cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4s7t3
title: Data from: The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins

description: Understanding the boundaries of breeding populations is of great
 importance for conservation efforts and estimates of extinction risk for
 threatened species. However, determining these boundaries can be difficult
 when population structure is subtle. Emperor penguins are highly reliant
 on sea ice, and some populations may be in jeopardy as climate change
 alters sea-ice extent and quality. An understanding of emperor penguin
 population structure is therefore urgently needed. Two previous studies
 have differed in their conclusions, particularly whether the Ross Sea, a
 major stronghold for the species, is isolated or not. We assessed emperor
 penguin population structure using 4,596 genome-wide single nucleotide
 polymorphisms (SNPs), characterized in 110 individuals (10–16 per colony)
 from eight colonies around Antarctica. In contrast to a previous
 conclusion that emperor penguins are panmictic around the entire
 continent, we find that emperor penguins comprise at least four
 metapopulations, and that the Ross Sea is clearly a distinct
 metapopulation. Using larger sample sizes and a thorough assessment of the
 limitations of different analytical methods, we have shown that population
 structure within emperor penguins does exist and argue that its
 recognition is vital for the effective conservation of the species. We
 discuss the many difficulties that molecular ecologists and managers face
 in the detection and interpretation of subtle population structure using
 large SNP data sets, and argue that subtle structure should be taken into
 account when determining management strategies for threatened species,
 until accurate estimates of demographic connectivity among populations can
 be made.
description: Emperor penguin neutral
 SNP datasetEP_final.vcf
DOI: 10.5061/dryad.5706p
title: Data from: Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

description: Molecular sequence data provide information about relative times only, and
 fossil-based age constraints are the ultimate source of information about
 absolute times in molecular clock dating analyses. Thus, fossil
 calibrations are critical to molecular clock dating, but competing methods
 are difficult to evaluate empirically because the true evolutionary time
 scale is never known. Here, we combine mechanistic models of fossil
 preservation and sequence evolution in simulations to evaluate different
 approaches to constructing fossil calibrations and their impact on
 Bayesian molecular clock dating, and the relative impact of fossil versus
 molecular sampling. We show that divergence time estimation is impacted by
 the model of fossil preservation, sampling intensity and tree shape. The
 addition of sequence data may improve molecular clock estimates, but
 accuracy and precision is dominated by the quality of the fossil
 calibrations. Posterior means and medians are poor representatives of true
 divergence times; posterior intervals provide a much more accurate
 estimate of divergence times, though they may be wide and often do not
 have high coverage probability. Our results highlight the importance of
 increased fossil sampling and improved statistical approaches to
 generating calibrations, which should incorporate the non-uniform nature
 of ecological and temporal fossil species distributions.
description: simulation-study-codeCode used to perform the simulationssimulation-study.zip
DOI: 10.5061/dryad.7v378
title: Data from: Carbon debt of Conservation Reserve Program (CRP) grasslands converted to bioenergy production

description: Over 13 million ha of former cropland are enrolled in the US Conservation
 Reserve Program (CRP), providing well-recognized biodiversity, water
 quality, and carbon (C) sequestration benefits that could be lost on
 conversion back to agricultural production. Here we provide measurements
 of the greenhouse gas consequences of converting CRP land to continuous
 corn, corn–soybean, or perennial grass for biofuel production. No-till
 soybeans preceded the annual crops and created an initial carbon debt of
 10.6 Mg CO2 equivalents (CO2e)·ha−1 that included agronomic inputs,
 changes in C stocks, altered N2O and CH4 fluxes, and foregone C
 sequestration less a fossil fuel offset credit. Total debt, which includes
 future debt created by additional changes in soil C stocks and the loss of
 substantial future soil C sequestration, can be constrained to 68 Mg
 CO2e·ha−1 if subsequent crops are under permanent no-till management. If
 tilled, however, total debt triples to 222 Mg CO2e·ha−1 on account of
 further soil C loss. Projected C debt repayment periods under no-till
 management range from 29 to 40 y for corn–soybean and continuous corn,
 respectively. Under conventional tillage repayment periods are three times
 longer, from 89 to 123 y, respectively. Alternatively, the direct use of
 existing CRP grasslands for cellulosic feedstock production would avoid C
 debt entirely and provide modest climate change mitigation immediately.
 Incentives for permanent no till and especially permission to harvest CRP
 biomass for cellulosic biofuel would help to blunt the climate impact of
 future CRP conversion.
description: Data from Carbon debt of
 Conservation Reserve Program (CRP) grasslands converted to bioenergy
 production. Gelfand et al., (2011)Data collected from four
 fields during year 2009, using eddy-covariance, static chambers methods,
 and measurements of management field activity. The data was used for
 calculations presented in the Gelfand et al., (2011).Gelfand_PNAS_2011.xlsx
DOI: 10.5061/dryad.58m3g
title: Data from: Temperature and consumer type dependencies of energy flows in natural communities

description: With the world continuously warming, a mechanistic understanding of how
 temperature affects interaction strengths, which are fundamental to
 food-web stability, is needed. As interaction strengths are determined by
 the flows of energy from resources to consumers, we investigated effects
 of temperature on animal energetics. We used newly compiled datasets on
 respiration rates and assimilation efficiencies to assess how temperature
 affects the energy use (respiration rates) and the efficiency of energy
 gain (assimilation efficiency) for different consumer types. Furthermore,
 we incorporated our findings in a simulation of temperature effects on
 maintenance feeding rates (i.e. energy consumption necessary to sustain
 life). Our analysis revealed a generally positive temperature dependence
 of assimilation efficiencies across consumer types thus implying a net
 energy gain with warming. The temperature scaling of respiration rates did
 not differ between consumer types. Based on these parameters we calculated
 maintenance feeding rates and compared them to empirically measured
 (realized) feeding rates. This comparison revealed that detritivores and
 herbivores have the potential to increase their biomasses under warming as
 their maintenance feeding rates increase less strongly than their realized
 feeding rates. For carnivores, however, we found a stronger increase of
 their maintenance feeding rates compared to their realized feeding rates,
 which should lead to decreased population sizes under warming. Overall,
 our results increase the understanding of climate change effects on
 ecosystems as they suggest profound energetic consequences for natural
 communities.
description: Dataset for respiration
 rates and assimilation efficienciesDataset for assimilation
 efficiencies and respiration rates for different ectotherm consumer types
 (carnivores, herbivores, detritivores). The dataset contains species
 names, taxonomic classification, resource for assimilation efficiency
 measurements, body mass and experimental temperature.Lang_et_al_2017_data.csvR-code for statistics and the simulation of maintenance feeding ratesR-code for a) the analysis of temperature and body mass dependencies of respiration rates and assimilation efficiencies across consumer types (carnivores, herbivores and detritivores) and b) the simulation of temperature effects on maintenance feeding rates based on the results of the dataset analyses (a). We also provide the R-code for c) statistics using an alternative random structure and d) statistics using only originally reported fresh weights.Lang_et_al_2017_Statistics_and_Simulations.rSupplementary InformationSupplement to "Temperature and consumer type dependencies of energy flows in natural communities", containing tables S1-S13.Lang_et_al_2017_SI.pdf
DOI: 10.5061/dryad.tv5mb
title: Data from: No evidence for extrinsic post-zygotic isolation in a wild Saccharomyces yeast system

description: Although microorganisms account for the largest fraction of Earth's
 biodiversity, we know little about how their reproductive barriers evolve.
 Sexual microorganisms such as Saccharomyces yeasts rapidly develop strong
 intrinsic post-zygotic isolation, but the role of extrinsic isolation in
 the early speciation process remains to be investigated. We measured the
 growth of F1 hybrids between two incipient species of Saccharomyces
 paradoxus to assess the presence of extrinsic post-zygotic isolation
 across 32 environments. More than 80% of hybrids showed either partial
 dominance of the best parent or over-dominance for growth, revealing no
 fitness defects in F1 hybrids. Extrinsic reproductive isolation therefore
 likely plays little role in limiting gene flow between incipient yeast
 species and is not a requirement for speciation.
description: Data and
 ScriptsRaw data and scripts
 required to reproduce results and analyses.Scripts_and_data_Charron_Landry_BiologyLetters.zip
DOI: 10.5061/dryad.bj5k0
title: Data from: Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community

description: Metabarcoding of vertebrate DNA derived from carrion flies has been
 proposed as a promising tool for biodiversity monitoring. To evaluate its
 efficacy, we conducted metabarcoding surveys of carrion flies on Barro
 Colorado Island (BCI), Panama, which has a well-known mammal community,
 and compared our results against diurnal transect counts and
 camera-trapping. We collected 1084 flies in 29 sampling days, conducted
 metabarcoding with mammal-specific (16S) and vertebrate-specific (12S)
 primers, and sequenced amplicons on Illumina MiSeq. For taxonomic
 assignment, we compared BLAST with the new program PROTAX, and we found
 that PROTAX improved species identifications. We detected 20 mammal, four
 bird, and one lizard species from carrion fly metabarcoding, all but one
 of which are known from BCI. Fly metabarcoding detected more mammal
 species than concurrent transect counts (29 sampling days, 13 species) and
 concurrent camera-trapping (84 sampling days, 17 species), and detected
 67% of the number of mammal species documented by eight years of transect
 counts and camera-trapping combined, although fly metabarcoding missed
 several abundant species. This study demonstrates that carrion fly
 metabarcoding is a powerful tool for mammal biodiversity surveys, and has
 the potential to detect a broader range of species than more commonly used
 methods.
description: protaxscriptsDirectory containing perl scripts used to run PROTAXmammal16S_OTUFasta file containing all mammal 16S OTU sequencesmammal12S_OTUFasta file containing all mammal 12S OTU sequencesmammal16S_refseqsFasta file containing mammal 16S reference sequences used in training PROTAXmammal12S_refseqsFasta file containing mammal 12S reference sequences used in training PROTAXMammalia_taxonomyFull Linnean taxonomy of mammal speciesprotax_trainBASH commands used to train unweighted PROTAX modelprotax_classifyBASH commands used to classify OTU sequences using unweighted PROTAX modelprotax_weighted_trainBASH commands used to train weighted PROTAX modelprotax_weighted_classifyBASH commands used to classify OTU sequences using weighted PROTAX modelBCI_sp_listList of species known to be present on BCIpanama_sp_listList of species known from Panama
DOI: 10.17632/872pjfmdjr
title: Replication Data for: Systematic risk profiling: Assessing compounding economic risks in developing countries

description: This repository contains the full replication package for the paper "Systematic risk profiling: Assessing compounding economic risks in developing countries."
It includes all necessary code and data to reproduce the analysis for Kenya, Rwanda, and Malawi. The package is organized into three parts following the Systematic Risk Profiling (SRP) approach:
- Sampling shock scenarios (R).
- CGE model simulations (GAMS).
- Ranking risks and generating final outputs (R).
See the included README.txt for step-by-step instructions on running the simulations and generating the tables/figures found in the manuscript.
DOI: 10.5061/dryad.bs935
title: Data from: Perfusion index in newborns during critical congenital heart disease screening at 24 hours in healthy newborns: retrospective observational study from the United States

description: Objective: To describe the distribution of Perfusion Index (PI) in
 asymptomatic newborns at 24 hours of life when screening for Critical
 Congenital Heart Disease (CCHD) using an automated data selection method.
 Design: This is a retrospective observational study. Setting: Newborn
 nursery in a California public hospital with 3500 to 4000 deliveries
 annually. Methods: We developed an automated program to select the PI
 values from CCHD screens. Included were term and late preterm infants who
 were screened for CCHD from November 2013 to January 2014 and from May
 2015 to July 2015. PI measurements were downloaded every 2 seconds from
 the pulse oximeter and median PI were calculated for each oxygen
 saturation screen in our cohort. Results: We included data from 2768
 oxygen saturation screens. Each screen had a median of 29 data points
 (interquartile range 17 to 49). The median PI in our study cohort was 1.8
 (95% confidence interval 1.8 to 1.9) with interquartile range 1.2 to 2.7.
 The median pre-ductal PI was significantly higher than the median
 post-ductal (1.9 vs. 1.8, p = 0.03) although this difference may not be
 clinically significant. Conclusion: Using an automated data selection
 method, the median PI in asymptomatic newborns at 24 hours of life is 1.8
 with a narrow interquartile range of 1.2 to 2.7. This automated data
 selection method may improve accuracy and precision compared to manual
 data collection method. Further studies are needed to establish external
 validity of this automated data selection method and its clinical
 application for CCHD screening.
description: Combined Raw Data -
 DataDryadThis is the raw data
 output downloaded from the Pulse Oximiter using Trendcom software (Masimo
 Corporation, Irvine, California).
DOI: 10.17632/872pjfmdjr.2
title: Replication Data for: Systematic risk profiling: Assessing compounding economic risks in developing countries

description: This repository contains the full replication package for the paper "Systematic risk profiling: Assessing compounding economic risks in developing countries."
It includes all necessary code and data to reproduce the analysis for Kenya, Rwanda, and Malawi. The package is organized into three parts following the Systematic Risk Profiling (SRP) approach:
- Sampling shock scenarios (R).
- CGE model simulations (GAMS).
- Ranking risks and generating final outputs (R).
See the included README.txt for step-by-step instructions on running the simulations and generating the tables/figures found in the manuscript.
DOI: 10.5061/dryad.8157n
title: Data from: Late Neolithic phytolith and charcoal records of human activities and vegetation change in Shijiahe culture, Tanjialing site, China

description: There is significant archaeological evidence marking the collapse of the
 Shijiahe culture in the middle reaches of the Yangtze River in China
 during the late Neolithic Period. However, the causes for this cultural
 collapse remain unclear. Our sedimentary records from a 3.3 m long profile
 and 76 phytolith and charcoal samples from the Tanjialing archaeological
 sites provide records of interactions between an ancient culture and
 vegetation change. During the early Shijiahe culture (c, 4850-4400 cal
 BP), the climate was warm and humid. Fire was intensively used to clear
 the vegetation. In the mid-period of the Shijiahe culture (c, 4400-4200
 cal BP), the climate became slightly dry-cold and this was accompanied by
 decreasing water, leading to settlements. From c, 4200 cal BP, severe
 drought eroded the economic foundation of rice-cultivation. These
 conditions forced people to abandon the Shijiahe ancient city to find
 water in other regions, leading to the collapse of the Shijiahe culture.
description: AMS 14C
 datingArchaeological
 strataconcentrationConcentration.cdrGeographical locationPercentagephytolithsPhytoliths.jpgRecord comparison
DOI: 10.5061/dryad.jj1tt
title: Data from: Tropical specialist versus climate generalist: diversification and demographic history of sister species of Carlia skinks from northwestern Australia

description: Species endemic to the tropical regions are expected to be vulnerable to
 future climate change due in part to their relatively narrow climatic
 niches. In addition, these species are more likely to have responded
 strongly to past climatic change, and this can be explored through
 phylogeographic analyses. To test the hypothesis that tropical specialists
 are more sensitive to climate change than climate generalists, we
 generated and analyze sequence data from mtDNA and ~2500 exons to compare
 scales of historical persistence and population fluctuation in two sister
 species of Australian rainbow skinks: the tropical specialist Carlia
 johnstonei and the climate generalist C. triacantha. We expect the
 tropical specialist species to have deeper and finer-scale phylogeographic
 structure and stronger demographic fluctuations relative to the closely
 related climate generalist species, which should have had more stable
 populations through periods of harsh climate in the late Quaternary.
 Within C. johnstonei, we find that populations from the northern Kimberley
 islands are highly divergent from mainland populations. In C. triacantha,
 one major clade occurs across the deserts and into the mesic Top End, and
 another occurs primarily in the Kimberley with scattered records
 eastwards. Where their ranges overlap in the Kimberley, both mitochondrial
 and nuclear DNA suggest stronger phylogeographic structure and range
 expansion within the tropical specialist, whereas the climate generalist
 has minimal structuring and no evidence of recent past range expansion.
 These results are consistent with the hypothesis that tropical specialists
 are more sensitive to past climatic change.
description: Scripts and datasets
 used in this studyThis is a compressed zip
 file of scripts to process the raw data and datasets used in analyses for
 this study.Dryad.zipND4 samples informationTable with information regarding all samples sequenced with mitochondrial gene ND4.ND4_samples_information.xlsx
DOI: 10.5061/dryad.bp096
title: Data from: Woodland ectomycorrhizal fungi benefit from large-scale reduction of nitrogen deposition in the Netherlands

description: 1.Woodland ectomycorrhizal (ECM) fungal species declined considerably in
 the Netherlands in the late 20th century, mainly due to raised levels of
 atmospheric nitrogen deposition. Environmental measures have been taken to
 reduce this deposition, but it remains unclear whether and to what extent
 ECM species have benefitted from this. 2.We hypothesised that ECM species,
 especially those species that are known to be nitrophobic, i.e. sensitive
 to nitrogen loading, have recovered to some extent from the reduction in
 nitrogen deposition after 1994. We further hypothesised that, due to
 legacy effects of deposition, recovery has been stronger in regions where
 deposition levels have previously been lower. 3.To test these hypotheses,
 we analysed long-term opportunistic data, i.e., observations collected
 without standardised field method. We applied data filtering and a
 modified List Length method to adjust for potential biases in these data.
 The removal of bias left us with two periods to examine ECM species
 trends: before (1965-1985) and after (1994-2013) deposition reduction
 started [in 1994]. 4.We compared trends in ECM species in 1965-1985 with
 those in 1994-2013. Multispecies indicators were used to summarise the
 findings of ECM species, and to compare these with results of litter
 saprotrophic species and wood saprotrophic and wood parasitic species.
 5.We found that (i) most trends switched in direction from negative to
 positive after the reduction of nitrogen deposition began, (ii) these
 trends were more pronounced for nitrophobic ECM species than for
 nitrotolerant ECM species; (iii) trends for ECM species differed from
 those of the other functional groups; and (iv) recovery was stronger in
 the region with a history of lower deposition. 6.Policy implications. Our
 results suggest that woodland ectomycorrhizal species benefit
 substantially from environmental measures to reduce nitrogen deposition.
 Our study is one of few scientific studies to date documenting evidence of
 success of large-scale (nation-wide) environmental measures. We have
 demonstrated that opportunistic citizen-science data can be used for the
 detection of species trends, but it is essential to examine and control
 for potential bias in the data.
description: ObservationsSpeciesSitesReadme
DOI: 10.5061/dryad.jc8kd
title: Data from: Significance and popularity in music production

description: Creative industries constantly strive for fame and popularity. Though
 highly desirable, popularity is not the only achievement artistic
 creations might ever acquire. Leaving a longstanding mark in the global
 production and influencing future works is an even more important
 achievement, usually acknowledged by experts and scholars. ‘Significant’
 or ‘influential’ works are not always well known to the public or have
 sometimes been long forgotten by the vast majority. In this paper, we
 focus on the duality between what is successful and what is significant in
 the musical context. To this end, we consider a user-generated set of tags
 collected through an online music platform, whose evolving co-occurrence
 network mirrors the growing conceptual space underlying music production.
 We define a set of general metrics aiming at characterizing music albums
 throughout history, and their relationships with the overall musical
 production. We show how these metrics allow to classify albums according
 to their current popularity or their belonging to expert-made lists of
 important albums. In this way, we provide the scientific community and the
 public at large with quantitative tools to tell apart popular albums from
 culturally or aesthetically relevant artworks. The generality of the
 methodology presented here lends itself to be used in all those fields
 where innovation and creativity are in play.
description: albums_time_dump.json.tarThis dataset contains data that allows for the complete reproducibility of the study. The data is a collection of json records, with the following information: name of the album, list of tags, Last.fm score of each tag, release date of the album.