitude ranges.
 Numerous biotic and abiotic factors have been proposed as determinants of
 altitude occupancy. We measured several aspects of thermal physiology of
 215 bird species across a 2·6-km altitude gradient in the Peruvian Andes.
 We predicted that highland species would show adaptation to the colder
 high-altitude climate and that energy costs of thermoregulation might
 limit upslope dispersal of lowland natives. We found reductions in thermal
 conductance, body temperature and lower critical temperature in highland
 birds compared with lowland species. These combine to make highland
 natives more resistant to heat loss. We did not find convincing evidence
 that acute thermal limits or energy costs of thermoregulation constrained
 altitude distributions. Heat-budget models predicted low-to-moderate
 long-term costs at native altitudes. Costs increased for lowland natives
 modelled in the highland climate, but for all but a few species, costs
 remained within putative expenditure limits. Although we did not test heat
 tolerances, we measured all species at temperatures similar to the hottest
 air temperatures at the lowland site. There was no evidence that high
 lowland temperatures preclude downslope movements of highland birds. While
 thermal tolerances probably do not directly determine altitude occupancy
 by most species, the additional energy cost of thermoregulation
 experienced by lowland species moving upslope may trade off against
 investment in important life-history components such as breeding, and
 thereby affect altitude range limits.
description: Raw Data Thermal
 conductanceRaw Data all data with
 conductance.pdfLondono_GA_SUPPLEMENTAL_MaterialLondono_GA_et al._SUPPLEMENTAL_Material.pdfLondono_GA_et al._MCC_tree_ThermCost
DOI: 10.5061/dryad.21b04
title: Data from: Reporting quality of randomized controlled trial abstracts among high-impact general medical journals: a review and analysis

description: Objective: To assess adherence to The Consolidated Standards of Reporting
 Trials (CONSORT) for Abstracts by five high-impact general medical
 journals and to assess whether quality of reporting was homogeneous across
 these journals. Design: Descriptive, cross-sectional study. Setting:
 Randomized Controlled Trial (RCT) abstracts in five high-impact general
 medical journals. Participants: We used up to 100 RCT abstracts published
 between 2011 and 2014 from each of the following journals: The New England
 Journal of Medicine (NEJM), the Annals of Internal Medicine (Annals IM),
 The Lancet, the British Medical Journal (The BMJ), and the Journal of the
 American Medical Association (JAMA). Main Outcome: The primary outcome was
 percent overall adherence to the 19-item CONSORT for abstracts checklist.
 Secondary outcomes included percent adherence in checklist subcategories
 and assessing homogeneity of reporting quality across the individual
 journals. Results: Search results yielded 466 abstracts, three of which
 were later excluded as they were not RCTs. Analysis was performed on 463
 abstracts (97 from NEJM, 66 from Annals IM, 100 from The Lancet, 100 from
 The BMJ, 100 from JAMA). Analysis of all scored items showed an overall
 adherence of 67% (95% CI, 66-68%) to the CONSORT for Abstracts checklist.
 The Lancet had the highest overall adherence rate (78%; 95% CI, 76-80%)
 while NEJM had the lowest (55%; 95% CI, 53-57%). Adherence rates to eight
 of the checklist items differed by greater than 25% between journals.
 Conclusion: Among the five highest-impact general medical journals, there
 is variable and incomplete adherence to the CONSORT for Abstracts
 reporting checklist of randomized trials, with substantial differences
 between individual journals. Lack of adherence to the CONSORT for
 Abstracts reporting checklist by high-impact medical journals impedes
 critical appraisal of important studies. We recommend diligent assessment
 of adherence to reporting guidelines by authors, reviewers, and editors to
 promote transparency and unbiased reporting of abstracts.
description: STATA_Reporting Quality
 of Randomized Controlled Trial Abstracts Among High-Impact General Medical
 Journals: A Review and AnalysisThe following file
 contains STATA data for the 2015 review and analysis of reporting quality
 of randomized controlled trial abstracts in five high-impact general
 medical journals based on adherence to the CONSORT for abstracts
 guidelines.STATA_Reporting Quality of
 Randomized Controlled Trial Abstracts Among High-Impact General Medical
 Journals.pdf
DOI: 10.5061/dryad.7kc09
title: Data from: The greenscape shapes surfing of resource waves in a large migratory herbivore

description: The Green Wave Hypothesis posits that herbivore migration manifests in
 response to waves of spring green-up (i.e. green-wave surfing).
 Nonetheless, empirical support for the Green Wave Hypothesis is mixed, and
 a framework for understanding variation in surfing is lacking. In a
 population of migratory mule deer (Odocoileus hemionus), 31% surfed plant
 phenology in spring as well as a theoretically perfect surfer, and 98%
 surfed better than random. Green-wave surfing varied among individuals and
 was unrelated to age or energetic state. Instead, the greenscape, which we
 define as the order, rate and duration of green-up along migratory routes,
 was the primary factor influencing surfing. Our results indicate that
 migratory routes are more than a link between seasonal ranges, and they
 provide an important, but often overlooked, foraging habitat. In addition,
 the spatiotemporal configuration of forage resources that propagate along
 migratory routes shape animal movement and presumably, energy gains during
 migration.
description: Aikens_etal_2017_DataThis zip folder contains three data files, please see README.pdf and the associated publication for more information.
DOI: 10.5061/dryad.1904
title: Data from: Evidence of extreme habitat stability in a Southeast Asian biodiversity hotspot based on the evolutionary analysis of neotenic net-winged beetles

description: The diversification of neotenic beetle lineages has not been studied,
 despite the potential for defining biodiversity hotspots and elucidating
 the history of regional faunas. Additionally, neotenics may provide
 insight into the process of speciation in small populations with extremely
 low dispersal ability and a limited range. Here, we used two rDNA and
 three mtDNA markers to investigate the phylogeny of Scarelus, a neotenic
 lineage endemic to Southeast Asian rainforests. Most genetic
 differentiation was associated with Palaeogene geographic divisions, which
 remain distinct despite temporary connections. Dispersal events were rare,
 with only two inferred for Scarelus: from Borneo to the Philippines 28.3
 million years ago (mya) and from Sumatra to Java 13.9 mya. The
 reproductive isolation depended on allopatric range fragmentation, and
 Scarelus diversified readily when conditions were favorable; in this case,
 at different times in the eastern (19.3–39.1 mya) and western (3.5–13.9
 mya) parts of Sundaland. The observed strong phenotypic similarity was
 preserved under speciation through complete allopatry. Neotenic Lycidae
 have survived for a long time in very stable habitats, and extremely low
 dispersal activity has not limited their existence; however, the long-term
 diversification rate of neotenics is low and diversification is
 nonexistent under stable conditions. The modern ranges of neotenic
 lineages are indicative of ancient rainforest refugia, and may be used in
 biodiversity conservation management. Most neotenics are at risk of
 extinction due to small ranges and a low dispersal potential.
description: ScarelusNEXUSMolEcolThe nexus matrices containing all sequences used for the phylogenetic analysis
DOI: 10.5061/dryad.601m8
title: Data from: Assessment of healthcare delivery in the early management of bacterial meningitis in UK young infants: an observational study

description: OBJECTIVE: To define early presenting features of bacterial meningitis in
 young infants in England and to review the adequacy of individual case
 management as compared with relevant national guidelines and an expert
 panel review. DESIGN: Retrospective medical case note review and parental
 recall using standardised questionnaires. SETTING: England and Wales.
 PARTICIPANTS: Infants aged &lt;90 days with bacterial meningitis
 diagnosed between July 2010 and July 2013. RESULTS: Of the 97 cases
 recruited across England and Wales, 66 (68%) were admitted from home and
 31 (32%) were in hospital prior to disease onset. Almost all symptoms
 reported by parents appeared at the onset of the illness, with very few
 new symptoms appearing subsequently. Overall, 20/66 (30%) infants were
 assessed to have received inappropriate pre hospital management. The
 median time from onset of first symptoms to first help was 5 hours (IQR:
 2-12) and from triage to receipt of first antibiotic dose was 2.0 hours
 (IQR: 1.0-3.3) hours, significantly shorter in infants with fever or
 seizures at presentation compared to those without (1.7 [IQR, 1.0-3.0] vs.
 4.2 [1.8-6.3] hours, p=0.02). Overall, 26 (39%) infants had a poor outcome
 in terms of death or neurological complication; seizures at presentation
 was the only significant independent risk factor (OR, 7.9; 95% CI: 2.3-
 207.0). For cases in hospital already, the median time from onset to first
 dose of antibiotics was 2.6 (IQR: 1.3-9.8) hours and 12/31 (39%) of
 infants had serious neurological sequelae at hospital discharge.
 CONCLUSIONS: Young infants with bacterial meningitis have non-specific
 symptoms and signs, with no clear progression of illness over time,
 highlighting the difficulties in early recognition by parents and
 healthcare professionals alike. A substantial proportion of infants
 received inappropriate pre- and post-hospital management. We propose a
 targeted campaign for education and harmonisation of practice with
 evidence-based management algorithms.
description: HCD
 dataDatafile
 PDFAll
 combo_dryad.pdf
DOI: 10.5061/dryad.j2qr4
title: Data from: Energetic and Ecological Constraints on Population Density of Reef Fishes

description: Population ecology has classically focused on pairwise species
 interactions, hindering the description of general patterns and processes
 of population abundance at large spatial scales. Here we use the Metabolic
 Theory of Ecology as a framework to formulate and test a model that yields
 predictions linking population density to the physiological constraints of
 body size and temperature on individual metabolism, and the ecological
 constraints of trophic structure and species richness on energy
 partitioning among species. Our model was tested by applying Bayesian
 quantile regression to a comprehensive reef-fish community database, from
 which we extracted density data for 5609 populations spread across 49
 sites around the world. Our results indicate that population density
 declines markedly with increases in community species richness and that,
 after accounting for richness, energetic constraints are manifested most
 strongly for the most abundant species, which generally are of small body
 size and occupy lower trophic groups. Overall, our findings suggest that,
 at the global scale, factors associated with community species richness
 are the major drivers of variation in population density. Given that
 populations of species-rich tropical systems exhibit markedly lower
 maximum densities, they may be particularly susceptible to stochastic
 extinction.
description: Reef-fish population
 vectorsThis dataset contains
 data on: abundance (individuals/m^2), standing biomass (g/ind),
 size-corrected biomass (g^alpha/ind), trophic group (herbivore, omnivore,
 planktivore, invertivore, piscivore), time-averaged temperature kinetics,
 community-level species richness (# of species) and sampling area (m^2).
 This dataset was collected by visual counts of 5609 populations of reef
 fishes spread across 49 sites around tropical and subtropical seas (see
 publication for full methods description).dryad_data.csv
DOI: 10.5061/dryad.m329j
title: Data from: Infectious adaptation: potential host range of a defensive endosymbiont in Drosophila

description: Maternally transmitted symbionts persist over macroevolutionary time
 scales by undergoing occasional lateral transfer to new host species. To
 invade a new species, a symbiont must survive and reproduce in the new
 host, undergo maternal transmission, and confer a selective benefit
 sufficient to overcome losses due to imperfect maternal transmission.
 Drosophila neotestacea is naturally infected with a strain of Spiroplasma
 that restores fertility to nematode-parasitized females, which are
 otherwise sterilized by parasitism. We experimentally transferred
 Spiroplasma from D. neotestacea to four other species of mycophagous
 Drosophila that vary in their ability to resist and/or tolerate nematode
 parasitism. In all four species, Spiroplasma achieved within-host
 densities and experienced rates of maternal transmission similar to that
 in D. neotestacea. Spiroplasma restored fertility to nematode-parasitized
 females in one of these novel host species. Based on estimates of maternal
 transmission fidelity and the expected benefit of Spiroplasma infection in
 the wild, we conclude that Spiroplasma has the potential to spread and
 become abundant within D. putrida, which is broadly sympatric with D.
 neotestacea and in which females are rendered completely sterile by
 nematode parasitism. Thus, a major adaptation within D. putrida could
 arise via lateral transmission of a heritable symbiont from D.
 neotestacea.
description: All
 dataThis is an Excel
 workbook containing spreadsheets on restoration of fertility (female egg
 count), Spiroplasma density (qPCR-Spiroplasma), Howardula motherworm size
 (Motherworm size), and maternal transmission (Maternal transmission).
 These data were collected in either the Perlman (University of Victoria)
 or Jaenike (University of Rochester), as indicated in the
 file.
DOI: 10.5061/dryad.q2764
title: Data from: Receiver discriminability drives the evolution of complex sexual signals by sexual selection

description: A hallmark of sexual selection by mate choice is the evolution of
 exaggerated traits, such as longer tails in birds and more acoustic
 components in the calls of birds and frogs. Trait elaboration can be
 opposed by costs such as increased metabolism and greater predation risk,
 but cognitive processes of the receiver can also put a brake on trait
 elaboration. For example, according to Weber's Law traits of a fixed
 absolute difference will be more difficult to discriminate as the absolute
 magnitude increases. Here we show that in the Emei music frog (Babina
 daunchina) increases in the fundamental frequency between successive notes
 in the male advertisement call, which increases the spectral complexity of
 the call, facilitates the female's ability to compare the number of
 notes between calls. These results suggest that female's
 discriminability provides the impetus to switch from enhancement of
 signaling magnitude (i.e. adding more notes into calls) to employing a new
 signal feature (i.e. increasing frequency among notes) to increase
 complexity. We suggest that increasing the spectral complexity of notes
 ameliorates some of the effects of Weber's Law, and highlights how
 perceptual and cognitive biases of choosers can have important influences
 on the evolution of courtship signals.
description: Flat
 stimulusFlat calls (F) in which
 the frequency among notes did not vary. This data if for
 Fig.1Natural
 stimulusNatural calls (N) in
 which the fundamental frequency (F0) increases in the species-typical
 manner (i.e. naturally) from note to note: 441 Hz, 551 Hz, 589 Hz, 606 Hz,
 618 Hz, 628 Hz, 628 Hz and 628 Hz, respectively.This data if for
 Fig.1Extra increase
 stimulusExaggerated frequency
 increase calls (E) in which the increase in frequency among notes was
 exaggerated artificially using Avisoft SAS-Lab Pro.This data if for
 Fig.1Phonotaxis data of the
 three group with different frequency increasePhonotaxis data of the
 three group with different frequency increase(before combine the data of
 ratio 0.6 and 0.625)Phonotaxis data of the
 three group with different frequency increase (after combine the ratios of
 0.6 and 0.625)Phonotaxis data of the
 three group with different frequency increase (after combine the ratios of
 0.6 and 0.625),this data is for Fig.2Phonotaxis data of the
 relative attractivenessPhonotaxis data of the
 relative attractiveness,this data is for Fig.3Phonotaxis data of the
 relative attractiveness(combined data)Phonotaxis data of the
 relative attractiveness,combined data of 4,5,6 note numbers to E-F,N-F,or
 E-N
DOI: 10.5061/dryad.605j6
title: Data from: Development and calibration of a novel sensor to quantify the water content of surface soils and biological soil crusts

description: The surface layer of soil as transition zone between pedosphere and
 atmosphere plays a crucial role in exchange processes of nutrients,
 atmospheric gases and water. Knowledge of its water content is essential,
 as it governs both physiological and transport mechanisms. In arid and
 semi-arid regions, this uppermost soil layer is commonly colonized by
 biological soil crusts (biocrusts), which play major roles in the global
 terrestrial carbon and nitrogen cycles. The water status of biocrusts is
 essential as it controls the activity, productivity and surface exchange
 of these poikilohydric communities. On-site analyses of the water content
 of both bare and crusted soils are thus urgently needed to correctly model
 the exchange processes of water, nutrients and trace gases at the soil
 surface. In this study, we present the biocrust wetness probe (BWP), which
 is the first to reliably measure the water content within biocrusts or the
 uppermost 5 mm of a substrate. Using a weak alternating current, the
 electrical conductivity is assessed over time. With an automatic
 calibration routine, conductivity values are temperature- corrected and
 converted into water contents and precipitation equivalents. During 1 year
 of continuous field measurements at 5-min intervals, 60 BWPs worked
 reliably without any failure. The probes responded immediately and
 individually upon rain events, showing substrate-specific water response
 curves, which are well represented by linear and exponential calibration
 curves. The BWP facilitates the spatio-temporal assessment and
 interpolation of surface soil wetness and thus bio- crust activity, which
 governs nutrient fluxes, trace gas release and biogeochemical cycles. Its
 implementation in distributed sensor networks is under development.
description: Data for
 repository_finalThe Excelfile provided
 comprises two data sheets. On the first sheet the calibration data for
 measurement 2-4 for the 60 sensors are given. On the second sheet, the
 minimum conductivity value measured in the field without any water present
 is given. The values are already temperature-corrected.