cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fv584
title: Data from: Feeder density enhances house finch disease transmission in experimental epidemics

description: [No abstract entered]
description: Aviary_Sampling_Data_FinalAll on-site sampling data (date, mass, eye score, etc.)flockmate_contacts_repeatedAggressive interactions by non-index birdflockmates.feeding.repeated.041717Feeding behaviors of non-index birdsfollowing_latencies_finalIndex following latenciesIndex_Contacts_RepeatedAggressive interactions (index birds)Index_Feeder_PreferenceTime index birds spent on individual feeders within the compartmentsIndex_Feeding_Repeated_041917Feeding behaviors of index birdsPathogen_LoadsqPCR data
DOI: 10.5061/dryad.1694
title: Data from: Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations

description: A possible consequence of planting GMOs in centers of crop origin is
 unintended gene flow into traditional landraces. In 2001, a study reported
 the presence of the transgenic 35S promoter in maize landraces sampled in
 2000 from the Sierra Juarez of Oaxaca, Mexico. Analysis of a large sample
 taken from the same region in 2003 and 2004 could not confirm the
 existence of transgenes, thereby casting doubt on the earlier results.
 These two studies were based on different sampling and analytical
 procedures and are thus hard to compare. Here we present new molecular
 data for this region that confirm the presence of transgenes in three of
 23 localities sampled in 2001. Transgene sequences were not detected in
 samples taken in 2002 from nine localities, while directed samples taken
 in 2004 from two of the positive 2001 localities were again found to
 contain transgenic sequences. These findings suggest the persistence or
 re-introduction of transgenes up until 2004 in this area. We address
 variability in recombinant sequence detection by analyzing the consistency
 of current molecular assays. We also present theoretical results on the
 limitations of estimating the probability of transgene detection in
 samples taken from landraces. The inclusion of a limited number of female
 gametes, but more importantly, aggregated transgene distributions may
 significantly lower detection probabilities. Our analytical and sampling
 considerations help explain discrepancies among different detection
 efforts, including the one presented here, and provide considerations for
 the establishment of monitoring protocols to detect the presence of
 transgenes among structured populations of landraces.
description: SuppFigure3replyGID.pdfSupplementary figure 3 to the reply to GID: BASTA resistance tests on maize plants from the 2001 collection.Suppfigure2replyGID.pdfSupplementary figure 2 of the reply to Genetic ID: ELISA tests for presence of recombinant proteins performed in maize samples collected in 2001.Suppfigure1replyGID.pdfSupplementary figure 1 of the reply to Genetic ID: variations in PCR amplification
DOI: 10.5061/dryad.7145v
title: Data from: Ice-VII inclusions in diamonds: evidence for aqueous fluid in Earth’s deep mantle

description: Water-rich regions in Earth’s deeper mantle are suspected to play a key
 role in the global water budget and the mobility of heat-generating
 elements. We show that ice-VII occurs as inclusions in natural diamond and
 serves as an indicator for such water-rich regions. Ice-VII, the residue
 of aqueous fluid present during growth of diamond, crystallizes upon
 ascent of the host diamonds but remains at pressures as high as 24
 gigapascals; it is now recognized as a mineral by the International
 Mineralogical Association. In particular, ice-VII in diamonds points
 toward fluid-rich locations in the upper transition zone and around the
 660-kilometer boundary.
description: M57666Figure 1 Diffraction
 dataSM458_001Figure S1b X-ray fluorescence mapFigS1b.jpgFigS3adiffraction dataBalas_16.txtFigS3bGRr1521_76.txtFigS3cdiffraction dataGRr1521_106.txtFigS3ddiffraction dataGRr1521_26.txtFigS3ediffraction dataGRr1521_35.txtFigS3fdiffraction dataGRR1507_372.txtFigS3gSM458_15.txtFigS3hGRr1518_33.txtFigS2Grr1507_372full.txtFigS4bdiffraction dataSM458_08.txt
DOI: 10.5061/dryad.r4454
title: Data from: The predictability of a lake phytoplankton community, over time-scales of hours to years

description: Forecasting changes to ecological communities is one of the central
 challenges in ecology. However, nonlinear dependencies, biotic
 interactions and data limitations have limited our ability to assess how
 predictable communities are. We used a machine learning approach and
 environmental monitoring data (biological, physical and chemical) to
 assess the predictability of phytoplankton cell density in one lake across
 an unprecedented range of time scales. Communities were highly predictable
 over hours to months: model R2 decreased from 0.89 at 4 hours to 0.75 at 1
 month, and in a long-term dataset lacking fine spatial resolution, from
 0.46 at 1 month to 0.32 at 10 years. When cyanobacterial and eukaryotic
 algal cell density were examined separately, model-inferred environmental
 growth dependencies matched laboratory studies, and suggested novel
 trade-offs governing their competition. High-frequency monitoring and
 machine learning can help elucidate the mechanisms underlying ecological
 dynamics and set prediction targets for process-based models.
description: Phytoplankton cell
 densities by scanning flow cytometry and environmental variation across
 depths from Lake Greifensee, Switzerland, in 2014 and
 2015This is a high-frequency
 dataset consisting of estimates of phytoplankton cell density every 4
 hours during the summer and autumn of 2014 and 2015, measured using
 scanning flow cytometry. It also includes associated environmental
 variables, some of which were measured at longer time scales, such as once
 to twice a week (as in the case of zooplankton and dissolved
 nutrients).Dataset_ELE_Greifensee_2014plus2015_TS_cytobuoy_env_logabund.csvPhytoplankton cell densities by microscopy and environmental variation from Lake Greifensee, Switzerland, from 1984 to 2016This is a dataset consisting of estimates of phytoplankton cell density every month from March 1984 to June 2016, measured using microscopy. It also includes associated environmental variables, most of which were measured at the same location and approximately the same time (as in the case of zooplankton densities and dissolved nutrients). Irradiance measurements have been estimated separately, based on published estimates from a nearby site (see paper for details). For the purpose of analysis, dates have been rounded to the beginning of the nearest month, and where duplicates emerge from this rounding, values have been averaged between the two.Dataset_ELE_Greifensee_long_term_TS_microscopy_env.csv
DOI: 10.5061/dryad.bq27d
title: Data from: Genome-wide evidence of environmentally mediated secondary contact of European green crab (Carcinus maenas) lineages in eastern North America

description: Genetic-environment associations are increasingly revealed through
 population genomic data and can occur through a number of processes,
 including secondary contact, divergent natural selection, or
 isolation-by-distance. Here we investigate the influence of the
 environment, including seasonal temperature and salinity, on the
 population structure of the invasive European green crab (Carcinus maenas)
 in eastern North America. Green crab populations in eastern North America
 are associated with two independent invasions, previously shown to consist
 of distinct northern and southern ecotypes, with a contact zone in
 southern Nova Scotia, Canada. Using a RAD-seq panel of 9137 genome-wide
 SNPs, we detected 41 SNPs (0.49%) whose allele frequencies were highly
 correlated with environmental data. A principal components analysis of 25
 environmental variables differentiated populations into northern,
 southern, and admixed sites in concordance with the observed genomic
 spatial structure. Furthermore, a spatial principal components analysis
 conducted on genomic and geographic data revealed a high degree of global
 structure (p&lt;0.0001) partitioning a northern and southern ecotype.
 Redundancy and partial redundancy analyses revealed that among the
 environmental variables tested, winter sea surface temperature had the
 strongest association with spatial structuring, suggesting that it is an
 important factor defining range and expansion limits of each ecotype.
 Understanding environmental thresholds associated with intraspecific
 diversity will facilitate the ability to manage current and predict future
 distributions of this aquatic invasive species.
description: Crab_Genepop_EnvironmentalOutliersA genepop file of green crab genotypes containing only SNPs identified as being correlated with environmental variables.Crab_Genepop_EnvOutliers.txtNeutral GenotypesGenepop file of neutral SNP genotypesNeutral_GP.txtGreenCrabEnvironmentalDataEnvironmental (temperature and salinity) data, and Cartesian coordinates for each sample site in our study.GreenCrabEnvData.csvCrabCoordinatesCoordinates for the sample locations, plus transformed Cartesian coordinates.
DOI: 10.5061/dryad.cs133
title: Data from: Haplotype-based genome-wide association study identifies loci and candidate genes for milk yield in Holsteins

description: Since milk yield is a highly important economic trait in dairy cattle, the
 genome-wide association study (GWAS) is vital to explain the genetic
 architecture underlying milk yield and to perform marker-assisted
 selection (MAS). In this study, we adopted a haplotype-based empirical
 Bayesian GWAS to identify the loci and candidate genes for milk yield. A
 total of 1 092 Holstein cows were sequenced by using the genotyping by
 genome reducing and sequencing (GGRS) method. After filtering, 164 312
 high-confidence SNPs and 13 476 haplotype blocks were identified to use
 for GWAS. The results indicated that 17 blocks were significantly
 associated with milk yield. We further identified the nearest gene of each
 haplotype block and annotated the genes with milk-associated quantitative
 trait locus (QTL) intervals and ingenuity pathway analysis (IPA) networks.
 Our analysis showed that four genes, DLGAP1, AP2B1, ITPR2 and THBS4, have
 relationships with milk yield, while another three, ARHGEF4, TDRD1 and
 KIF19, were inferred to have potential relationships. Additionally, a
 network derived from the IPA containing one inferred (ARHGEF4) and all
 four confirmed genes likely regulates milk yield. Our findings add to the
 understanding of identifying the causal genes underlying milk production
 traits and could guide follow up studies for further confirmation of the
 associated genes, pathways and biological networks.
description: genotype and phenotype
 of 1092 cowsgenotype_phenotype_of_1092cows.rar
DOI: 10.5061/dryad.v08p7
title: Data from: Competing for blood: the ecology of parasite resource competition in human malaria-helminth co-infections

description: Ecological theory suggests that co-infecting parasite species can interact
 within hosts directly, via host immunity and/or via resource competition.
 In mice, competition for red blood cells (RBCs) between malaria and
 bloodsucking helminths can regulate malaria population dynamics, but the
 importance of RBC competition in human hosts was unknown. We analyzed
 infection density (i.e. the concentration of parasites in infected hosts),
 from a 2-year deworming study of over 4,000 human subjects. After
 accounting for resource-use differences among parasites, we find evidence
 of resource competition, priority effects, and a competitive hierarchy
 within co-infected individuals. For example, reducing competition via
 deworming increased Plasmodium vivax densities 2.8-fold, and this effect
 is limited to bloodsucking hookworms. Our ecological, resource-based
 perspective sheds new light into decades of conflicting outcomes of
 malaria-helminth co-infection studies with significant health and
 transmission consequences. Beyond blood, investigating within-human
 resource competition may bring new insights for improving human health.
description: Competing for blood -
 dataData (first tab) and
 explanation of variable names (second tab).
DOI: 10.5061/dryad.3b04j
title: Data from: Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers

description: Although resolving phylogenetic relationships and establishing species
 limits is a primary goal of systematics, these tasks remain challenging at
 both conceptual and analytical levels. Here, we integrated genomic and
 phenotypic data and employed a comprehensive suite of coalescent-based
 analyses to develop and evaluate competing phylogenetic and species
 delimitation hypotheses in a recent evolutionary radiation of grasshoppers
 (Chorthippus binotatus group) composed of two species and eight putative
 subspecies. To resolve the evolutionary relationships within this complex,
 we first evaluated alternative phylogenetic hypotheses arising from
 multiple schemes of genomic data processing and contrasted genetic-based
 inferences with different sources of phenotypic information. Second, we
 examined the importance of number of loci, demographic priors, number and
 kind of phenotypic characters, and sex-based trait variation for
 developing alternative species delimitation hypotheses. The best-supported
 topology was largely compatible with phenotypic data and showed the
 presence of two clades corresponding to the nominative species groups, one
 including three well-resolved lineages and the other comprising a
 four-lineage polytomy and a well-differentiated sister taxon. Integrative
 species delimitation analyses indicated that the number of employed loci
 had little impact on the obtained inferences but revealed the higher power
 provided by an increasing number of phenotypic characters and the
 usefulness of assessing their phylogenetic information-content and
 differences between sexes in among-taxa trait variation. Overall, our
 study highlights the importance of integrating multiple sources of
 information to test competing phylogenetic hypotheses and elucidate the
 evolutionary history of species complexes representing early-stages of
 divergence where conflicting inferences are more prone to appear.
description: Landmarks coordinates of
 pronota and forewingThis ZIP file includes
 the raw coordinates of the landmarks employed to characterize the shape
 variation of the forewing and pronota. Trait shape was characterized
 separately for each sex. The landmarks are stored in TPS
 format.01_Landmarks_raw
 coordinates_Pronota and
 forewings.zipSVDquartets and SNAPP
 input filesThis ZIP file includes
 the different inputs files for SVDquartets and SNAPP to species tree
 estimation. For SVDquartets analyses, six SNP matrices were employed which
 were obtained by setting in PyRAD different values of clustering
 thresholds (Wclust = 0.85 and 0.90) and minimum taxon coverage in a given
 locus (minCov = 4, 10 and 20). SNAPP analyses were performed employing a
 SNP matrix generated using Wclust = 0.90 and minCov =
 10.02_SVDquartets-SNAPP input
 files.zipBPP and iBPP input
 filesThis ZIP file includes
 the genetic and morphological matrices that were used to perform the BPP
 and iBPP analyses.03_BPP-iBPP input
 files.zip
DOI: 10.5061/dryad.kt741
title: Data from: Spatial prioritisation of EU’s LIFE-Nature program to strengthen the conservation impact of Natura 2000

description: 1. Despite advances in conservation efforts within Europe during recent
 decades, assessments highlight a need for adequate financing mechanisms to
 support the Natura 2000 network; the centrepiece of the EU´s Biodiversity
 Strategy. Besides the need for greater investment (currently only covering
 a fifth of the estimated cost of the network), better planning for this
 investment could help better achieve conservation goals. 2. We demonstrate
 a method that could be used to identify priority Natura 2000 sites, and
 species therein, that could guide investment in the future. We first used
 the lists of key species associated with each Natura 2000 site to map the
 distribution of all priority species covered by the Birds and Habitats
 Directives. We then used Marxan software to prioritise allocation of
 conservation funds among all Natura 2000 sites, while trying to mimic the
 observed conservation effort implemented under the LIFE Program, the main
 financial tool of the EU´s Biodiversity Strategy, in the period 1992-2013.
 3. Some Natura 2000 sites show exceptional value, holding species that
 either do not, or only very rarely, occur elsewhere in the network. These
 priority sites were concentrated mainly on islands and in the south
 western, eastern and northern extremes of Europe´s mainland thus
 reflecting patterns in species richness and endemism. 4. We found a poor
 relationship between the priorities identified here and the way funds had
 been distributed in previous LIFE-Nature Programs. 5. Policy implications.
 We propose that prioritisation exercises like the one shown here could be
 used to inform a top-down EU regulation mechanism by providing lists of
 site and species priorities that better reflect European conservation
 needs. These recommendations, performed at continental scale, could then
 help guide LIFE project proposals from the Member States and fill the
 current gap in the coverage of priority species. This top-down control
 mechanism could be integrated in the current system of budget
 distribution, rather than replacing it completely, to enhance the
 efficiency of conservation investment in the EU and achievement of
 continental goals.18-Jan-2018
description: Hermoso et
 alDistribution of key
 species in Natura 2000, used in this study
DOI: 10.5061/dryad.nm35n
title: Data from: Gender equity at scientific events

description: Although the proportion of women in science, and in evolutionary biology
 in particular, has substantially increased over the last century, women
 remain underrepresented in academia, especially at senior levels.
 Moreover, their scientific achievements do not always receive the same
 level of recognition as do men’s, which can be reflected in a lower
 relative representation of women among invited speakers at conferences or
 specialized courses. Using announcements sent to the EvolDir mailing list
 between April 2016 and July 2017, and the symposium programs of three
 large evolutionary biology congresses held in summer 2017, we quantified
 the representation of women announced as invited speakers in conferences,
 congress symposia and specialized courses. We compared the proportion of
 invited women to a baseline estimated using membership data of the
 associated scientific societies, and surveyed organizers to investigate
 their influence and that of potential gender-ratio guidelines on the
 proportion of invited women. We find that the average proportion of
 invited women is comparable (conferences), significantly lower
 (specialized courses) or significantly higher (congress symposia) than the
 current baseline (32% women). It is positively correlated to the
 proportion of women among the organizers, and it is on average higher for
 events whose organizers considered gender when choosing speakers than for
 those whose organizers did not. To investigate the impact of Equal
 Opportunity guidelines, we then collected longitudinal data on the
 proportion of invited women at two series of conferences, covering the
 2001-2017 period. The proportion of invited women is higher when Equal
 Opportunity guidelines are announced. Encouraging women to sit on
 organizing committees of scientific events, and the establishment of
 visible Equal Opportunity guidelines, thus could be ways to ensure higher
 number of invited female speakers in the future. Our results suggest that
 change, if desired, requires deliberate actions.
description: Debarre-Rode-Ugelvig_2018_20180104Data and analysis scripts; please see README file for more details.
DOI: 10.5061/dryad.88s50
title: Data from: Acid secretion by the boring organ of the burrowing giant clam, Tridacna crocea

description: The giant clam Tridacna crocea, native to Indo-Pacific coral reefs, is
 noted for its unique ability to bore fully into coral rock and is a major
 agent of reef bioerosion. However, T. crocea’s mechanism of boring has
 remained a mystery despite decades of research. By exploiting a new,
 two-dimensional pH-sensing technology and manipulating clams to press
 their presumptive boring tissue (the pedal mantle) against pH-sensing
 foils, we show that this tissue lowers the pH of surfaces it contacts by
 more than 2 pH units below seawater pH day and night. Acid secretion is
 likely mediated by vacuolar-type H+-ATPase, which we demonstrate (by
 immunofluorescence) is abundant in the pedal mantle outer epithelium. Our
 discovery of acid secretion solves this decades-old mystery and reveals
 that, during bioerosion, T. crocea can liberate reef constituents directly
 to the soluble phase, rather than producing sediment alone as earlier
 assumed.
description: ME_ST_XX_00001Individual ID: Clam 1 (Day) ; Time: 10 March 2017 14:40ME_ST_XX_00006Individual ID: Clam 5 (Day) ; Time: 10 March 2017 14:40ME_ST_XX_00011Individual ID: Clam 3 (Day) ; Time: 10 March 2017 14:40ME_ST_XX_00013Individual ID: Clam 6 (Day) ; Time: 10 March 2017 14:40ME_ST_XX_00018Individual ID: Clam 7 (Day) ; Time: 10 March 2017 14:40ME_ST_XX_00021Individual ID: Clam 8 (Day) ; Time: 10 March 2017 14:40ME_ST_XX_00026Individual ID: Clam 1 (Night) ; Time: 10 March 2017 20:45ME_ST_XX_00034Individual ID: Clam 5 (Night) ; Time: 10 March 2017 20:45ME_ST_XX_00040Individual ID: Clam 3 (Night) ; Time: 10 March 2017 20:45ME_ST_XX_00042Individual ID: Clam 6 (Night) ; Time: 10 March 2017 20:45ME_ST_XX_00044Individual ID: Clam 7 (Night) ; Time: 10 March 2017 20:45ME_ST_XX_00049Individual ID: Clam 8 (Night) ; Time: 10 March 2017 20:45ME_ST_XX_00031Individual ID: Clam 4 (Day) ; Time: 10 March 2017 14:40ME_ST_XX_00076Individual ID: Clam 4 (Night) ; Time: 10 March 2017 20:45ME_ST_XX_00059Individual ID: Clam 2 (Day) ; Time: 11 March 2017 14:06ME_ST_XX_00061Individual ID: Clam 9 (Day) ; Time: 11 March 2017 14:06ME_ST_XX_00083Individual ID: Clam 9 (Night) ; Time: 11 March 2017 22:24ME_ST_XX_00088Individual ID: Clam 2 (Day) ; Time: 11 March 2017 14:06
DOI: 10.5061/dryad.pv12j
title: Data from: Sulfur resistance of Ce-Mn/TiO2 catalysts for low-temperature NH3–SCR

description: Ce-Mn/TiO2 catalyst prepared using a simple impregnation method
 demonstrated a better low-temperature selective catalytic reduction of NO
 with NH3 (NH3-SCR) activity in comparison with the sol-gel method. The
 Ce-Mn/TiO2 catalyst loading with 20% Ce had the best low-temperature
 activity and achieved a NO conversion rate higher than 90% at 140-260°C
 with a 99.7% NO conversion rate at 180 °C. The Ce-Mn/TiO2 catalyst only
 had a 6% NO conversion rate decrease after 100 ppm of SO2 was added to the
 stream. When the SO2 was removed from the stream, the catalyst was able to
 recover completely. The crystal structure, morphology, textural
 properties, and valence state of the metals involving the novel catalysts
 were investigated using X-ray diffraction (XRD), N2 adsorption and
 desorption analysis, X-ray photoelectron spectroscopy (XPS), scanning
 electron microscopy (SEM), and energy dispersive spectroscopy (EDS),
 respectively. The decrease of NH3-SCR performance in the presence of 100
 ppm SO2 was due to the decrease of the surface area, change of the pore
 structure, the decrease of Ce4+ and Mn4+ concentration, and the formation
 of the sulfur phase chemicals which blocked the active sites and changed
 the valence status of the elements.
description: Raw data of catalyst
 characterization and laboratory tests data_Quan Xu & Wenjing Yang et
 al.Raw data of the all
 characterization and laboratory tests. It contains origin files, figures
 and excel of data. X-ray diffraction (XRD), N2 adsorption and desorption
 analysis, X-ray photoelectron spectroscopy (XPS), scanning electron
 microscopy (SEM), and energy dispersive spectroscopy
 (EDS).raw
 dota.rar