cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gm6kk
title: Data from: Illuminating prey selection in an insectivorous bat community, exposed to artificial light at night

description: 1.Light pollution has been increasing around the globe and threatens to
 disturb natural rhythms of wildlife species. Artificial light impacts the
 behaviour of insectivorous bats in numerous ways, including foraging
 behaviour, which may in turn lead to altered prey selection. 2.In a
 manipulative field experiment, we collected faecal samples from six
 species of insectivorous bats in naturally dark and artificially lit
 conditions, and identified prey items using molecular methods to
 investigate effects of light pollution on prey selection. 3.Proportional
 differences of identified prey were not consistent and appeared to be
 species specific. Red bats, little brown bats, and gray bats exhibited
 expected increases in moths at lit sites. Beetle-specialist big brown bats
 had a sizeable increase in beetle consumption around lights, while
 tri-colored bats and evening bats showed little change in moth consumption
 between experimental conditions. Dietary overlap was high between
 experimental conditions within each species, and dietary breadth only
 changed significantly between experimental conditions in one species, the
 little brown bat. 4.Policy implications. Our results, building on others,
 demonstrate that bat-insect interactions may be more nuanced than the
 common assertion that moth consumption increases around lights. They
 highlight the need for a greater mechanistic understanding of bat-light
 interactions to predict which species will be most affected by light
 pollution. Given differences in bat and insect communities, we advocate
 biologists, land stewards, and civil planners work collaboratively to
 determine lighting solutions that minimize changes in foraging behaviour
 of species in the local bat community. Such efforts may allow stakeholders
 to more effectively craft management strategies to minimize unnatural
 shifts in prey selection caused by artificial lights.
description: Cravens_et_al_2017_dataThe data in this file is the data used in the analysis of Cravens et al. 2017. The data has been filtered from the raw output from the 'Bold' package in program R. Please see the 'remarks' worksheet for explanations of the abbreviations used in the data file. We can provide the raw, unfiltered output from the 'Bold' package if one is interested.Representative sequences for identification of insects in BOLD databaseThis data file contains the data, in fasta file format, of each of the representative sequences obtained from clustering and filtering, that were input into the BOLD database for identification.Cravens_et_al_2017_rep_seqs.fna
DOI: 10.5061/dryad.6fj3v
title: Data from: Effect of reaction solvent on hydroxyapatite synthesis in sol-gel process

description: Synthesis of hydroxyapatite (HA) through sol–gel process in different
 solvent systems is reported. Calcium nitrate tetrahydrate (CNTH) and
 diammonium hydrogen phosphate (DAHP) were used as calcium and phosphorus
 precursors, respectively. Three different synthesis reactions were carried
 out by changing the solvent media, while keeping all other process
 parameters constant. A measure of 0.5 M aqueous DAHP solution was used in
 all reactions while CNTH was dissolved in distilled water, tetrahydrofuran
 (THF) and N,N-dimethylformamide (DMF) at a concentration of 0.5 M. Ammonia
 solution (28–30%) was used to maintain the pH of the reaction mixtures in
 the 10–12 range. All reactions were carried out at 40 ± 2°C for 4 h. Upon
 completion of the reactions, products were filtered, washed and calcined
 at 500°C for 2 h. It was clearly demonstrated through various techniques
 that the dielectric constant and polarity of the solvent mixture strongly
 influence the chemical structure and morphological properties of calcium
 phosphate synthesized. Water-based reaction medium, with highest
 dielectric constant, mainly produced β-calcium pyrophosphate (β-CPF) with
 a minor amount of HA. DMF/water system yielded HA as the major phase with
 a very minor amount of β-CPF. THF/water solvent system with the lowest
 dielectric constant resulted in the formation of pure HA.
description: Supplementary
 DataThis file contains
 supplementary data for the manuscript. The images herein are also included
 below in .tif format.XRD diffractogram of
 water based synthesisXRD diffractogram of
 water based synthesis. Corresponds to figure (a) in the supplementary data
 document.XRD diffractogram of DMF
 based synthesisXRD diffractogram of DMF
 based synthesis. Corresponds to figure (b) in the supplementary data
 document.XRD diffractogram of THF
 based synthesisXRD diffractogram of THF
 based synthesis. Corresponds to figure (c) in the supplementary data
 document.
DOI: 10.5061/dryad.h9q13
title: Data from: Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S attenuata) dolphins, from SNP data

description: Little is known about global patterns of genetic connectivity in pelagic
 dolphins, including how circumtropical pelagic dolphins spread globally
 following the rapid and recent radiation of the subfamily delphininae. In
 this study, we tested phylogeographic hypotheses for two circumtropical
 species, the spinner dolphin (Stenella longirostris) and the pantropical
 spotted dolphin (Stenella attenuata), using &gt;3,000 nuclear DNA
 single nucleotide polymorphisms (SNPs) in each species. Analyses for
 population structure indicated significant genetic differentiation between
 almost all subspecies and populations in both species. Bayesian
 phylogeographic analyses of spinner dolphins showed deep divergence
 between Indo-Pacific, Atlantic, and eastern tropical Pacific Ocean (ETP)
 lineages. Despite high morphological variation, our results show very
 close relationships between endemic ETP spinner subspecies in relation to
 global diversity. The dwarf spinner dolphin is a monophyletic subspecies
 nested within a major clade of pantropical spinner dolphins from the
 Indian and western Pacific Ocean populations. Population-level division
 among the dwarf spinner dolphins was detected–with the northern Australia
 population being very different from that in Indonesia. In contrast to
 spinner dolphins, the major boundary for spotted dolphins is between
 offshore and coastal habitats in the ETP, supporting the current
 subspecies-level taxonomy. Comparing these species underscores the
 different scale at which population structure can arise, even in species
 that are similar in habitat (i.e., pelagic) and distribution.
description: LeslieMorin_DolphinPhylogeography_R_environment_data_resultsThis R environment is the one used to generate the results for this manuscript within it are filtered data and many outputs based on analyses in the accompanying R-script.Convert2strataG_10July17.rdataConvert2StrataG_10July2017_LowHet_cleanWith this R script, one can input the .rdata file attached - calculate the FST and DAPC measures presented in this manuscript and generate the plots presented therein.
DOI: 10.5061/dryad.9n153
title: Data from: Taxonomic reassessment of Clevosaurus latidens Fraser, 1993 (Lepidosauria, Rhynchocephalia) and rhynchocephalian phylogeny based on parsimony and Bayesian inference

description: The Late Triassic rhynchocephalian Clevosaurus latidens Fraser, 1993 is
 known from the fissure deposits of Cromhall Quarry, England. Many studies
 have questioned its referral to the genus Clevosaurus and some
 phylogenetic analyses suggest a close relationship with herbivorous
 rhynchocephalians. We reexamine the type specimens and referred material
 of C. latidens to elucidate its taxonomic identity. Additionally, we
 provide new phylogenetic analyses of the Rhynchocephalia using both
 parsimony and Bayesian approaches. Our taxonomic review and both
 phylogenetic analyses reveal that C. latidens is not referable to
 Clevosaurus, but represents a new genus. We reassess C. latidens and
 provide an amended diagnosis for the new genus Fraserosphenodon gen. nov.
 Both parsimony and Bayesian analyses recover similar topologies and we
 propose formal names for two higher clades within Rhynchocephalia:
 Eusphenodontia and Neosphenodontia.
description: Phylogenetic analysis
 Supplementary Data SetThis file includes the
 complete results of the phylogenetic analysis including the character
 matrix, ACCTRAN and DELTRAN optimizations and the scripts used in each
 analysis.Phylogenetic_analysis_Supplementary_Data_Set.zip
DOI: 10.5061/dryad.n8147
title: Data from: Population genomics and geographical parthenogenesis in Japanese harvestmen (Opiliones, Sclerosomatidae, Leiobunum)

description: Naturally-occurring population variation in reproductive mode presents an
 opportunity for researchers to test hypotheses regarding the evolution of
 sex. Such populations frequently assume a geographical pattern, in which
 parthenogenesis-dominated populations are widely dispersed, with narrowly
 distributed sexual populations. We evaluate the geographic distribution of
 genomic signatures associated with parthenogenesis using nuclear and
 mitochondrial DNA sequence data from two Japanese harvestman sister taxa,
 Leiobunum manubriatum and L. globosum. Asexual reproduction is putatively
 facultative in these species, and female-biased localities are common in
 habitat margins. Past karyotypic and current cytometric work indicates L.
 globosum is entirely tetraploid, while L. manubriatum may be either
 diploid or tetraploid. We estimated species phylogeny, genetic
 differentiation, diversity, and mitonuclear discordance in females
 collected across the species range in order to identify range expansion
 towards marginal habitat, potential for hybrid origin, and persistence of
 asexual lineages. Our results point to northward expansion of a tetraploid
 ancestor of L. manubriatum and L. globosum, coupled with support for
 greater male gene flow in southern L. manubriatum localities. Specimens
 from localities in the Tohoku and Hokkaido regions were indistinct,
 particularly those of L. globosum, potentially due to little mitochondrial
 differentiation or haplotypic variation. Although L. manubriatum overlaps
 with L. globosum across its entire range, L. globosum was reconstructed as
 monophyletic with strong support using mtDNA, and marginal support with
 nuclear loci. Ultimately, we find evidence for continued sexual
 reproduction in both species, and describe opportunities to clarify the
 rate and mechanism of parthenogenesis.
description: GMgbs2ploidyR script for application of gbs2ploidy packageDAPC and statistics scriptR script to compute population statistics and DAPC analysesDAPCstats.RBEAST *.xml files*.xml-formatted files for L. globosum, L. manubriatum, and all specimensBEASTfiles.zipFiles for DAPC and population statisticsFolder of *.phy, STRUCTURE and tab delimited files for F-statistics calculation and DAPC analyses in RRfiles.zipgbs2ploidy filesEdited heterozygous allele depth files and FACS-assigned ploidy for all specimens to use in gbs2ploidy analyses in R.ploidyfiles.zip
DOI: 10.5061/dryad.826kd
title: Data from: Environmental DNA reveals that rivers are conveyer belts of biodiversity information

description: DNA sampled from the environment (eDNA) is a useful way to uncover
 biodiversity patterns. By combining a conceptual model and empirical data,
 we test whether eDNA transported in river networks can be used as an
 integrative way to assess eukaryotic biodiversity for broad spatial scales
 and across the land–water interface. Using an eDNA metabarcode approach,
 we detect 296 families of eukaryotes, spanning 19 phyla across the
 catchment of a river. We show for a subset of these families that eDNA
 samples overcome spatial autocorrelation biases associated with the
 classical community assessments by integrating biodiversity information
 over space. In addition, we demonstrate that many terrestrial species are
 detected; thus suggesting eDNA in river water also incorporates
 biodiversity information across terrestrial and aquatic biomes.
 Environmental DNA transported in river networks offers a novel and
 spatially integrated way to assess the total biodiversity for whole
 landscapes and will transform biodiversity data acquisition in ecology.
description: Taxonomic assignments
 for all reads reported in figure 2This excel file contains
 the meta data for all sequenced reads with their taxonomic assignment
 reported in figure 2 as well as the file used to construct table 1.
 Worksheet titled, “all_data_confirmed_taxonomy” contains all reads by site
 that were confirmed to at least the family level as described in the
 manuscript. The full taxonomic name associated with the reference sequence
 is listed, but this is not to be interpreted as the assignment for the
 read below the family level in all cases. See Supplementary Data 1, 2, 3
 and 4 in manuscript for which families and species were considered
 confirmed as described in the methods section. Worksheet titled,
 “Pivot_all_confirmed_Table 1” contains a PIVOT table whereby we calculated
 the values reported in Table 1 columns 8, 9 and 10.reads per
 site_dryad.xlsx
DOI: 10.5061/dryad.8t201
title: Data from: Covariation between the physiological and behavioral components of pathogen transmission: host heterogeneity determines epidemic outcomes

description: Although heterogeneity in contact rate, physiology, and behavioral
 response to infection have all been empirically demonstrated in
 host–pathogen systems, little is known about how interactions between
 individual variation in behavior and physiology scale-up to affect
 pathogen transmission at a population level. The objective of this study
 is to evaluate how covariation between the behavioral and physiological
 components of transmission might affect epidemic outcomes in host
 populations. We tested the consequences of contact rate covarying with
 susceptibility, infectiousness, and infection status using an
 individual-based, dynamic network model where individuals initiate and
 terminate contacts with conspecifics based on their behavioral
 predispositions and their infection status. Our results suggest that both
 heterogeneity in physiology and subsequent covariation of physiology with
 contact rate could powerfully influence epidemic dynamics. Overall, we
 found that 1) individual variability in susceptibility and infectiousness
 can reduce the expected maximum prevalence and increase epidemic
 variability; 2) when contact rate and susceptibility or infectiousness
 negatively covary, it takes substantially longer for epidemics to spread
 throughout the population, and rates of epidemic spread remained
 suppressed even for highly transmissible pathogens; and 3) reductions in
 contact rate resulting from infection-induced behavioral changes can
 prevent the pathogen from reaching most of the population. These effects
 were strongest for theoretical pathogens with lower transmissibility and
 for populations where the observed variation in contact rate was higher,
 suggesting that such heterogeneity may be most important for less
 infectious, more chronic diseases in wildlife. Understanding when and how
 variability in pathogen transmission should be modelled is a crucial next
 step for disease ecology.
description: Oikos 04527 Dryad
 DepositoryZip file containing code
 used to run and analyze simulations, as well as raw and processed data
 files.DryadDepository.zip
DOI: 10.5061/dryad.87n81
title: Data from: Individual size variation reduces spatial variation in abundance of tree community assemblage, not of tree populations

description: Research on individual trait variation has gained much attention because
 of its implication for ecosystem functions and community ecology. The
 effect of individual variation on population and community abundance
 (number of individuals) variation remains scarcely tested. Using two
 established ecological scaling laws (Taylor's law and abundance–size
 relationship), we derived a new scaling relationship between the
 individual size variation and spatial variation of abundance. Tested
 against multi-plot tree data from Diaoluo Mountain tropical forest in
 Hainan, China, the new scaling relationship showed that individual size
 variation reduced the spatial variation of community assemblage abundance,
 but not of taxon-specific population abundance. The different responses of
 community and population to individual variation were reflected by the
 validity of the abundance–size relationship. We tested and confirmed this
 scaling framework using two measures of individual tree size: aboveground
 biomass and diameter at breast height. Using delta method and
 height-diameter allometry, we derived the analytic relation of scaling
 exponents estimated under different individual size measures. In addition,
 we used multiple regression models to analyze the effect of taxon richness
 on the relationship between individual size variation and spatial
 variation of population or community abundance, for taxon-specific and
 taxon-mixed data, respectively. This work offers empirical evidence and a
 scaling framework for the negative effect of individual trait variation on
 spatial variation of plant community. It has implications for forest
 ecosystem and management where the role of individual variation in
 regulating population or community spatial variation is important but
 understudied.
description: Diaoluo tree sample
 dataTree sample data from
 Diaoluo Mountain tropical forest in 2010 and 2015 separately. Each row
 records one individual with its diameter at breast height (cm), height
 (m), wood density (g/cm3), and aboveground biomass (g)DiaoluoTreeSample.csv
DOI: 10.5061/dryad.67n73
title: Data from: Grow with the flow: a latitudinal cline in physiology is associated with more variable precipitation in Erythranthe cardinalis

description: Local adaptation is commonly observed in nature: organisms perform well in
 their natal environment, but poorly outside it. Correlations between
 traits and latitude, or latitudinal clines, are among the most common
 pieces of evidence for local adaptation, but identifying the traits under
 selection and the selective agents is challenging. Here, we investigated a
 latitudinal cline in growth and photosynthesis across 16 populations of
 the perennial herb Erythranthe cardinalis (Phrymaceae). Using machine
 learning methods, we identify interannual variation in precipitation as a
 likely selective agent: southern populations from more variable
 environments had higher photosynthetic rates and grew faster. We
 hypothesize that selection may favour a more annualized life history –
 grow now rather than save for next year – in environments where severe
 droughts occur more often. Thus, our study provides insight into how
 species may adapt if Mediterranean climates become more variable due to
 climate change.
description: Source code for: Grow
 with the flow: a latitudinal cline in physiology is associated with more
 variable precipitation in Erythranthe cardinalisRelease v1.0 of source
 code for this manuscript. Download this repository to your machine. Open
 'card-cline.Rproj' in RStudio. Install R packages if necessary.
 To generate manuscript, simply open ms/ms.Rnw and compile using
 RStudio.card-cline.zip
DOI: 10.5061/dryad.6s386
title: Data from: Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria)

description: A highly divergent 16S rRNA gene was found in one of the five ribosomal
 operons present in a species complex currently circumscribed as Scytonema
 hyalinum (Nostocales, Cyanobacteria) using clone libraries. If 16S rRNA
 sequence macroheterogeneity among ribosomal operons due to insertions,
 deletions or truncation is excluded, the sequence heterogeneity observed
 in S. hyalinum was the highest observed in any prokaryotic species thus
 far (7.3–9.0%). The secondary structure of the 16S rRNA molecules encoded
 by the two divergent operons was nearly identical, indicating possible
 functionality. The 23S rRNA gene was examined for a few strains in this
 complex, and it was also found to be highly divergent from the gene in
 Type 2 operons (8.7%), and likewise had nearly identical secondary
 structure between the Type 1 and Type 2 operons. Furthermore, the 16S-23S
 ITS showed marked differences consistent between operons among numerous
 strains. Both operons have promoter sequences that satisfy consensus
 requirements for functional prokaryotic transcription initiation.
 Horizontal gene transfer from another unknown heterocytous cyanobacterium
 is considered the most likely explanation for the origin of this molecule,
 but does not explain the ultimate origin of this sequence, which is very
 divergent from all 16S rRNA sequences found thus far in cyanobacteria. The
 divergent sequence is highly conserved among numerous strains of S.
 hyalinum, suggesting adaptive advantage and selective constraint of the
 divergent sequence.
description: Alignment for 16S rRNA
 gene phylogenetic analysisThis is the alignment
 used to generate Figure 1 in the publication. All OTUs have NCBI GenBank
 accession numbers at the end of the descriptor line.Scytonema_hyalinum_16S_alignment.txtAlignment for 3 loci phylogenetic analysisThis is the alignment file for the sequence data for three loci, rpoC1 (838 bp), rbcLX (600 bp), and nifD (233 bp), respectively, used in the analysis shown in Figure 5. All three sequences are partial genes.Scytonema_hyalinum_3loci_alignment.txtPhylogenetic analysis based on 16S rRNA gene sequencesPhylogenetic analysis based on 16S rRNA gene sequences of heterocytous cyanobacterial strains, all OTUs shown. Source phylogeny for Figure 1 in the publication.Scytonema_hyalinum_16S_BI_tree.epsPhylogenetic analysis based on concatenated sequences for three lociThis is the phylogenetic analysis based on three loci (rpoC1, rbcLX, and nifD, that is the source for Figure 5 in the publication.Scytonema_hyalinum_3loci_BI_tree.eps