cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9b9c1
title: Data from: Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample

description: Subtribe Spiranthinae is the most species-rich lineage of terrestrial
 Neotropical orchids, encompassing &gt; 500 species and 40 genera. We
 conducted maximum parsimony and maximum likelihood phylogenetic analyses
 of DNA sequence data of plastid matK-trnK and trnL-trnF and nuclear
 ribosomal ITS sequences for 36 genera and 182 species of Spiranthinae plus
 appropriate outgroups. The results strongly support monophyly of
 Spiranthinae (minus Discyphus, Discyphinae and Galeottiella,
 Galeottiellinae) and five major lineages, namely monospecific Cotylolabium
 (sister to the remaining Spiranthinae) and the Eurystyles, Pelexia,
 Spiranthes and Stenorrhynchos clades. Eighteen of the 27 genera of
 Spiranthinae for which more than one species was included in our analyses
 are monophyletic. Paraphyly of large genera, such as Cyclopogon and
 Sarcoglottis, resulted from segregation of particular species or groups of
 species exhibiting minor modifications of structures directly involved in
 pollination (e.g. nectary, rostellum and viscidium). Conversely, polyphyly
 has resulted from convergent evolution of floral attributes in distantly
 related species (e.g. Mesadenus). Some of the morphological characters
 used traditionally for generic delimitation and in non-molecular cladistic
 analyses of Spiranthinae are discussed against the evolutionary framework
 set by our molecular trees, emphasizing putative synapomorphies and
 problems derived from inappropriate character coding or incorrect homology
 assessments. Our ancestral area analysis indicates that Spiranthinae
 originated in eastern South America, with subsequent migrations and
 secondary radiations in Mesoamerica and North America, plus a derived
 migration from the latter region to the Old World (Spiranthes).
description: Combined matrix of
 Spiranthinae and outgroups (matK-trnK, trnL-F and nrITS)Interleaved matrix in
 NEXUS format including nucleotide sequences of matK-trnK (2169
 characters), trnL-F (2002 characters) and nrITS (760 characters)
 regions.matrix
 combined.txt
DOI: 10.17632/sbh6m2yw23.1
title: Hematopoietic stem cells activate a latent differentiation pathway to facilitate recovery after 5-fluorouracil-induced myeloablation

description: Mendeley Data Figures and Tables for Zhang et al., 2025.
DOI: 10.5061/dryad.407tq
title: Data from: Loss of miR-143 and miR-145 in condyloma acuminatum promotes cellular proliferation and inhibits apoptosis by targeting NRAS

description: The expression profile of miRNAs and their function in condyloma
 acuminatum (CA) remains unknown. In this study, we aimed to detect the
 effects of miR-143 and miR-145, the most downregulated in CA samples using
 high-throughput sequencing, on cell proliferation and apoptosis, to
 determine a novel therapeutic target for CA recurrence. RT-qPCR was used
 to validate the lower expression of miR-143 and miR-145 in a larger size
 of CA samples, and the expression of NRAS in CA samples was significantly
 higher than self-controls as determined western blotting assay. Luciferase
 assay was performed to confirm that miR-143 or miR-145 targeted NRAS
 directly. Transduction of LV-pre-miR-143 or LV-pre-miR-145 to human
 papilloma virus (HPV)-infected SiHa cells led to reduced proliferation,
 greater apoptosis, and inhibition of expression of NRAS, PI3Kp110α, and
 pAKT. However, knockout of miR-143 or miR-145 in human epidermal
 keratinocytes (HEKs) by delivery of CRISPR/CAS9-gRNA for target miRNAs
 protected cells from apoptosis and upregulated expression of target genes
 as described above. MiR-143 and miR-145 sensitized cells to nutlin-3a, a
 p53 activator and MDM2 antagonist, while their loss protected cells from
 the stress of nutlin-3a. Furthermore, siRNA targeting NRAS showed similar
 effects on proliferation and apoptosis as miR-143 or miR-145. Taken
 together, our results suggest that loss of miR-143 or miR-145 in CA
 protects HPV-infected cells from apoptosis induced by environmental
 stress, in addition to promoting cellular proliferation and inhibiting
 apoptosis by targeting NRAS/PI3K/ATK. Restoration of miR-143 or miR-145
 might provide an applicable and novel approach to block the recurrence and
 progression of CA.
description: Fw_ Raw data of
 multiArray assay for Treat vs Control
DOI: 10.5061/dryad.2mk56
title: Data from: Positive size-speed relationships in gametes and vegetative cells of Chlamydomonas reinhardtii; implications for the evolution of sperm.

description: It is commonly held that differences in gametes of the two sexes
 (anisogamy) evolved from ancestors whose gametes were similar in size and
 behaviour (isogamy). Underlying many hypotheses explaining anisogamy are
 assumed relationships between cell size and speed in the ancestral
 isogamous population. Using the isogamous alga Chlamydomonas reinhardtii,
 we explored size-speed distributions in vegetative and gamete cells of ten
 cell lines, and clonal data from within two cell lines. We applied an
 independent speed selection approach to gamete populations of C.
 reinhardtii, monitoring correlated responses in size following selection
 for high speed. We demonstrate positive size-speed relationships in
 clones, cell lines and artificially selected speed selection lines. We
 found different size-speed relationships in the two cell types of C.
 reinhardtii even though they overlap in size, suggesting that cell
 composition and/or programs of gene expression are capable of altering
 this relationship, and that the relationship is evolvable. The positive
 genetic size-speed correlation means that the division of parent
 vegetative cells into numerous gametes trades off against not only size
 but also speed, a trade-off that has not received previous attention. Our
 results support re-evaluating the role of speed selection in the evolution
 of anisogamy.
description: Combined data files Seed
 and Tomkins 2018 DRYAD
DOI: 10.5061/dryad.4dp8c
title: Data from: Concede or clash? Solitary sharks competing for food assess rivals to decide.

description: To adapt to their environment, organisms can either directly interact with
 their surroundings or use social information, namely information provided
 by neighbouring individuals. Social information relates to the external
 features of surrounding peers, and little is known about its use by
 solitary species. Here, we investigated the use of social cues in a
 solitary marine predator by creating artificial aggregations of
 free-ranging sicklefin lemon sharks (Negaprion acutidens). Using a novel
 monitoring protocol, we analysed both dominance interactions and tolerance
 associations between sharks competing for food in relation with the
 number, the morphology and the behaviour of rivals. Sharks produced more
 agonistic displays and spent more time around the bait as competitors were
 more abundant. Moreover, the morphological attributes of competitors had
 very limited influence on the structure of shark social interactions.
 Instead, sharks appeared to establish tolerance relationships with
 competitors according to their individual behaviour. Furthermore, the more
 two sharks were observed together at a given study site, the fewer
 agonistic interactions they exchanged. We discuss these findings as
 evidence of the use of social cues in a non-gregarious predatory species
 and suggest directions for future research.
description: _AttributesNEWSharks individual attributes._BehaviorsNEWShark agonistic displays._AssociationsShark tolerance associations._Groups.csv_Time at FeederTime at Cage values.
DOI: 10.5061/dryad.s9r98
title: Data from: How scientists perceive the evolutionary origin of human traits: results of a survey study

description: Various hypotheses have been proposed for why the traits distinguishing
 humans from other primates originally evolved, and any given trait may
 have been explained both as an adaptation to different environments and as
 a result of demands from social organization or sexual selection. To find
 out how popular the different explanations are among scientists, we
 carried out an online survey among authors of recent scientific papers in
 journals covering relevant fields of science (palaeoanthropology,
 palaeontology, ecology, evolution, human biology). Some of the hypotheses
 were clearly more popular among the 1266 respondents than others, but none
 was universally accepted or rejected. Even the most popular of the
 hypotheses were assessed “very likely” by &lt;50 % of the respondents,
 but many traits had 1–3 hypotheses that were found at least moderately
 likely by &gt;70 % of the respondents. An ordination of the hypotheses
 identified two strong gradients. Along one gradient, the hypotheses were
 sorted by their popularity, measured by the average credibility score
 given by the respondents. The second gradient separated all hypotheses
 postulating adaptation to swimming or diving into their own group. The
 average credibility scores given for different subgroups of the hypotheses
 were not related to respondent’s age or number of publications authored.
 However, (palaeo)anthropologists were more critical of all hypotheses, and
 much more critical of the water-related ones, than were respondents
 representing other fields of expertise. Although most respondents did not
 find the water-related hypotheses likely, only a small minority found them
 unscientific. The most popular hypotheses were based on inherent drivers,
 i.e. they assumed the evolution of a trait to have been triggered by the
 prior emergence of another human-specific behavioural or morphological
 trait, but opinions differed as to which of the traits came first.
description: survey1Full data of the survey, except column Country is left empty to prevent identification of individuals. Columns 124-137 are not from the questionnaire but calculated based on other columns (see file survey1_questions).survey1_questionsTitle names and explanations for columns in the surveySurvey data as R objects on Opasnet. Analysis code.Data of the study survey. Data is available as R objects (data.frames) from Opasnet repository by using the code on the linked page. The page also contains the codes that were used to perform the statistical analyses and draw figures of the article.
DOI: 10.5061/dryad.v1d32
title: Data from: Phylogenomics of a rapid radiation: the Australian rainbow skinks

description: Background: The application of target capture with next-generation
 sequencing now enables phylogenomic analyses of rapidly radiating clades
 of species. But such analyses are complicated by extensive incomplete
 lineage sorting, demanding the use of methods that consider this process
 explicitly, such as the multi-species coalescent (MSC) model. However, the
 MSC makes strong assumptions about divergence history and population
 structure, and when using the full Bayesian implementation, current
 computational limits mean that relatively few loci and samples can be
 analysed for even modest sized radiations. We explore these issues through
 analyses of an extensive (&gt;1000 loci) dataset for the Australian
 rainbow skinks. This group consists of 3 genera and 39 described species,
 which likely diversified rapidly in Australia during the mid-late Miocene
 to occupy rainforest, woodland, and rocky habitats with corresponding
 diversity of morphology and breeding colouration. Previous phylogenetic
 analyses of this group have revealed short inter-nodes and high
 discordance among loci, limiting the resolution possible. A further
 complication is that many species have deep phylogeographic structure -
 this poses the question of how to sample individuals within species for
 analyses using the MSC. Results: Phylogenies obtained using concatenation
 and summary coalescent species tree approaches to the full dataset are
 well resolved with generally consistent topology, including for previously
 intractable relationships near the base of the clade. As expected, branch
 lengths at the tips are substantially overestimated using concatenation.
 Comparisons of different strategies for sampling haplotypes for full
 Bayesian MSC analyses (for one clade and using smaller sets of loci)
 revealed, unexpectedly, that combining haplotypes across divergent
 phylogeographic lineages yielded consistent species trees. Conclusions:
 This study of more than 1000 loci provides a strongly-supported estimate
 of the phylogeny of the Australian rainbow skinks, which will inform
 future research on the evolution and taxonomy of this group. Our analyses
 suggest that species tree estimation with the MSC can be quite robust to
 violation of the assumption that the individuals representing a taxon are
 sampled from a panmictic population.
description: archiveArchive containing code and data
DOI: 10.5061/dryad.813mf
title: Data from: Patterns of genome-wide nucleotide diversity in the gynodioecious plant Thymus vulgaris are compatible with recent sweeps of cytoplasmic genes

description: Gynodioecy is a sexual dimorphism where females coexist with hermaphrodite
 individuals. In most cases, this dimorphism involves the interaction of
 cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Two
 scenarios can account for how these interactions maintain gynodioecy.
 Either CMS genes recurrently enter populations at low frequency via
 mutation or migration and go to fixation unimpeded (successive sweeps), or
 CMS genes maintain polymorphism over evolutionary time through
 interactions with a nuclear restorer allele (balanced polymorphism). To
 distinguish between these scenarios, we used transcriptome sequencing in
 gynodioecious Thymus vulgaris and surveyed genome-wide diversity in 18
 naturally occurring individuals sampled from populations at a local
 geographic scale. We contrast the amount and patterns of nucleotide
 diversity in the nuclear and cytoplasmic genome, and find ample diversity
 at the nuclear level (π = 0.019 at synonymous sites) but reduced genetic
 diversity and an excess of rare polymorphisms in the cytoplasmic genome
 relative to the nuclear genome. Our finding is incompatible with the
 maintenance of gynodioecy via scenarios invoking long-term balancing
 selection, and instead suggests the recent fixation of CMS lineages in the
 populations studied.
description: Galaxy9-[F__ORFs]Fasta format file containing contigs with ORFS used in the study. Contigs were a subset of denovo assembly of the transcriptome reads obtained for this study. The raw reads are available from SRA (see original publication for accession numbers)popGenFilt3Tabular text file containing the diversity statistics and extra information on each contig that was polymorphic. See the readme file for details on the meaning of each statistic
DOI: 10.17632/y5577s2f63
title: WOMEN IN JUSTICE AND SECURITY WORLDWIDE

description: The paper examines the evolution of women's roles in these fields throughout history. Initially relegated to secondary roles, women have gained presence and recognition thanks to feminist movements, legal reforms, and gender equality policies. Today, women actively participate in police forces, the military, and the judiciary, facing and overcoming challenges such as discrimination and harassment. Their presence has strengthened the justice and security sectors, contributing to more inclusive and effective approaches to conflict resolution and the administration of justice. Despite the progress, it is important to continue promoting female participation to improve efficiency and equity in these systems globally.
DOI: 10.5061/dryad.h5vk5
title: Data from: Climate change and functional traits affect population dynamics of a long-lived seabird

description: 1. Recent studies unravelled the effect of climate changes on populations
 through their impact on functional traits and demographic rates in
 terrestrial and freshwater ecosystems, but such understanding in marine
 ecosystems remains incomplete. 2. Here, we evaluate the impact of the
 combined effects of climate and functional traits on population dynamics
 of a long-lived migratory seabird breeding in the southern ocean: the
 black-browed albatross (Thalassarche melanophris, BBA). We address the
 following prospective question: ''Of all the changes in the
 climate and functional traits, which would produce the biggest impact on
 the BBA population growth rate?'' 3. We develop a structured
 matrix population model that includes the effect of climate and functional
 traits on the complete BBA life cycle. A detailed sensitivity analysis is
 conducted to understand the main pathway by which climate and functional
 trait changes affect the population growth rate. 4. The population growth
 rate of BBA is driven by the combined effects of climate over various
 seasons and multiple functional traits with carry-over effects across
 seasons on demographic processes. Changes in Sea Surface Temperature (SST)
 during late winter cause the biggest changes in the population growth
 rate, through their effect on juvenile survival. Adults appeared to
 respond to changes in winter climate conditions by adapting their
 migratory schedule rather than by modifying their at-sea foraging
 activity. However, the sensitivity of the population growth rate to SST
 affecting BBA migratory schedule is small. BBA foraging activity during
 the pre-breeding period has the biggest impact on population growth rate
 among functional traits. Finally, changes in SST during the breeding
 season have little effect on the population growth rate. 5. These results
 highlight the importance of early life histories and carry-over effects of
 climate and functional traits on demographic rates across multiple seasons
 in population response to climate change. Robust conclusions about the
 roles of various phases of the life cycle and functional traits in
 population response to climate change rely on an understanding of the
 relationships of traits to demographic rates across the complete life
 cycle.
description: Climate change and
 functional traits affect population dynamics of a long-lived
 seabirdSee Supplementary:
 Climate change and functional traits affect population dynamics of a
 long-lived seabirddryadJENOUVRIER2018.zip
DOI: 10.17632/y5577s2f63.1
title: WOMEN IN JUSTICE AND SECURITY WORLDWIDE

description: The paper examines the evolution of women's roles in these fields throughout history. Initially relegated to secondary roles, women have gained presence and recognition thanks to feminist movements, legal reforms, and gender equality policies. Today, women actively participate in police forces, the military, and the judiciary, facing and overcoming challenges such as discrimination and harassment. Their presence has strengthened the justice and security sectors, contributing to more inclusive and effective approaches to conflict resolution and the administration of justice. Despite the progress, it is important to continue promoting female participation to improve efficiency and equity in these systems globally.
DOI: 10.5061/dryad.75625
title: Data from: Mutation dynamics and fitness effects followed in single cells

description: Mutations have been investigated for more than a century but remain
 difficult to observe directly in single cells, which limits the
 characterization of their dynamics and fitness effects. By combining
 microfluidics, time-lapse imaging, and a fluorescent tag of the mismatch
 repair system in Escherichia coli, we visualized the emergence of
 mutations in single cells, revealing Poissonian dynamics. Concomitantly,
 we tracked the growth and life span of single cells, accumulating ~20,000
 mutations genome-wide over hundreds of generations. This analysis revealed
 that 1% of mutations were lethal; nonlethal mutations displayed a
 heavy-tailed distribution of fitness effects and were dominated by
 quasi-neutral mutations with an average cost of 0.3%. Our approach has
 enabled the investigation of single-cell individuality in mutation rate,
 mutation fitness costs, and mutation interactions.
description: Data from MV and microMA
 experimentsA description of the
 data can be found in the readme file.All_data.zip
DOI: 10.15468/dl.6afqj7
title: Occurrence Download

description: A dataset containing 1782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Laurus novocanariensis"
 ]
}

 The dataset includes 1782 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001526-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.33410
title: Data from: Microenvironment and functional-trait context dependence predict alpine plant community dynamics

description: Predicting the structure and dynamics of communities is difficult.
 Approaches linking functional traits to niche boundaries, species
 co‐occurrence and demography are promising, but have so far had limited
 success. We hypothesized that predictability in community ecology could be
 improved by incorporating more accurate measures of fine‐scale
 environmental heterogeneity and the context‐dependent function of traits.
 We tested these hypotheses using long term whole‐community demography data
 from an alpine plant community in Colorado. Species distributions along
 microenvironmental gradients covaried with traits important for
 below‐ground processes. Positive associations between species
 distributions across life stages could not be explained by abiotic
 microenvironment alone, consistent with facilitative processes. Rates of
 growth, survival, fecundity and recruitment were predicted by the direct
 and interactive effects of trait, microenvironment, macroenvironment and
 neighbourhood axes. Synthesis. Context‐dependent interactions between
 multiple traits and microenvironmental axes are needed to predict
 fine‐scale community structure and dynamics.
description: Appendix 1 Metadata
 (CSV)Appendix 1
 Metadata.csvAppendix 1
 (GRD)Kriged maps of
 microenvironment variables in global coordinates (Arc Grid
 format).Appendix
 1.grdAppendix 1
 (GRI)Kriged maps of
 microenvironment variables in global coordinates (Arc Grid
 format).Appendix
 1.griAppendix 2 Metadata
 (CSV)Appendix 2
 Metadata.csvAppendix 2
 (CSV)Functional trait values
 (means and standard deviations) for species occurring in the plots (CSV
 format with text metadata).Appendix
 2.csvAppendix 3 Metadata
 (CSV)Appendix 3
 Metadata.csvAppendix 3
 (CSV)Complete plant census
 data in all plots for years 2014-2017, transformed into format suitable
 for spatial analyses (CSV format with text metadata).Appendix
 3.csvAppendix 4 Metadata
 (CSV)Appendix 4
 Metadata.csvAppendix 4
 (CSV)Complete census data in
 all plots for years 2014-2017, transformed into format suitable for
 demographic regression (CSV format with text metadata).Appendix
 4.csv