cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kt056q7
title: Data from: PbbHLH4 regulates floral monoterpene biosynthesis in Phalaenopsis orchids

description: Floral scent is an important factor in attracting pollinators and
 repelling florivores. In Phalaenopsis bellina (Orchidaceae), the major
 floral scent components are monoterpenoids. Previously, we have identified
 that expression of GERANYL DIPHOSPHATE SYNTHASE (PbGDPS) is highly
 correlated with monoterpene biosynthesis in Phalaenosis orchids. Here, we
 showed that both cis- and trans-regulation were present on the GDPS
 promoters, with trans-regulation playing a key role. To investigate the
 regulation of floral scent biosynthesis, we compared the transcriptomic
 data of two Phalaenopsis orchids with contrasting scent phenotypes. Eight
 transcription factors (TFs) with sequential elevation expressions through
 floral development stages in P. bellina were identified, and their
 transcript levels were higher in the scent orchid than the scentless one.
 Five of these TFs transactivated several structural genes involved in
 monoterpene biosynthesis pathway to various extent, including PbbHLH4,
 PbbHLH6, PbbZIP4, PbERF1, and PbNAC1. Ectopic transient expression of
 these TFs in scentless orchids revealed that terpenoid biosynthesis was
 all stimulated. PbbHLH4 most profoundly induced the monoterpene phenotype
 with a 950-fold increase of monoterpenoid production in the scentless
 orchid. In conclusion, the orchid floral monoterpenes biosynthesis was
 regulated sequentially and elaborately, and with PbbHLH4 playing a crucial
 role for monoterpene phenotype.
description: Dataset
 1Includes three
 spreadsheets with the gene expression levels of two orchid transcriptome
 analyzed in this study.Dataset
 2Includes one spreadsheet
 with the STEM clustering results for associating expression patterns of
 the transccription factors analyzed in this study.Supplementary Figures
 and TablesIncludes nine
 supplementary figures (Fig. S1-9.jpg), supplementary figure legends
 (SuppFL.pdf), and supplementary tables (SuppTable.pdf).Supp.zipAlignment FilesIncludes four sequence alignment files in a plain text format for Fig. S1, S4, S6 and S9.Align.zip
DOI: 10.5061/dryad.h1r1pg7
title: Data from: Nets versus spraying: a spatial modelling approach reveals indoor residual spraying targets Anopheles mosquito habitats better than mosquito nets in Tanzania

description: The global implementation of malaria interventions has averted hundreds of
 millions of clinical malaria cases in the last decade. This study assesses
 predicted Anopheles mosquito distributions across the United Republic of
 Tanzania before large-scale insecticide-treated net (ITN) rollouts and
 indoor residual spraying (IRS) initiatives to determine whether mosquito
 net usage by children under the age of five and IRS are targeted to areas
 where historical evidence indicates mosquitoes thrive. Demographic and
 Health Surveys data from 2011-2012 and 2015-2016 include detailed
 measurements of mosquito net and IRS use across Tanzania. Anopheline data
 are far less intensively collected, but we constructed a Maxent-built
 baseline mosquito habitat suitability (MHS) map (AUC=0.872) with Tanzanian
 Anopheles occurrence records from 1999-2003. This MHS model was tested
 against independently-observed georeferenced Plasmodium falciparum cases
 from the Malaria Atlas Project, with ~87% of cases from 1999-2003 (n=107)
 and ~84% of cases from 1985-2012 (n=919) occurring in areas of high
 predicted suitability for mosquitoes. We compared the validated MHS with
 subsequent malaria interventions using mixed effects logistic regression.
 Specifically, we assessed whether Anopheles habitat suitability related to
 the frequency that ≥1 child in a household reportedly slept under a
 mosquito net when that intervention later became widely available, and
 whether IRS was reportedly applied to dwellings over a one-year period.
 There was no evidence that mosquito net use the night before the survey
 related to MHS from 2011-2012 and marginally significant evidence
 (p&lt;0.05) from 2015-2016 (β=1.466, 95% C.I.=0.848-2.103, marginal
 R2=0.020, respectively). However, the likelihood of IRS treatments rose
 relatively strongly in the 12 months prior to both surveys (β=13.466, 95%
 C.I.=10.488-16.456, marginal R2=0.144, and β=6.817, 95% C.I.=5.439-8.303,
 marginal R2=0.136, respectively). IRS treatments have therefore been
 targeted more effectively than mosquito nets toward areas where anopheline
 habitat suitability was previously found to be high.
description: Maxent_dataThis zipped file contains the ASCII files representing the environmental factors used to make the Maxent model and map.Anopheles_c2001This CSV file contains the combined Anopheles mosquito coordinates, where mosquitoes were collected in Tanzania between 1999-2003, for the building of the Maxent model. These data, combined with the ASCII environmental files, will reproduce the Maxent model and map when used as input in the Maxent software.
DOI: 10.5061/dryad.vk245pd
title: Data from: Targeted sequencing of venom genes from cone snail genomes improves understanding of conotoxin molecular evolution

description: To expand our capacity to discover venom sequences from the genomes of
 venomous organisms, we applied targeted sequencing techniques to
 selectively recover venom gene superfamilies and non-toxin loci from the
 genomes of 32 cone snail species (family, Conidae), a diverse group of
 marine gastropods that capture their prey using a cocktail of neurotoxic
 peptides (conotoxins). We were able to successfully recover conotoxin gene
 superfamilies across all species with high confidence (&gt; 100X
 coverage) and used these data to provide new insights into conotoxin
 evolution. First, we found that conotoxin gene superfamilies are composed
 of 1-6 exons and are typically short in length (mean = ~85bp). Second, we
 expanded our understanding of the following genetic features of conotoxin
 evolution: (a) positive selection, where exons coding the mature toxin
 region were often three times more divergent than their adjacent noncoding
 regions, (b) expression regulation, with comparisons to transcriptome data
 showing that cone snails only express a fraction of the genes available in
 their genome (24%-63%), and (c) extensive gene turnover, where Conidae
 species varied from 120-859 conotoxin gene copies. Finally, using
 comparative phylogenetic methods, we found that while diet specificity did
 not predict patterns of conotoxin evolution, dietary breadth was
 positively correlated with total conotoxin gene diversity. Overall, the
 targeted sequencing technique demonstrated here has the potential to
 radically increase the pace at which venom gene families are sequenced and
 studied, reshaping our ability to understand the impact of genetic changes
 on ecologically relevant phenotypes and subsequent diversification.
description: Data from study
 recovering conotoxins from genomic DNAI have included: (1) The
 target sequences the baits were designed from (2) the bait sequences
 themselves (3) the final phylogenetic alignment and (4) the final venom
 sequences.dryad.zip
DOI: 10.5061/dryad.50jf82v
title: Data from: “The CarP‐N neutral Project”: removal, processing and reuse of invasive fish in local terrestrial conservation projects

description: 1. Proliferation of problematic non-indigenous fish species is major
 biosecurity problem in many countries. 2. In Southern Hemisphere lowland
 rivers, species such as introduced common carp (Cyprinus carpio) take
 advantage of nutrient rich conditions and a temperate climate and often
 dominate the fish biomass in invaded waterbodies. 3. These invasive
 organisms assimilate nutrients into their flesh and also release nutrients
 through re-suspension and defecation re-directing the pathway of energy
 transfer and use in aquatic systems. 4. We describe an invasive fish
 ‘recycling’ programme where a semi-automated trap selectively captures
 pest fish and transfers them to a thermophilic digester where bacteria
 efficiently process them into nutrient rich meal. 5. Developing products
 from invasive fish meal to support other conservation efforts while
 simultaneously providing a funding source to offset the costs of harvest
 and de-incentivise spread are key objectives. 6. We showcase two trials to
 substantiate our concept; a dune planting experiment where we demonstrate
 the transfer of processed invasive fish nutrient from an over-fertilised
 aquatic ecosystem to coastal sand dunes where nutrients are depleted but
 were formerly higher. We also illustrate the potential for using this
 locally derived recycled nutrient to replace imported synthetic fertiliser
 tablets typically used in dune planting. 7. The second trial demonstrates
 use of invasive fish as a lure in terrestrial trapping programmes for
 controlling other problematic invasive pests. Synthesis and applications:
 We consider this concept to be a shift in restoration thinking whereby an
 aquatic biosecurity problem is being used to improve indigenous
 biodiversity outcomes in other ecosystems. We propose that this project is
 a useful vehicle to promote thought that more accurately embodies the
 concept of sustainability by being more cognisant of the traceability of
 nutrient flow from harvest and processing through to use within and
 between ecosystems. It illustrates alternate ways in which invasive
 products can be applied to these systems for positive environmental
 outcomes and to generate programme cost recovery. A similar philosophy
 should be applicable to problematic and abundant invasive species
 elsewhere, particularly where those organisms are susceptible to either
 point source control and or efficient mass harvest.08-Mar-2018
description: Supplementary
 information relating to : JAPPL-2017-00650A word file decribing
 results of dune planting fertiliser trialsSupp_info_finalv3revclean.docx
DOI: 10.5061/dryad.n0vf77m
title: Data from: Sympatric serpentine endemic Monardella (Lamiaceae) species maintain habitat differences despite hybridization

description: Ecological differentiation and genetic isolation are thought to be
 critical in facilitating coexistence between related species, but the
 relative importance of these phenomena, and the interactions between them,
 are not well understood. Here we examine divergence in abiotic habitat
 affinity and the extent of hybridization and introgression between two
 rare species of Monardella (Lamiaceae) that are both restricted to the
 same serpentine soil exposure in California. Although broadly sympatric,
 they are found in microhabitats that differ consistently in soil
 chemistry, slope, rockiness, and vegetation. We identify one active hybrid
 zone at a site with intermediate soil and above-ground characteristics,
 and we document admixture patterns indicative of extensive and asymmetric
 introgression from one species into the other. We find that genetic
 distance among heterospecific populations is related to geographic
 distance, such that the extent of apparent introgression is partly
 explained by the spatial proximity to the hybrid zone. Our work shows that
 plant species can maintain morphological and ecological integrity in the
 face of weak genetic isolation, intermediate habitats can facilitate the
 establishment of hybrids, and that the degree of apparent introgression a
 population experiences is related to its geographic location rather than
 its local habitat characteristics.
description: BedassleModel_codeZip file containing all the R and STAN code required to fun the Bedassle-like spatial and environmental covariance models for the SNP data.IsolationByDistanceZip file containing the data file and R code for the MLPE isolation by distance analysesMonardella_structure_infileInput file for STRUCTURE analyses, with SNP loci in the header row, and each individual in a row. Missing data is indicated with -9.Monardella_Treemix_infileTreeMix input file.soil_tissue_PCA_regressionZip file containing data and R code for soil and site principal components analyses and tissue v. soil regression analyses and model comparison.
DOI: 10.5061/dryad.dg5hv06
title: Data from: A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

description: DNA barcoding has proved difficult in a number of woody plant genera,
 including the ecologically important oak genus Quercus. In this study, we
 utilized restriction-site associated DNA sequencing (RAD-seq) to develop
 an economical single-nucleotide polymorphism (SNP) DNA barcoding system
 that suffices to distinguish eight common, sympatric eastern North
 American white oak species. Two de novo clustering pipelines, PyRAD and
 Stacks, were used in combination with post-clustering bioinformatic tools
 to generate a list of 291 potential SNPs, 80 of which were included in a
 barcoding toolkit that is easily implemented using MassARRAY mass
 spectrometry technology. As a proof-of-concept, we used the genotyping
 toolkit to infer potential hybridization between North American white oaks
 transplanted outside of their native range (Q. michauxii, Q. montana, Q
 muehlenbergii/ Q. prinoides and Q. stellata) among natural forests of
 locally native trees (Q. alba and Q. macrocarpa) in the living collection
 at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering
 analyses suggested low rates of hybridization between cultivated and
 native species, with the exception of one Q. michauxii mother tree, the
 acorns of which exhibited high admixture from either Q. alba or Q.
 stellata and Q. macrocarpa; and a hybrid between Q. stellata that appears
 to have backcrossed almost exclusively to Q. alba. Together, RAD-seq and
 MassARRAY technologies allow for efficient development and implementation
 of a multispecies barcode for one of the more challenging forest tree
 genera.
description: SNP_extract_stringent_approachCustom bash script for SNP detection using stringent approach after PyRAD/RADami analysis.Oakcoding_locus.fastaLocus alignment sequences used to create the SNPs.Sequenome_SNP_matrix_1stscreenSEQUENCE output file of the first SNP screening. The file is separated into four sheets detailing i) assay summary ii) sample summary iii) genotypes and iv) genotype areaSequenome_SNP_matrix_2ndscreenSEQUENCE output file of the second SNP screening. The file is separated into four sheets detailing i) assay summary ii) sample summary iii) genotypes and iv) genotype areaSequenome_SNP_matrix_potentialparentsSEQUENCE output file for genotyping potential parent individuals. The file is separated into three sheets detailing i) assay summary ii) sample summary and iii) genotypes
DOI: 10.5061/dryad.5q39d8q
title: Data from: The burning question: does fire affect habitat selection and forage preference of the black rhinoceros Diceros bicornis in East African savannahs?

description: Endangered species conservation requires information on how management
 activities influence habitat quality. The black rhinoceros (Diceros
 bicornus) is critically endangered and restricted to savannas representing
 ~5% of its historical range. Fire is used extensively in savanna, but
 little is known about how rhinos respond to burning. Our aim was to
 understand rhino responses to fire by studying habitat selection and
 foraging at multiple scales. We used resource selection functions and GPS
 locations of 31 rhinos from 2014-2016 to study rhino habitat use in
 Serengeti National Park, Tanzania. Rhino selectivity was quantified by
 comparing forage consumption to plant species availability in randomly
 sampled vegetation plots; rhino diets were subsequently verified through
 DNA-metabarcoding analysis of fecal samples. Rhino habitat use was a
 unimodal function of fire history, with highly occupied sites having fire
 frequencies of &lt; 0.6 fires yr-1 and maximum occupancy occurring at
 a fire frequency of 0.1 fires yr-1. Foraging stations had characteristic
 plant communities, with 17 species statistically associated with rhino
 foraging. Rhinos were associated with, and disproportionately consumed,
 woody plants, forbs and legumes all of which decreased in abundance with
 increasing fire frequency. In contrast to common management practices,
 multiple lines of evidence suggest that the current fire regime in
 Serengeti negatively influences rhino habitat use and foraging and that
 frequent fire limits rhino access to preferred forage. We conclude with a
 conceptual model to guide managers and conservationists in the use of fire
 under variable savanna conditions.
description: Anderson-et-al-Oryx-fire-datasetThis is an R file which provides code to read-in and view the MODIS-derived fire products from the Serengeti ecosystem between the years of 2000 and 2016. The two main products which accessed via the code is a raster of fire frequency from 2000 – 2016 (Anderson-et-al-Oryx-fire-frequency-2000-2016.tif) and the spatial distribution of annual burns from 2000 – 2016 provided as a set of stacked rasters (Anderson-et-al-Oryx-annual-fire-bands-2000-2016.tif).Anderson-et-al-Oryx-fire-frequency-2000-2016This is a raster in .tif format of MODIS-derived fire frequency between the years 2000 – 2016; the CRS of the raster is in the sinusoidal projection (+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs).Anderson-et-al-Oryx-annual-fire-bands-2000-2016This is a stack of 16 rasters in .tif format showing the spatial locations of annual fires between the years 2000 – 2016 as derived from MODIS; the CRS of the rasters are in the sinusoidal projection (+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs).
DOI: 10.5061/dryad.20r509g
title: Data from: Age and area predict patterns of species richness in pumice rafts contingent on oceanic climatic zone encountered

description: The Theory of Island Biogeography predicts that area and age explain
 species richness patterns (or alpha diversity) in insular habitats. Using
 a unique natural phenomenon, pumice rafting, we measured the influence of
 area, age and oceanic climate on patterns of species richness. Pumice
 rafts are formed simultaneously when submarine volcanoes erupt, the pumice
 clasts break-up irregularly, forming irregularly shaped pumice stones
 which while floating through the ocean are colonised by marine biota. We
 analyse two eruption events and more than 5000 pumice clasts collected
 from 29 sites and three climatic zones. Overall the older and larger
 pumice clasts held more species. Pumice clasts arriving in tropical and
 subtropical climates showed this same trend, where in temperate locations
 species richness (alpha diversity) increased with area but decreased with
 age. Beta diversity analysis of the communities forming on pumice clasts
 that arrived in different climatic zones showed that tropical and
 subtropical clasts transported similar communities while species
 composition on temperate clasts differed significantly from both tropical
 and subtropical arrivals. Using these thousands of insular habitats, we
 find strong evidence that area and age but also climatic conditions
 predict the fundamental dynamics of species richness colonising pumice
 clasts.
description: Combined_data_Home_and_Havre_Dryad_Eleanor_Velasquez_6_3_18This file contains data collected on the presence of marine invertebrates attached to floating pumice which washed ashore on the east coast of Australia and islands in the Pacific. This occurred following two marine volcano eruption events. The Home reef eruption occurred in 2006 and the Havre in 2012. Both events were used so that we could compare and contrast the differences and similarities between the two.
DOI: 10.5061/dryad.8vn80rv
title: Data from: What can mixed-species flock movement tell us about the value of Amazonian secondary forests? insights from spatial behavior

description: The value of secondary forest for rainforest species remains an important
 question for conservation in the 21st century. Here, we describe the
 spatial behavior of understory mixed-species flocks in a heterogeneous
 landscape in central Amazonia. Understory mixed-species flocks represent a
 diverse, highly organized component of the rich Amazonian avifauna. We
 recorded movements within 26 flock home ranges in primary forest,
 secondary forest, interfaces between forest types, and forest fragments.
 We describe frequency and movement orientation in relation to forest
 edges, movement patterns and proportion of use between secondary and
 primary forest, the relation between home range sizes and vegetation
 height, and home range configuration. Flocks visited only a small portion
 of forest edges, and showed a tendency for moving parallel to edges next
 to less-developed secondary forest. Movement patterns in secondary forests
 did not show significant differences compared to primary forests. Time
 spent in secondary forests increased in proportion to mean canopy height.
 Flocks were consistently present in secondary forests where vegetation
 height averaged over 15 m, but home ranges were nearly twice as large
 compared to primary forest. Home range limits tended to be aligned with
 disturbed vegetation, essentially rearranging a territorial configuration
 normally adjusted by topography. The spatial behavior of this important
 subset of the Amazonian avifauna shows that secondary forests are
 tolerated above a certain development threshold, but perceived as sub
 optimal habitat until canopy height closely matches primary forests.
description: Mix_sp_flocks_BDFFPTracking data for mixed species flocks at the Biological Dynamics of Forest Fragments Project in Brazil. Data is in GPX format. Each file is an aggregate of several days following flocks. Files with (...)_dry_2500(...) are a subsamples from flocks sampled for 100+ hours and only for the dry season. For a comprehensive list of sampling effort, check the supplementary material. Lidar data is split in Canopy height models (CHM) and Digital elevation models (DHM) all in TIF format.
DOI: 10.5061/dryad.413d4t5
title: Data from: Alcohol reduces muscle fatigue through atomistic interactions with nicotinic receptors

description: Alcohol consumption affects many organs and tissues, including skeletal
 muscle. However, the molecular mechanism of ethanol action on skeletal
 muscle remains unclear. Here, using molecular dynamics simulations and
 single channel recordings, we show that ethanol interacts with a
 negatively charged amino acid within an extracellular region of the
 neuromuscular nicotinic acetylcholine receptor (nAChR), thereby altering
 its global conformation and reducing the single channel current amplitude.
 Charge reversal of the negatively charged amino acid abolishes the
 nAChR-ethanol interaction. Moreover, using transgenic animals harboring
 the charge-reversal mutation, ex vivo measurements of muscle force
 production show that ethanol counters fatigue in wild type but not
 homozygous αE83K mutant animals. In accord, in vivo studies of motor
 coordination following ethanol administration reveal an approximately
 twofold improvement for wild type compared to homozygous mutant animals.
 Together, the converging results from molecular to animal studies suggest
 that ethanol counters muscle fatigue through its interaction with
 neuromuscular nAChRs.
description: in vivo and ex vivo
 data