cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5266bm8
title: Data from: Will natural resistance result in populations of ash trees remaining in British woodlands after a century of ash dieback disease?

description: Novel pests and diseases are becoming increasingly common, and often cause
 additional mortality to host species in the newly contacted communities.
 This can alter the structure of the community up to, and including, the
 extinction of host species. In the last twenty years, ash dieback disease
 (ADB) has spread into Europe from East Asia. It has caused substantial
 mortality in ash tree (Fraxinus excelsior L.) populations. However, a
 proportion of the individuals in most populations appears to be less
 susceptible to ADB and resistance seems to have high heritability. These
 observations have led to suggestions that ash populations may be
 sustainable after the disease. In order to test this hypothesis, I
 modified an existing model of UK woodland (parameterised for Wytham Woods,
 Oxfordshire) to take into account the impact of ADB, and allowed offspring
 to inherit resistance traits from their parent. The results suggest that
 ash populations would still exist in 100 years but at lower levels than
 they are currently. For example, when the initial proportion of resistant
 individuals is about 10% and heritability of resistance is 0.5, then the
 population of ash falls to about one third of present levels. The
 proportion of individuals initially resistant to ADB had a larger effect
 on population size after 100 years than the heritability of resistance.
 The fact that the initial size of the resistant population is important to
 achieving a high population size in the presence of ADB suggests that a
 selective breeding programme with the intention of augmenting the natural
 ash populations would be beneficial.
description: SORTIE Code for Ash
 Dieback PaperA zipped archive
 containing all the necessary code and input files to run the SORTIE
 program used in the paper
DOI: 10.5061/dryad.739sh81
title: Data from: Altitudinal biodiversity patterns of seed plants along Gongga Mountain in the southeastern Qinghai-Tibetan Plateau

description: The mechanisms underlying elevation patterns in species and phylogenetic
 diversity remain a central issue in ecology and are vital for effective
 biodiversity conservation in the mountains. Gongga Mountain, located in
 the southeastern Qinghai-Tibetan Plateau, represents one of the longest
 elevational gradients (ca. 6500 m, from ca. 1000 - 7556 m) in the world
 for studying species diversity patterns. However, the elevational gradient
 and conservation of plant species diversity and phylogenetic diversity in
 this mountain remain poorly studied. Here, we compiled the elevational
 distributions of 2,667 native seed plant species occurring in Gongga
 Mountain, and estimated the species diversity, phylogenetic diversity,
 species density, and phylogenetic relatedness across ten elevation belts
 and five vegetation zones. The results indicated that species diversity
 and phylogenetic diversity of all seed plants showed a hump-shaped
 pattern, peaking at 1800 - 2200 m. Species diversity was significantly
 correlated with phylogenetic diversity and species density. The floras in
 temperate coniferous broad-leaved mixed forests, sub-alpine coniferous
 forests and alpine shrublands and meadows were significantly
 phylogenetically clustered, whereas the floras in evergreen broad-leaved
 forests had phylogenetically random structure. Both climate and human
 pressure had strong correlation with species diversity, phylogenetic
 diversity and phylogenetic structure of seed plants. Our results suggest
 that the evergreen broad-leaved forests and coniferous broad-leaved mixed
 forests at low to mid elevations deserve more conservation efforts. This
 study improves our understanding on the elevational gradients of species
 and phylogenetic diversity and their determinants, and provides support
 for improving seed plants conservation in Gongga Mountain.
description: Altitudinal biodiversity
 patterns of seed plants along Gongga MountainData supporting on the
 analysis for this manuscript.
DOI: 10.5061/dryad.p20km22
title: Data from: Identifying genetic markers for a range of phylogenetic utility–from species to family level

description: Resolving the phylogenetic relationships of closely related species using
 a small set of loci is challenging as sufficient information may not be
 captured from a limited sample of the genome. Relying on few loci can also
 be problematic when conflict between gene-trees arises from incomplete
 lineage sorting and/or ongoing hybridization, problems especially likely
 in recently diverged lineages. Here, we developed a method using limited
 genomic resources that allows identification of many low copy candidate
 loci from across the nuclear and chloroplast genomes, design probes for
 target capture and sequence the captured loci. To validate our method we
 present data from Eucalyptus and Melaleuca, two large and phylogenetically
 problematic genera within the Myrtaceae family. With one annotated genome,
 one transcriptome and two whole-genome shotgun sequences of one Eucalyptus
 and four Melaleuca species, respectively, we identified 212 loci
 representing 263 kbp for targeted sequence capture and sequencing. Of
 these, 209 were successfully tested from 47 samples across five related
 genera of Myrtaceae. The average percentage of reads mapped back to the
 reference was 57.6% with coverage of more than 20 reads per position
 across 83.5% of the data. The methods developed here should be applicable
 across a large range of taxa across all kingdoms. The core methods are
 very flexible, providing a platform for various genomic resource
 availabilities and are useful from shallow to deep phylogenies.
description: README of Supplementary
 Materials on DRYAD of Kuelheim et al. 2019 (Plos ONE),
 DOI:10.1371/journal.pone.0218995Readme file to all
 Supplementary Archives deposited on DRYAD of Kuelheim et al. 2019 (Plos
 ONE)Kuelheim_et_al_2019_DRYAD_README.pdfSupplementary Archive 1Supplementary Archive 1: This archive contains all reference sequences and sequences used for probe design (FASTA format) of 212 loci and of one Eucalyptus and a consensus of four Melaleuca species.Supplementary_Archive_1.zipSupplementary Archive 2Supplementary Archive 2: Short read archive (raw reads) of 47 multiplexed Myrtaceae samples for the target enrichment approach for 212 loci.Supplementary_Archive_2.zipSupplementary Archive 3Supplementary Archive 3: This archive contains following subdirectories i) subdirectory supermatrix_209_loci and ii) subdirectory ML_inference (see README)Supplementary_Archive_3.zip
DOI: 10.5061/dryad.4ss043q
title: Data from: On the physical origin of linguistic laws and lognormality in speech

description: Physical manifestations of linguistic units include sources of variability
 due to factors of speech production which are by definition excluded from
 counts of linguistic symbols. In this work we examine whether linguistic
 laws hold with respect to the physical manifestations of linguistic units
 in spoken English. The data we analyze comes from a phonetically
 transcribed database of acoustic recordings of spontaneous speech known as
 the Buckeye Speech corpus. First, we verify with unprecedented accuracy
 that acoustically transcribed durations of linguistic units at several
 scales comply with a lognormal distribution, and we quantitatively justify
 this ‘lognormality law’ using a stochastic generative model. Second, we
 explore the four classical linguistic laws (Zipf’s law, Herdan’s law,
 Brevity law, and Menzerath-Altmann’s law) in oral communication, both in
 physical units and in symbolic units measured in the speech
 transcriptions, and find that the validity of these laws is typically
 stronger when using physical units than in their symbolic counterpart.
 Additional results include (i) coining a Herdan’s law in physical units,
 (ii) a precise mathematical formulation of Brevity law, which we show to
 be connected to optimal compression principles in information theory and
 allows to formulate and validate yet another law which we call the
 size-rank law, or (ii) a mathematical derivation of Menzerath-Altmann’s
 law which also highlights an additional regime where the law is inverted.
 Altogether, these results support the hypothesis that statistical laws in
 language have a physical origin.
description: Postprocess data Buckeye
 corpusPostprocess data from
 Buckeye Corpus.TablaTranscripcion.csv
DOI: 10.5061/dryad.cv66j09
title: Data from: Male black widows parasitize mate-searching effort of rivals to find females faster

description: Mate-searching success is a critical precursor to mating, but there is a
 dearth of research on traits and tactics that confer a competitive
 advantage in finding potential mates. Theory and available empirical
 evidence suggest that males locate mates using mate-attraction signals
 produced by receptive females (personal information) and avoid
 inadvertently-produced cues from rival males (social information) that
 indicate a female has likely already mated. Here we show that western
 black widow males use both kinds of information to find females
 efficiently, parasitizing the searching effort of rivals in a way that
 guarantees competition over mating after reaching a female’s web. This
 tactic may be adaptive because female receptivity is transient, and we
 show that (a) mate searching is risky (88% mortality) and (b) a strongly
 male-biased operational sex ratio (from 1.2:1 to &gt;10:1) makes
 competition inevitable. Males with access to rivals’ silk trails moved at
 higher speeds than those with only personal information, and located
 females even when personal information was unreliable or absent. We show
 that following rivals can increase the potential for sexual selection on
 females as well as males and argue it may be more widespread in nature
 than is currently realized.
description: Scott-data2-malesize-procBData used to calculate male body condition indexScott-data3-race2016-procBData from 2016 male mate-searching field experimentScott-data4-race2017-procBData from 2017 male mate-searching field experimentScott-data5-race2016b-procBData from additional 2016 male mate-searching field experiment (described in ESM1)Scott-data6-xrace-procBData from laboratory X-maze experimenrtScott-data7-male-movements-procBMale movement data (shown in Fig. S2 in ESM1)Scott-data8-cage-distributions-procBDistributions of pheromone traps and male capture in 2-16 and 2017 field experiments.Scott-analysis-forProcBR file with code for all analyses described in the paperScott-analysis-forProcBHTML file showing output from the R code contained in Scott-analysis-forProcB.RScott-data1-OSR-procBData used to calculate OSR in the fieldScott_procB_readmeThis file contains descriptions of all the files associated with this Dryad package.
DOI: 10.5061/dryad.sc20b6g
title: Data from: The influence of landscape context on short- and long-term forest change following a severe ice storm

description: 1. When deforestation results in small forest fragments surrounded by a
 non-forest matrix, forest stands within these fragments experience changes
 in structure and community composition. They also continue to experience
 natural disturbances like hurricanes and ice storms. It is unclear whether
 the landscape context of forest stands influences plant community response
 to natural disturbances. 2. Using data from surveys of forested plots in
 the years immediately following and 19 years after a severe ice storm, we
 measured changes in woody stem density, species richness, and beta
 diversity. 3. Plots with greater storm damage had greater gains in stems
 and species, and greater shifts in community composition. In addition,
 there were interactions between the degree of storm damage and landscape
 context. The short-term effects of storm damage were magnified in plots
 with less forest on the surrounding landscape and farther from the forest
 edge. In plots with high damage, a return towards pre-storm conditions
 over the long-term occurred more often in plots farther from the forest
 edge compared to those close to the edge. 4. Synthesis: Future climate
 scenarios predict increases in severe weather and accompanying ecosystem
 disturbance. Our results show that it is important to consider landscape
 context when assessing the response of forest communities to such
 disturbances.
description: Lloren_etal_2019_JEcol This data package contains two types of spreadsheets: (1) Matrices showing the abundance of each plant species observed in our study at each plot for each year (2) Summary table for each plot in our study Lloren_etal_2019_The_influence_of_landscape_context.zip
DOI: 10.5061/dryad.10h185k
title: Data from: Genome-wide identification of microsatellites and transposable elements in the dromedary camel genome using whole genome sequencing data

description: Transposable elements (TEs) along with simple sequence repeats (SSRs) are
 prevalent in eukaryotic genome, especially in mammals. Repetitive
 sequences form approximately one-third of the camelid genomes, so study on
 this part of genome can be helpful in providing deeper information from
 the genome and its evolutionary path. Here, in order to improve our
 understanding regarding the camel genome architecture, the whole genome of
 the two dromedaries (Yazdi and Trodi camels) was sequenced. Totally, 92-
 and 84.3-Gb sequence data were obtained and assembled to 137,772 and
 149,997 contigs with a N50 length of 54,626 and 54,031 bp in Yazdi and
 Trodi camels, respectively. Results showed that 30.58% of Yazdi camel
 genome and 30.50% of Trodi camel genome were covered by TEs. Contrary to
 the observed results in the genomes of cattle, sheep, horse, and pig, no
 endogenous retrovirus-K (ERVK) elements were found in the camel genome.
 Distribution pattern of DNA transposons in the genomes of dromedary,
 Bactrian, and cattle was similar in contrast with LINE, SINE, and long
 terminal repeat (LTR) families. Elements like RTE-BovB belonging to LINEs
 family in cattle and sheep genomes are dramatically higher than genome of
 dromedary. However, LINE1 (L1) and LINE2 (L2) elements cover higher
 percentage of LINE family in dromedary genome compared to genome of
 cattle. Also, 540,133 and 539,409 microsatellites were identified from the
 assembled contigs of Yazdi and Trodi dromedary camels, respectively. In
 both samples, di-(393,196) and tri-(65,313) nucleotide repeats contributed
 to about 42.5% of the microsatellites. The findings of the present study
 revealed that non-repetitive content of mammalian genomes is approximately
 similar. Results showed that 9.1 Mb (0.47% of whole assembled genome) of
 Iranian dromedary’s genome length is made up of SSRs. Annotation of
 repetitive content of Iranian dromedary camel genome revealed that 9,068
 and 11,544 genes contain different types of TEs and SSRs, respectively.
 SSR markers identified in the present study can be used as a valuable
 resource for genetic diversity investigations and marker-assisted
 selection (MAS) in camel-breeding programs.
description: Genome-wide TEs and
 Microsatellites in dromedary camelGenome_information_of_Dromedary_camel_1.tar.gz
DOI: 10.5061/dryad.7cn76k3
title: Data from: Inhibition behavior of mild steel by three new benzaldehyde thiosemicarbazone derivatives in 0.5 M H2SO4: Experimental and computational study

description: Three new benzaldehyde thiosemicarbazone derivatives namely benzaldehyde
 thiosemicarbazone (BST), 4-carboxyl benzaldehyde thiosemicarbazone (PBST)
 and 2-carboxyl benzaldehyde thiosemicarbazone (OCT) were synthesized and
 their inhibition effects on mild steel corrosion in 0.5 M H2SO4 solution
 were studied systematically using gravimetric and electrochemical
 measurements. Weight loss results revealed that PBST exhibited the highest
 inhibition efficiency of 96.6% among the investigated compounds when the
 concentration was 300 μM. The analysis of polarization curves indicated
 that the three benzaldehyde thiosemicarbazone derivatives acted as mixed
 type inhibitors and PBST and OCT predominantly anodic. The adsorption
 process of all these benzaldehyde thiosemicarbazone derivatives on Q235
 steel surface in 0.5 M H2SO4 solution conformed to Langmuir adsorption
 isotherm. Scanning electron microscopy was conducted to show the presence
 of benzaldehyde thiosemicarbazone derivatives on Q235 mild steel surface.
 The results of theoretical calculations were in good agreement with that
 of experimental measurements.
description: Data
DOI: 10.5061/dryad.64hm348
title: Data from: Individual variation in early-life telomere length and survival in a wild mammal

description: Individual variation in survival probability due to differential responses
 to early-life environmental conditions is important in the evolution of
 life-histories and senescence. A biomarker allowing quantification of such
 individual variation, and which links early-life environmental conditions
 with survival by providing a measure of conditions experienced, is
 telomere length. Here, we examined telomere dynamics among 24 cohorts of
 European badgers (Meles meles). We found a complex cross-sectional
 relationship between telomere length and age, with no apparent loss over
 the first 29 months, but with both decreases and increases in telomere
 length at older ages. Overall, we found low within-individual consistency
 in telomere length across individual lifetimes. Importantly, we also
 observed increases in telomere length within individuals, which could not
 be explained by measurement error alone. We found no significant sex
 differences in telomere length, and provide evidence that early-life
 telomere length predicts lifespan. However, while early-life telomere
 length predicted survival to adulthood (≥1 year old), early-life telomere
 length did not predict adult survival probability. Furthermore, adult
 telomere length did not predict survival to the subsequent year. These
 results show that the relationship between early-life telomere length and
 lifespan was driven by conditions in early-life, where early-life telomere
 length varied strongly among cohorts. Our data provide evidence for
 associations between early-life telomere length and individual
 life-history, and highlight the dynamics of telomere length across
 individual lifetimes due to individuals experiencing different early-life
 environments.
description: Data - individual
 variation in early-life telomere lengthData for analyses in
 individual variation in early-life telomere length and survival in a wild
 mammal
DOI: 10.5061/dryad.8rm2dn0
title: Data from: CRISPR-Cas9 mediated CD133 knockout inhibits colon cancer invasion through reduced epithelial-mesenchymal transition

description: We previously reported that CD133, as a putative cancer stem cell marker,
 plays an important role in cell proliferation and invasion in colon
 cancer. To understand the role of CD133 expression in colon cancer, we
 evaluated the inhibitory effect of CD133 in colon cancer cells. In this
 study, we generated CD133knockout colon cancer cells (LoVo) using the
 CRISPR-Cas9 gene editing system. CD133+ colon cancer cells (LoVo) were
 infected with the lentiviral vector carrying CD133 gRNA and purified cell
 by culturing single cell colonies. CD133knockout cells was validated by
 western blot and flow cytometry analysis. In functional study, we observed
 a significant reduction in cell proliferation and colony formation in
 CRISPR-Cas9 mediated CD133 knockout cells in compare with control (P
 &lt; 0.001). We also found the anticancer effect of stattic was
 dependent on CD133 expression in colon cancer cells. Although
 CD133knockout cells could not completely block the tumorigenic property,
 they showed remarkable inhibitory effects on the ability of cell migration
 and invasion (P &lt; 0.001). In addition, we examined the epithelial
 mesenchymal transition (EMT)-related protein expression by western blot.
 The result clearly showed a loss of vimentin expression in CD133knockout
 cells. Therefore, CRISPR-Cas9 mediated CD133knockout can be an effective
 treatment modality for CD133+ colon cancer through reducing the
 characteristics of cancer stem cells.
description: S1 raw images of
 CRISPR-Cas9 mediated CD133 knockout inhibit cancer invasion through
 reduced EMTOriginal images of
 western blot and additional repeated western blots. Raw data of colony
 formation and transwell migration assay.
DOI: 10.5061/dryad.nn7188m
title: Data from: An ecological history of the relict genetic lineage of Arabidopsis thaliana

description: The combination of extensive population sampling with whole-genome
 sequencing in the annual plant Arabidopsis thaliana has recently allowed
 the identification of a genetically differentiated relict lineage. The
 most important nuclei of relict A. thaliana is found in the Iberian
 Peninsula and North Africa, although relict accessions have also been
 found scattered across Atlantic oceanic islands, eastern Mediterranean
 Basin, South and East Africa and China. We hypothesised that relict A.
 thaliana long survived and adapted to a wide array of environments in the
 Iberian Peninsula and North Africa due to the fact that the region
 repeatedly acted as glacial refugia. Given the lack of evidence to support
 this hypothesis, we addressed this issue by studying the ecological
 history of Iberian and North African relict A. thaliana. To this end, we
 analysed the relationship between the current habitat suitability of
 relict A. thaliana, estimated with species distribution models, and the
 vegetation dynamics in the region over the last millennia using pollen
 fossil data from sediment cores and reconstructions of past distribution
 ranges of the most important tree species occurring in the region.
 Overall, our results indicated that a higher current habitat suitability
 of relict A. thaliana was correlated with more stable vegetation dynamics
 since the Last Glacial Maximum and during the Holocene. Given that relict
 A. thaliana is known to harbour genetic variation specific to its relict
 nature, we also evaluated the differentiation between relict and
 non-relict A. thaliana accessions at the functional genetic level for the
 known flowering genes, CRY2 and TSF. Genomic surveys detected the
 existence of haplogroups of these genes occurring at very high frequency
 only among relict accessions. Overall, our study reinforced the relict
 character of this lineage thought to be at the base of the species'
 early history. We stress the need to sample in depth other geographic
 areas harbouring relict A. thaliana and conduct further functional genetic
 analyses between relict and non-relict accessions to keep disentangling
 the evolutionary trajectory of this annual plant.
description: Arabidopsis_data_RELICTS_8jul19This file includes the following: (1) the predictors used in the species distribution model, (2) the paleobotanical data of three broad climatic periods (present, Holocene, Young Dryas - Allerod), and (3) the haplogroups of CRY2 and TSF genes obtained from publicly available whole-genome sequences.