cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1gv57s0
title: Data from: Indirect effects of a large mammalian herbivore on small mammal populations: context-dependent variation across habitat types, mammal species and seasons

description: Multiple consumer species frequently co-occur in the same landscape and,
 through effects on surrounding environments, can interact in direct and
 indirect ways. These interactions can vary in occurrence and importance,
 and focusing on this variation is critical for understanding the dynamics
 of interactions among consumers. Large mammalian herbivores are important
 engineers of ecosystems worldwide, have substantial impacts on vegetation
 and can indirectly affect small-mammal populations. However, the degree to
 which such indirect effects vary within the same system has received
 minimal attention. We used a 16-year-old exclosure experiment, stratified
 across a heterogeneous landscape, to evaluate the importance of
 context-dependent interactions between tule elk (Cervus canadensis
 nannodes) and small mammals [deer mice (Peromyscus maniculatus), meadow
 voles (Microtus californicus) and harvest mice (Reithrodontymys
 megalotis)] in a coastal grassland in California. Effects of elk on voles
 varied among habitats and seasons: in open grasslands, elk reduced vole
 numbers during fall 2013 but not summer 2014; in Lupinus-dominated
 grasslands, elk reduced vole numbers during summer 2014 but not fall 2013;
 and in Baccharis-dominated grasslands, elk had no effect on vole numbers
 in either season. Effects of elk on the two mice species also varied among
 habitats and seasons, but often in different ways from voles and each
 other. In fall 2013, elk decreased mice abundances in Lupinus-dominated
 grasslands, but not in Baccharis-dominated or open grasslands. In summer
 2014, elk decreased the abundance of harvest mice consistently across
 habitat types. In contrast, elk increased deer-mice numbers in open
 grasslands but not other habitats. Within the same heterogenous study
 system, the influence of elk on small mammals was strongly context
 dependent, varying among habitats, mammal species and seasons. We
 hypothesize that such variability is common in nature, and that failure to
 consider it may yield inaccurate findings and limit our understanding of
 interactions among co-occurring consumers.
description: Captures_By_Trap_PEMA_REMECapture data for deer mice and harvest mice.Ellis_Cushman_MICACapture data for meadow voles (Microtus californicus)seedremovalData for seed removal experiment
DOI: 10.5061/dryad.2vh4h
title: Data from: Mode and tempo of sequence and floral evolution within the Anserineae

description: The Chenopodiaceae Tribe Anserineae Dumort was proposed to include the
 genus Spinacia and the genus Blitum. In addition to the recent
 domestication of Spinacia, the tribe demonstrates extensive evolution
 within its floral development. We test whether the development of dioecy,
 monoecy, and protogyny is reflected differentially among floral
 developmental versus non-floral developmental genes, and whether recent
 domestication leaves traces in the phylogenetic relationship within the
 genus Spinacia. The phylogenetic predictions consistently support the
 sister relationship of Spinacia sp. to a Blitum clade consisting of Blitum
 bonus-henricus, Blitum virgatum, and Blitum nuttallianum. Relative rates
 tests indicate a generally faster rate of nucleotide substitutions within
 Spinacia. Tests of selection indicate that there is generally purifying
 selection acting on the sequences. In addition, insertion/deletion (indel)
 events occur more prominently within the Spinacia clade and occur in both
 coding and intron regions. The phylogenetic relationships within this
 tribe calls into question the hypothesis that dioecy in Spinacia evolved
 from a monoecious grade. The evidence for purifying selection in Spinacia
 suggests that the increased nucleotide substitution rates are not driving
 protein evolution, in contrast to evidence of protein sequence and
 structure evolution driven by indels. There is no footprint of
 domestication on sequence evolution, and we cannot detect phylogenetic
 signals that would support separation of the Spinacia accessions into
 three distinct taxa.
description: Anserineae_UFOAlignment of UFO gene from Anserineae with C. album as an outgroup.Anserineae_rbcSAlignment of rbcS sequences from Anserineae. C. album is outgroup.Anserineae_rbcLAlignment of rbcL sequences from Anserineae. B. vulgare and C. album are outgroups.Anserineae_PIAlignment of PI sequences from Anserineae. Sequences include introns. C. album is outgroup.Anserineae_PIcdnAlignment of PI sequences from Anserineae. Sequences derived from mRNA and do not include introns. C. album is the outgroup.Anserineae_ConcatenatedAlignment of seven concatenated genes (rbcS, rbcL, matK, UFO, AG, AP3, PI) from the Anserineae. C. album is the outgroup. Introns are included.Anserineae_matKAlignment of matK sequences from Anserineae. C. album is the outgroup.Anserineae_AP3Alignment of AP3 sequences from Anserineae. Sequences include introns. C. album is the outgroup.Anserineae_AP3cdnAlignment of AP3 sequences from Anserineae. Sequences derived from mRNA and do not include introns. C. album is the outgroup.Anserineae_AGcdnAlignment of AG sequences from Anserineae. Sequences derived from mRNA and do not include introns. C. album is the outgroup.Anserineae_AGAlignment of PI sequences from Anserineae. Sequences include introns. C. album is the outgroup.
DOI: 10.5061/dryad.8t475
title: Data from: Evaluating citizen vs. professional data for modelling distributions of a rare squirrel

description: To realize the potential of citizens to contribute to conservation efforts
 through the acquisition of data for broad-scale species distribution
 models, scientists need to understand and minimize the influences of
 commonly observed sample selection bias on model performance. Yet
 evaluating these data with independent, planned surveys is rare, even
 though such evaluation is necessary for understanding and applying data to
 conservation decisions. We used the state-listed fox squirrel Sciurus
 niger in Florida, USA, to interpret the performance of models created with
 opportunistic observations from citizens and professionals by validating
 models with independent, planned surveys. Data from both citizens and
 professionals showed sample selection bias with more observations within
 50 m of a road. While these groups showed similar sample selection bias in
 reference to roads, there were clear differences in the spatial coverage
 of the groups, with citizens observing fox squirrels more frequently in
 developed areas. Based on predictions at planned field surveys sites,
 models developed from citizens generally performed similarly to those
 developed with data collected by professionals. Accounting for potential
 sample selection bias in models, either through the use of covariates or
 via aggregating data into home range size grids, provided only slight
 increases in model performance. Synthesis and applications. Despite sample
 selection biases, over a broad spatial scale opportunistic citizen data
 provided reliable predictions and estimates of habitat relationships
 needed to advance conservation efforts. Our results suggest that the use
 of professionals may not be needed in volunteer programmes used to
 determine the distribution of species of conservation interest across
 broad spatial scales.
description: Squirrel
 locationsFox squirrel locations
 entered on website from public and professionals. File contains x,y
 coordinates and associated covariatespresencedata_final.csvSquirrel validation pointsFox squirrel occurrence data from camera trappingvalid_final.csv
DOI: 10.5061/dryad.pm20b46
title: Data from: Haplodeficiency of diabetes-associated gene GLIS3 impairs insulin sensitivity in male mice

description: [No abstract entered]
description: Supplementary Figures
 1-5
DOI: 10.5061/dryad.4rp76r87
title: Data from: Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1

description: Local adaptation provides an opportunity to study the genetic basis of
 adaptation and investigate the allelic architecture of adaptive genes. We
 study DELAY OF GERMINATION 1 (DOG1), a gene controlling natural variation
 in seed dormancy in Arabidopsis thaliana and investigate evolution of
 dormancy in 41 populations distributed in four regions separated by
 natural barriers. Using F_ST and Q_ST comparisons, we compare variation at
 DOG1 with neutral markers and quantitative variation in seed dormancy.
 Patterns of genetic differentiation among populations suggest that the
 gene DOG1 contributes to local adaptation. Although Q_ST for seed dormancy
 is not different from F_ST for neutral markers, a correlation with
 variation in summer precipitation supports that seed dormancy is adaptive.
 We characterize dormancy variation in several F_2-populations and show
 that a series of functionally distinct alleles segregate at the DOG1
 locus. Theoretical models have shown that the number and effect of alleles
 segregating at QTLs have important consequences for adaptation. Our
 results provide support to models postulating a large number of alleles at
 quantitative trait loci involved in adaptation.
description: Kronholm_data
DOI: 10.5061/dryad.71pp6
title: Data from: Developmental expression of drug metabolizing enzymes: impact on disposition in neonates and young children

description: Profound changes in drug metabolizing enzyme expression occurs during
 development that impacts drug efficacy and the risk of adverse events in
 the neonate and young child. A review of our current knowledge suggests
 individual hepatic drug metabolizing enzymes can be categorized into one
 of three classes based on developmental trajectories. The time frame for
 the perinatal changes observed for both Class 1 and Class 3 enzymes varies
 considerably between different enzymes. However, for a given enzyme,
 significant interindividual variation is observed in the timing of the
 perinatal changes, creating windows of hypervariability. Genetic variation
 clearly impacts drug disposition in children. However, developmental
 factors can dominate pharmacogenetic factors. Thus, a major challenge in
 applying pharmacogenomics to improve pediatric drug safety is determining
 at what age functional genetic variants identified in adults become a
 major determinant of expression in children. Developmental and genetic
 data on drug metabolizing enzyme ontogeny, as well as age-dependent
 changes in other physiological factors impacting drug disposition, can be
 integrated into physiologically-based pharmacokinetic models. Such models
 have proven useful in predicting the range of expected metabolic
 capacities at a given age.
description: Xenobiotic Metabolizing
 Enzyme Ontogeny Master DatabaseA Microsoft Excel file
 containing three data sheets of individual donor data: Enzyme Specific
 Content, Enzyme Specific Activity, GenotypeXME Ontogeny Master
 Database.xlsxXenobiotic Metabolizing
 Enzme Specific ContentA comma separated format
 file containing individual enzyme specific content donor
 dataXME
 Specific Content.csvXenobiotic Metabolizing
 Enzyme Specific ActivityA comma separated file
 containing individual enzyme specific activity donor
 dataXME
 Specific Activity.csvXenobiotic Metabolizing
 Enzyme GenotypeA comma separated format
 file containing individual genotype information for individual
 donors.XME
 Genotype.csv
DOI: 10.5061/dryad.mj846
title: Data from: Molecular phylogenetics and the evolution of fruit and leaf morphology of Dichaea (Orchidaceae: Zygopetalinae)

description: BACKGROUND AND AIMS: The orchid genus Dichaea, with over 100 species found
 throughout the neotropics, is easily recognized by distichous leaves on
 long stems without pseudobulbs and flowers with infrastigmatic ligules.
 The genus has previously been divided into four sections based primarily
 on presence of ovary bristles and a foliar abscission layer. The aim of
 this work is to use DNA sequence data to estimate phylogenetic
 relationships within Dichaea and map the distribution of major
 morphological characters that have been used to delimit
 subgenera/sections. METHODS: Sequence data for the nuclear ribosomal
 internal transcribed spacers and plastid matK, trnL intron, trnL-F spacer
 and ycf1 for 67 ingroup and seven outgroup operational taxonomic units
 were used to estimate phylogenetic relationships within Dichaea. Taxa from
 each of the four sections were sampled, with the greatest representation
 from section Dichaea, the most diverse and taxonomically puzzling group.
 KEY RESULTS: Molecular data and morphology support monophyly of Dichaea.
 Results indicate that section Dichaeopsis is polyphyletic and based on
 symplesiomorphies, including deciduous leaves and smooth ovaries that are
 widespread in Zygopetalinae. There are at least three well-supported
 clades within section Dichaeopsis. Section Pseudodichaea is monophyletic
 and defined by setose ovaries and leaves with an abscission layer.
 Sections Dichaea and Dichaeastrum are monophyletic and defined by pendent
 habit and persistent leaves. Section Dichaeastrum, distinguished from
 section Dichaea primarily by a glabrous ovary, is potentially
 polyphyletic. CONCLUSIONS: The leaf abscission layer was lost once,
 occurring only in the derived sections Dichaea and Dichaeastrum. The
 setose fruit is a more homoplasious character with several losses and
 gains within the genus. We propose an informal division of the genus based
 upon five well-supported clades.
description: Dichaea
 4geneNexus matrix of nrITS,
 matK, trnL intron, trnL-F spacer and ycf1 sequences of Dichaea
 (Zygopetalinae: Orchidaceae).
DOI: 10.5061/dryad.hj5m4
title: Data from: Adaptive patterns of phenotypic plasticity in laboratory and field environments in Drosophila melanogaster

description: Identifying mechanisms of adaptation to variable environments is essential
 in developing a comprehensive understanding of evolutionary dynamics in
 natural populations. Phenotypic plasticity allows for phenotypic change in
 response to changes in the environment, and as such may play a major role
 in adaptation to environmental heterogeneity. Here, the plasticity of
 stress response in D. melanogaster originating from two distinct
 geographic regions and ecological habitats was examined. Adults were given
 a short-term, 5-day exposure to combinations of temperature and
 photoperiod to elicit a plastic response for three fundamental aspects of
 stress tolerance that vary adaptively with geography. This was replicated
 in both the laboratory and in outdoor enclosures in the field. In the
 laboratory, geographic origin was the primary determinant of the stress
 response. Temperature and the interaction between temperature and
 photoperiod also significantly affected stress resistance. In the outdoor
 enclosures, plasticity was distinct among traits and between geographic
 regions. These results demonstrate that short-term exposure of adults to
 ecologically relevant environmental cues results in predictable effects on
 multiple aspects of fitness. These patterns of plasticity vary among
 traits and are highly distinct between the two examined geographic
 regions, consistent with patterns of local adaptation to climate and
 associated environmental parameters.
description: Mathur_Schmidt_rawdataThis is all of the phenotypic information and data analyzed in the paper.
DOI: 10.5061/dryad.m1831
title: Data from: Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor

description: Sensory systems define an animal's capacity for perception and can
 evolve to promote survival in new environmental niches. We have uncovered
 a noncanonical mechanism for sweet taste perception that evolved in
 hummingbirds since their divergence from insectivorous swifts, their
 closest relatives. We observed the widespread absence in birds of an
 essential subunit (T1R2) of the only known vertebrate sweet receptor,
 raising questions about how specialized nectar feeders such as
 hummingbirds sense sugars. Receptor expression studies revealed that the
 ancestral umami receptor (the T1R1-T1R3 heterodimer) was repurposed in
 hummingbirds to function as a carbohydrate receptor. Furthermore, the
 molecular recognition properties of T1R1-T1R3 guided taste behavior in
 captive and wild hummingbirds. We propose that changing taste receptor
 function enabled hummingbirds to perceive and use nectar, facilitating the
 massive radiation of hummingbird species.
description: DRYAD_Figure2_3_S3_S4_S5Luminescence assay data for Figures 2, 3, S3, S4, and S5.DRYAD_Fig4ABehavioral data used in Figure 4ADRYAD_Fig4B_S6Behavioral data used in Figure 4B and S6DRYAD_Alignment_labelsFigure1AlignmentS1_AllT1RAlignmentT1R1AlignmentT1R3Alignment
DOI: 10.5061/dryad.sr42j
title: Data from: Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis)

description: The evolution of reproductive isolation in an ecological context may
 involve multiple facets of species divergence on which divergent selection
 may operate. These include variation in quantitative phenotypic traits,
 regulation of gene expression, and differential transmission of particular
 allelic combinations. Thus, an integrative approach to the speciation
 process involves identifying the genetic basis of these traits, in order
 to understand how they are affected by divergent selection in nature and
 how they ultimately contribute to reproductive isolation. In the Lake
 Whitefish (Coregonus clupeaformis), dwarf and normal species pairs
 sympatrically occur in several North American postglacial lakes. The
 limnetic dwarf whitefish distinguishes from its normal benthic relative by
 numerous life history, behavioural, morphological and gene expression
 traits, in relation with the exploitation of distinct ecological niches.
 Here, we have applied the RAD-Sequencing method to a hybrid backcross
 family to reconstruct a high-density genetic linkage map and perform QTL
 mapping in the Lake Whitefish. The 3061 cM map encompassed 3438
 segregating RAD markers distributed over 40 linkage groups, for an average
 resolution of 0.89 cM. We mapped phenotypic and expression QTL underlying
 ecologically important traits as well as transmission ratio distortion
 QTL, and identified genomic regions harbouring clusters of such QTL. A
 narrow genomic region strongly associated with sex determination was also
 evidenced. Positional and functional information revealed in this study
 will be useful in ongoing population genomic studies to illuminate our
 understanding of the genomic architecture of reproductive isolation
 between whitefish species pairs.
description: Genotypes_Phenotypes_Expression_data
DOI: 10.5061/dryad.d1r5g
title: Data from: Fabrication and electromagnetic performance of talc/NiTiO 3 composite

description: In this study, the electromagnetic (EM) performance of talc/NiTiO3
 composite was evaluated. The morphology of talc displayed a lamella
 structure; there were many nanoparticles of NiTiO3 coated on the talc
 lamella. Thermal destruction occurred, which increased the surface area
 from 2.51 m2 g−1 to 79.09 m2 g−1 at the calcined stage at 650°C. The
 presence of NiTiO3 increased dielectric loss and magnetic loss of talc.
 The calculation of EM wave absorption of talc/NiTiO3 obtained a maximum
 reflection loss of −11.94 dB at the thickness of 6.85 mm; the optimum
 thickness for microwave absorption is 6.3–7.3 mm. This study revealed a
 new approach for fabricating an EM absorber and broadening applications of
 both talc and NiTiO3 in EM absorption.
description: XRD
 dataXRD data of talc, TN
 450, TN 550, and TN 650BET and Pore size
 dataNitrogen adsorption and
 desorption curves and pore size distribution of talc and TN 450, TN 550,
 and TN 650Permittivity and
 Permeability dataPermittivity and
 Permeability of talc, TN 450, TN 550 and TN 650 with volume fraction of 50
 % and thickness of 2 mm; reflection loss data of talc/NiTiO3 composite as
 a function of thickness.Permittivity and permeability
 data.xlsx
DOI: 10.5061/dryad.v0n20
title: Data from: Genetic structure and hybridization in the species group of Ficus auriculata: can closely related sympatric Ficus species retain their genetic identity while sharing pollinators?

description: Obligate mutualistic nursery pollination systems between insects and
 plants have led to substantial co-diversification involving at least some
 parallel cladogenesis, as documented in Yucca, Ficus and Phyllanthaceae.
 In such systems pollinators are generally species specific thus limiting
 hybridization and introgression among interfertile host species.
 Nevertheless, in the three systems, cases of one insect pollinating
 several plant species are reported. In most cases host plants sharing
 pollinators are allopatric. However in the case of the species group of
 Ficus auriculata, forms may co-occur over large parts of their range. We
 show here that the species group of F. auriculata is constituted by four
 well-defined genetic entities that share pollinators. We detected hybrids
 in nature mainly when both parental forms were growing nearby. Controlled
 crosses showed that F1 offspring could be successfully backcrossed. Hence,
 despite sharing pollinators and despite hybrid viability, the different
 forms have preserved their genetic and morphological identity. We propose
 that ecological differentiation among forms, coupled with limited overlap
 of reproductive season has facilitated the maintenance of these
 inter-fertile forms. As such, establishment of pollinator host specificity
 may not be a prerequisite for sympatric diversification in Ficus.
description: Dataset_CytbCytb sequences for phylogenetic inference (Agaonidae)Dataset_EFEF sequences for phylogenetic inference (Agaonidae)TreeML_CytbML tree from the analysis of Cytb sequencesTreeML_EFML tree from the analysis of EF sequencesTables S1-S3 : Ficus genotypesTable S1 Genotypes of parents and offspring in controlled crosses. Table S2 Parent and offspring probability of assignation to genetic cluster using Structure. Table S3 Genotypes at the 7 retained loci of 355 individuals used for the global analysis.TablesS1-S2-S3.docxTableS4_WaspSamplingList of wasp specimens included in this study