cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34810/data2689
title: Replication Data for: Long-term protection of crystalline zinc phosphide under atmospheric conditions

description: Earth-abundant zinc phosphide (Zn3P2) holds great promise as a photovoltaic
absorber for thin-film applications, owing to its direct bandgap of approximately
1.5 eV and its high absorption coefficient in the visible spectrum.
Nonetheless, questions remain about the material’s stability in atmospheric
environments, given its tendency to react with surrounding water vapor and
oxygen. This work presents a comprehensive long-term study to understand
how environmental exposure impacts high-quality, monocrystalline epitaxial
zinc phosphide. Through a combination of various experimental techniques,
such as ellipsometry, Raman spectroscopy, X-ray diffraction measurements,
scanning transmission electron microscopy, energy dispersive X-ray spectroscopy,
secondary ion mass spectroscopy, and X-ray photoelectron spectroscopy,
we reveal that exposure to atmosphere causes substantial oxidation
of the thin film surface, penetrating several tens of nanometers into the bulk
material. Finally, we show that degradation can be effectively prevented by applying a thin dielectric layer, such as Si3N4 ,or simply by storing the unprotected
thin films under vacuum. These findings provide valuable guidelines
for the proper handling of the material prior to device fabrication.
DOI: 10.5061/dryad.7g4c9
title: Data from: A phylogenetic analysis of egg size, clutch size, spawning mode, adult body size, and latitude in reef fishes

description: Theoretical treatments of egg size in fishes suggest that constraints on
 reproductive output should create trade-offs between the size and number
 of eggs produced per spawn. For marine reef fishes, the observation of
 distinct reproductive care strategies (demersal guarding, egg scattering,
 and pelagic spawning) has additionally prompted speculation that these
 strategies reflect alternative fitness optima with selection on egg size
 differing by reproductive mode and perhaps latitude. Here, we aggregate
 data from 278 reef fish species and test whether clutch size, reproductive
 care, adult body size, and latitudinal bands (i.e., tropical, subtropical,
 and temperate) predict egg size, using a statistically unified framework
 that accounts for phylogenetic correlations among traits. We find no
 inverse relationship between species egg size and clutch size, but rather
 that egg size differs by reproductive mode (mean volume for demersal eggs
 = 1.22 mm3, scattered eggs = 0.18 mm3, pelagic eggs = 0.52 mm3) and that
 clutch size is strongly correlated with adult body size. Larger eggs were
 found in temperate species compared with tropical species in both demersal
 guarders and pelagic spawners, but this difference was not strong when
 accounting for phylogenetic correlations, suggesting that differences in
 species composition underlies regional differences in egg size. In
 summary, demersal guarders are generally small fishes with small clutch
 sizes that produce large eggs. Pelagic spawners and egg scatterers are
 variable in adult and clutch size. Although pelagic spawned eggs are
 variable in size, those of scatterers are consistently small.
description: Supplemental_methods_Kasimatis_Riginos_DryadSupplementary methodsSupplemental_tables_Kasimatis_Riginos_Oct2015_DryadSupplementary Tables (ESM Tables 1-5)Data_source_appendix_Kasimatis_Riginos_Oct2015_dryadAppendix - includes references for original data sources and raw data (ESM Table 6)SuppFig1_sppnumbESM Figure S1Supp_fig2_chrongramESM Figure S2Kasimatis_Riginos_data_Oct2015Excel worksheet containing all raw data for analyses.volume_Oct2015CSV formatted infile with egg volume data. (Also represented in the excel file.)clutch_Oct2015CSV formatted infile with clutch size data. (Also represented in the excel file.)geography_Oct2015CSV formatted infile with geographic data. (Also represented in the excel file.)Fish_egg_size_tree_S1000_chronogram_Oct2015Nexus file containing chronogram used with PGLS analyses.Scripts_Kasimiatis_Riginos_Oct15 copyR scripts used for all presented analyses
DOI: 10.5061/dryad.jf2f5
title: Data from: Floral trait evolution associated with shifts between insect and wind pollination in the dioecious genus Leucadendron (Proteaceae)

description: Transitions between animal and wind pollination have occurred in many
 lineages and have been linked to various floral modifications, but these
 have seldom been assessed in a phylogenetic framework. In the dioecious
 genus Leucadendron (Proteaceae), transitions from insect to wind
 pollination have occurred at least four times. Using analyses that
 controlled for relatedness among Leucadendron species, we investigated how
 these transitions shaped the evolution of floral structural and signaling
 traits, including the degree of sexual dimorphism in these traits. Pollen
 grains of wind-pollinated species were found to be smaller, more numerous,
 and dispersed more efficiently in wind than were those of
 insect-pollinated species. Wind-pollinated species also exhibited a
 reduction in spectral contrast between showy subtending leaves and
 background foliage, reduced volatile emissions, and a greater degree of
 sexual dimorphism in color and scent. Uniovulate flowers and inflorescence
 condensation are conserved ancestral features in Leucadendron and likely
 served as exaptations in shifts to wind pollination. These results offer
 insights into the key modifications of male and female floral traits
 involved in transitions between insect and wind pollination.
description: Wind tunnel
 dataPollen dispersal
 capability in a wind tunnel at different speeds and
 distances.Wind_Tunnel.xlsxSpectral reflectance dataThe spectral reflectance of the subtending leaves surrounding inflorescences for male and female plants of Leucadendron species over the waveband of 300-700nm using a reflectance spectrophotometer (Ocean Optics In. Dunedin, Fla.)Spectral_Reflectance.xlsxPollen production in Leucadendron speciesThe number of pollen grains in one pre-dehiscent male flower. Pollen grains are counted in five subsamples of 2 μl from each sample and extrapolated total pollen production per flower from the initial sample volume of 1 ml.Pollen_Production.xlsxMeasurements of pollen grain sizeVertical height (h) and base (b) of pollen grains were measured by imaging pollen grains with a Scanning Electron Microscope (Zeiss Evo LS 15) and using AnalySis ® (version 3.2) on the SEM photographs with the scale bar as reference.Pollen_Size.xlsInflorescence measurementsMeasurements of flowers per inflorescence, size of inflorescence and inflorescences per branch.Inflorescence.xlsxPGEE tableThe table use to conduct PGEE analysis for several floral traits in Leucadendron.PGEE_table.xlsx
DOI: 10.5061/dryad.2jc88
title: Data from: The Rickettsia endosymbiont of Ixodes pacificus contains all the genes of de novo folate biosynthesis

description: Ticks and other arthropods often are hosts to nutrient providing bacterial
 endosymbionts, which contribute to their host’s fitness by supplying
 nutrients such as vitamins and amino acids. It has been detected, in our
 lab, that Ixodes pacificus is host to Rickettsia species phylotype G021.
 This endosymbiont is predominantly present, and 100% maternally
 transmitted in I. pacificus. To study roles of phylotype G021 in I.
 pacificus, bioinformatic and molecular approaches were carried out. MUMmer
 genome alignments of whole genome sequence of I. scapularis, a close
 relative to I. pacificus, against completely sequenced genomes of R.
 bellii OSU85-389, R. conorii, and R. felis, identified 8,190 unique
 sequences that are homologous to Rickettsia sequences in the NCBI Trace
 Archive. MetaCyc metabolic reconstructions revealed that all folate gene
 orthologues (folA, folC, folE, folKP, ptpS) required for de novo folate
 biosynthesis are present in the genome of Rickettsia buchneri in I.
 scapularis. To examine the metabolic capability of phylotype G021 in I.
 pacificus, genes of the folate biosynthesis pathway of the bacterium were
 PCR amplified using degenerate primers. BLAST searches identified that
 nucleotide sequences of the folA, folC, folE, folKP, and ptpS genes
 possess 98.6%, 98.8%, 98.9%, 98.5% and 99.0% identity respectively to the
 corresponding genes of Rickettsia buchneri. Phylogenetic tree
 constructions show that the folate genes of phylotype G021 and homologous
 genes from various Rickettsia species are monophyletic. This study has
 shown that all folate genes exist in the genome of Rickettsia species
 phylotype G021 and that this bacterium has the genetic capability for de
 novo folate synthesis.
description: S1
 TableS1 Table: Endosymbiotic
 rickettsial genes and their encoding proteins identified by the MUMmer
 alignment software and BLASTX in the Trace Archive of the Ixodes
 scapularis genome sequencing project. Column 1 and 2 are call numbers.
 Column 3 is the GenBank accession numbers of homologous proteins. Column 4
 is the names of the homologous proteins. Column 5 is the names of the
 bacterial species. Column 6 and 7 are the percentage identity to top
 BLASTX results. Column 8 is the AT% for the DNA. Column 9 is the sequences
 obtained by the MUMmer alignment.S1
 FileS1 File: SequenceSearch
 script code.S2
 FileS2 File:
 NucleotideReader script code.
DOI: 10.5061/dryad.4n86v
title: Data from: Optimizing regulatory requirements to aid in the implementation of compensatory mitigation

description: Governments, companies, and conservation organizations seek to minimize
 the impacts of development through application of the mitigation
 hierarchy: avoid, minimize, restore, and offset (McKenney &
 Kiesecker 2010). Around the world, policies and performance standards for
 compensatory mitigation are being strengthened not just to reduce impacts
 to biodiversity, but to achieve goals for biodiversity that range from “no
 net loss” to “net gains” (IFC 2012). Although use of offsets is still in
 its infancy, offsets are gaining traction globally as a goal of public
 policy (Madsen et al. 2011; Villarroya, Barros & Kiesecker 2014),
 corporate practices (Rainey et al. 2014), and lending standards (IFC 2012;
 Equator Principles 2013). As such, these new policies and standards will
 be important drivers for companies to improve mitigation practices.
description: JAPPL2015-0045_SOCHIFile geodatabase of inputs, including project area, planning units, conservation targets (including vector and raster) created in ArcGIS v10.1, for Marxan analysis on offset mitigation in the San Juan area of Colorado, USA.
DOI: 10.5061/dryad.q1r50
title: Data from: Plant–plant interactions as a mechanism structuring plant diversity in a Mediterranean semi-arid ecosystem

description: Plant–plant interactions are among the fundamental processes that shape
 structure and functioning of arid and semi-arid plant communities. Despite
 the large amount of studies that have assessed the relationship between
 plant–plant interactions (i.e., facilitation and competition) and
 diversity, often researchers forget a third kind of interaction, known as
 allelopathy. We examined the effect of plant–plant interactions of three
 dominant species: the perennial grass Lygeum spartum, the allelopathic
 dwarf shrub Artemisia herba-alba, and the nurse shrub Salsola vermiculata,
 on plant diversity and species composition in a semi-arid ecosystem in NE
 Spain. Specifically, we quantified the interaction outcome (IO) based on
 species co-occurrence, we analyzed diversity by calculation of the
 individual species–area relationship (ISAR), and compositional changes by
 calculation of the Chao-Jaccard similarity index. We found that S.
 vermiculata had more positive IO values than L. spartum, and A. herba-alba
 had values between them. Lygeum spartum and A. herba-alba acted as
 diversity repellers, whereas S. vermiculata acted as a diversity
 accumulator. As aridity increased, A. herba-alba transitioned from
 diversity repeller to neutral and S. vermiculata transitioned from neutral
 to diversity accumulator, while L. spartum remained as diversity repeller.
 Artemisia herba-alba had more perennial grass species in its local
 neighborhood than expected by the null model, suggesting some tolerance of
 this group to its “chemical neighbor”. Consequently, species that coexist
 with A. herba-alba were very similar among different A. herba-alba
 individuals. Our findings highlight the role of the nurse shrub S.
 vermiculata as ecosystem engineer, creating and maintaining patches of
 diversity, as well as the complex mechanism that an allelopathic plant may
 have on diversity and species assemblage. Further research is needed to
 determine the relative importance of allelopathy and competition in the
 overall interference of allelopathic plants.
description: Interaction Outcome
 datasetData of co-occurrences
 (Real coex. column) and expected co-occurrences (Expected coex. column)
 between target species (A. herba-alba, S. vermiculata and L. spartum) and
 the other plant species found intransects. Data is separate in different
 sheets for different study sites. Species code can be found in the first
 sheet.Interaction_Outcome_dataset.xlsxISAR datasetNumber of species found around each individual of target species (A. herba-alba, S. vermiculata and L. spartum) from d=0 to d=400cm, every 20 cm.ISAR_dataset.xlsxChao-Jaccard datasetMatrix of coexistences between target species (A. herba-alba, S. vermiculata and L. spartum) and the other species found in transects. Data is separate in different sheets for different study sites. Species code can be found in the first sheet.Chao_jaccard_dataset.xlsx
DOI: 10.5061/dryad.49p7f
title: Data from: A global bionomic database for the dominant vectors of human malaria

description: Anopheles mosquitoes were first recognised as the transmitters of human
 malaria in the late 19th Century and have been subject to a huge amount of
 research ever since. Yet there is still much that is unknown regarding the
 ecology, behaviour (collectively ‘bionomics’) and sometimes even the
 identity of many of the world’s most prominent disease vectors, much less
 the within-species variation in their bionomics. Whilst malaria
 elimination remains an ambitious goal, it is becoming increasingly clear
 that knowledge of vector behaviour is needed to effectively target control
 measures. A database of bionomics data for the dominant vector species of
 malaria worldwide has been compiled from published peer-reviewed
 literature. The data identification and collation processes are described,
 together with the geo-positioning and quality control methods. This is the
 only such dataset in existence and provides a valuable resource to
 researchers and policy makers in this field.
description: Bionomic database for
 the dominant vectors of malaria in AfricaCompilation of bionomics
 data for the dominant vectors of malaria in Africa from published and
 unpublished sources reporting data collected from
 1985-2013.Bionomics
 Africa.csvBionomic database for
 the dominant vectors of malaria in the AmericasCompilation of bionomics
 data for the dominant vectors of malaria in the Americas from published
 sources reporting data collected from 1985-2014.Bionomics
 Americas.csvBionomic database for
 the dominant vectors of malaria in the Asia-PacificCompilation of bionomics
 data for the dominant vectors of malaria in the Asia-Pacific from
 published sources reporting data collected from
 1985-2014.Bionomics
 Asia-Pacific.csv
DOI: 10.5061/dryad.84kj5
title: Data from: Functional diversity and structural disorder in the human ubiquitination pathway

description: The ubiquitin-proteasome system plays a central role in cellular
 regulation and protein quality control (PQC). The system is built as a
 pyramid of increasing complexity, with two E1 (ubiquitin activating), few
 dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase)
 enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE
 database and literature, we assembled a coherent dataset of 563 human E3s
 and analyzed their various physical features. We found an increase in
 structural disorder of the system with multiple disorder predictors
 (IUPred – E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and
 substrate simultaneously (single subunit E3, ssE3) have significantly
 higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger,
 mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate
 recognition subunits, 17.33%) functions are separated. In ssE3s, the
 disorder was localized in the substrate/adaptor binding domains, whereas
 the E2-binding RING/HECT-domains were structured. To demonstrate the
 involvement of disorder in E3 function, we applied normal modes and
 molecular dynamics analyses to show how a disordered and highly flexible
 linker in human CBL (an E3 that acts as a regulator of several tyrosine
 kinase-mediated signalling pathways) facilitates long-range conformational
 changes bringing substrate and E2-binding domains towards each other and
 thus assisting in ubiquitin transfer. E3s with multiple interaction
 partners (as evidenced by data in STRING) also possess elevated levels of
 disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB
 uncovered 21 distinct human E3 interactions, in 7 of which the disordered
 region of E3s undergoes induced folding (or mutual induced folding) in the
 presence of the partner. In conclusion, our data highlights the primary
 role of structural disorder in the functions of E3 ligases that manifests
 itself in the substrate/adaptor binding functions as well as the mechanism
 of ubiquitin transfer by long-range conformational transitions.
description: Supplementary_Materials_Chapter2Supplementary Table 2.1Supplementary Table 2.2Supplementary Table 2.3Supplementary Table 2.5Supplementary_Zip_Files_S2.1
DOI: 10.5061/dryad.sv056
title: Data from: Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations, and introgression between winged and wingless forms

description: Insect flight-loss is a repeated phenomenon in alpine habitats, where wing
 reduction is thought to enhance local recruitment and increase fecundity.
 One predicted consequence of flight loss is reduced dispersal ability,
 which should lead to population genetic differentiation and perhaps
 ultimately to speciation. Using a dataset of 15,123 SNP loci, we present
 comparative analyses of fine-scale population structure in co-distributed
 Zelandoperla stonefly species, across three parallel altitudinal transects
 in New Zealand's Rock and Pillar mountain range. We find that winged
 populations (altitude 200–500m; Z. decorata) show no genetic structuring
 within or among streams, suggesting substantial dispersal mediated by
 flight. By contrast, wingless populations (Z. fenestrata; altitude
 200–1100m) exhibit distinct genetic clusters associated with each stream,
 and additional evidence of isolation by distance within streams. Our data
 support the hypothesis that wing-loss can initiate diversification in
 alpine insect populations over small spatial scales. The often deep
 phylogenetic placement of lowland Z. fenestrata within their
 stream-specific clades suggests the possibility of independent alpine
 colonization events for each stream. Additionally, the detection of
 winged, interspecific hybrid individuals raises the intriguing possibility
 that a previously flightless lineage could reacquire flight via
 introgression.
description: Individual genotypic
 dataIndividual genotypic
 data for 180 samples scored at 15,123 SNP loci.Zelandoperla_180samp.15123snp.nex
DOI: 10.5061/dryad.t671s
title: Data from: Evidence of divergent selection for drought and cold tolerance at landscape and local scales in Abies alba Mill. in the French Mediterranean Alps

description: Understanding local adaptation in forest trees is currently a key research
 and societal priority. Geographically and ecologically marginal
 populations provide ideal case studies, because environmental stress along
 with reduced gene flow can facilitate the establishment of locally adapted
 populations. We sampled European silver fir (Abies alba Mill.) trees in
 the French Mediterranean Alps, along the margin of its distribution range,
 from pairs of high and low elevation plots on four different mountains
 situated along a 170 km east-west transect. The analysis of 267 SNP loci
 from 175 candidate genes suggested a neutral pattern of east-west
 isolation-by-distance among mountain sites. FST outlier tests revealed 16
 SNPs that showed patterns of divergent selection. Plot climate was
 characterized using both in-situ measurements and gridded data that
 revealed marked differences between and within mountains with different
 trends depending on the season. Association between allelic frequencies
 and bio-climatic variables revealed eight genes that contained candidate
 SNPs of which two were also detected using FST outlier methods. All SNPs
 were associated with winter drought and one of them showed strong evidence
 of selection with respect to elevation. QST - FST tests for fitness
 related traits measured in a common garden, suggested adaptive divergence
 for the date of bud flush and for growth rate. Overall, our results
 suggest a complex adaptive picture for A. alba in the southern French Alps
 where, during the east to west Holocene recolonization, locally
 advantageous genetic variants established both at the landscape and local
 scales.
description: common_garden_data_and_Qst-Fst_testsA series of files containing common garden data (budburst, survival and growth) from a nursery tests (see Sagnard et al. 2002) and R scripts to perform the Qst-Fst tests with the QstFstComp packageenvironmental_dataA list of environmental variables characterizing the four studied sites from southern France (Ventoux, Lure, Issole and Vésubie)IBE_vs_IBD_testsR scripts to perform the Mantel tests for detecting isolation-by-distance and isolation by-environment patterns using the ecodist packageKASP_detailsSequences (raw data) on which primer design for KASP assay was based and SNPs thereinoutlier_testsResults of outlier tests using Bayescan, FLK, hFDIST and LFMM, and R scripts for running LFMM using the LEA packagesampling_sitesLambert 3 coordinates and altitude of all sampled individualsSTRUCTUREShell scripts and results of the STRUCTURE analysis with K=1 to 9SNP_dataRaw SNP data called from transcriptome accession no.: JV134525–JV157085 TSA NCBI, and inferred SNP data using the software PHASE