cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7pvmcvf3x
title: Data and code from: Distinct transmission sites within a synapse for strengthening and homeostasis

description: We used patch-clamp electrophysiology from mouse brain slices to record
 miniature excitatory postsynaptic currents (mEPSC), evoked EPSCs, and
 EPSCs with two-photon glutamate uncaging at single spines (uEPSC) to
 determine the synaptic properties in visual cortex layer 2/3 pyramidal
 neurons during development from postnatal day (P) 10 until P30. Different
 parameters of the synaptic responses, such as amplitude, half-width, and
 frequency of mEPSCs were determined. These data and their analysis are
 documented in the Excel file Data_for_Figures. We also constructed a
 synaptic model to explain our results. The model for silent synapses is
 documented in the Excel file SS_simulation. The synaptic model was
 developed in MatLab, and the code is included in the file Figure_7_code.
 The fitting of the mEPSC amplitude distribution is documented in the file
 Figure_4_code.
description: # Data and code from: Distinct transmission sites within a synapse for
 strengthening and homeostasis
 [https://doi.org/10.5061/dryad.7pvmcvf3x](https://doi.org/10.5061/dryad.7pvmcvf3x) ## Description of the data and file structure Files are stored in matlab (.mat) format or Excel format (.xlsx). They were used to create the fits for the data in Figure 4 and the simulation in Figure 7. See the manuscript for details of parameter space. The file Data_for_Figures.xlsx is organized into sheets. Each sheet is named after the Figure panel for which it contains the data. The columns are generally named by the data set as described in the Figure. In addition, the mean and standard error of the mean (SEM) are presented. n represents the number of neurons, while m represents the number of animals. In some sheets, e.g., Fig. 2B, the data set name is illustrated before the column for SEM. Then, the column with the data set name contains the respective mean values. In some sheets, e.g., Fig 1H, the data is organized into rows. See Figure legends for additional information. The file SS_simulation.xlsx performs the simulation for the failure analysis to assess the % silent synapses. The parameter space for the simulation is entered in the yellow fields. Columns H and further contain the values of each simulated cell with 50 trials in the rows. The column success #syn reports the number of responding synapses and the success #trial reports a success as 1 and failure as 0. 1st and 2nd round are two consecutive simulations for holding the cell at -60mV and NMDA trials is for holding the cell at +40mV. Altogether 20 cells are simulated each round and the results reported in column A to G and rows 15 to 42. The % silent synapses is calculated as described in the methods of the manuscript. ### Files and variables Figure 4 code.zip contains the code for figure 4. Figure 7 code.zip contains the code for figure 7. SS_simulation.xlsx contains the simulation for silent synapses in figure S2 Data_for_Figures.xlsx contains the data for the Figures of the manuscript. ## Code/software Matlab Excel
DOI: 10.5061/dryad.r2280gbnv
title: Empowering regional conservation: Genetic diversity assessments as a tool for eelgrass management

description: To halt the loss of biodiversity, collaboration among scientists, managers
 and decision makers is vital. Although biodiversity loss is a global
 problem, management actions influencing diversity are often on a local to
 regional scale. Our study is an example of a regional conservation genomic
 assessment developed in collaboration between scientists and managers. We
 used 2bRAD sequencing to assess 18 eelgrass (Zostera marina) meadows in
 northwestern Sweden, an area that has experienced large losses of eelgrass
 since the 1980s. Genetic diversity was comparable to other assessed
 meadows in the Atlantic, but an order of magnitude lower than eelgrass in
 the Pacific. All but one meadow showed high rates of sexual reproduction.
 Almost all meadows were divergent but grouped into five genetic clusters.
 Four of the clusters correspond to geographic regions that can be used to
 define management units. Meadows in areas with a high decline in eelgrass
 between the 1980s to 2020s are more inbred than meadows in areas with an
 increase in eelgrass. Overall, our results indicate that striving to
 protect a number of large eelgrass meadows within each genetic cluster is
 important for maintaining genetic diversity and connectivity of eelgrass
 in northwestern Sweden and is likely beneficial for the wider ecosystem.
 We estimate current indicators and essential biodiversity variables and
 discuss their challenges in marine facultative clonal species. We showcase
 how regional-scale conservation genomic assessments can serve as a
 foundation for protection and restoration of a priority species.
description: # Empowering regional conservation: Genetic diversity assessments as a
 tool for eelgrass management * zostera_PRJNA1043091_ALL_5849.vcf.gz vcf
 file including all individuals, with a total of 5849 SNPs and 404 samples
 * zostera_meta_data.tsv Metadata of all individuals region = name of the
 waterbody site = site code = site code indv = individual labels latitude =
 latitude longitude = longitude year = sampling year meadow_type = level of
 impact on meadow meadow_size = if meadow is small&lt;20ha or large &gt;
 20ha MLL = multilocus lineage kept = yes, if the sample is kept after
 clone correction and included in zostera_PRJNA1043091_MLLs_4864.vcf.gz All
 raw sequences are available on the NCBIs Sequence Read Archive (BioProject
 PRJNA1043091)
DOI: 10.5061/dryad.z612jm6nc
title: Data from: Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of Crataegus shandongensis (Rosaceae, Maleae)

description: The recent recognition of the five-subgenera classification within
 Crataegus has prompted discussion about the maternal phylogenetic
 relationships among these subgenera, with inconsistencies in taxon
 sampling, marker selection, and inference methods contributing to
 differing interpretations. In this study, we performed deep genome
 skimming sequencing and assembled 63 whole plastomes, including 58 from
 Crataegus and five from related genera as the outgroups. We employed
 multiple phylogenetic inference methods (Maximum Likelihood and Bayesian
 Inference) to reconstruct an accurate phylogeny. The whole plastome-based,
 maternally inherited trees consistently supported two major clades within
 Crataegus: one comprising C. subg. Crataegus and C. subg.
 Brevispinae, the other encompassing the remaining three subgenera. Within
 the latter clade, C. subg. Sanguineae and C. subg. Americanae formed a
 sister group, which together were sister to C. subg. Mespilus. Our
 analysis also revealed a close maternal relationship between C.
 shandongensis and C. pinnatifida var. major, suggesting shared maternal
 ancestry. Furthermore, we updated the description of C. shandongensis
 based on extensive specimen examination and designated the lectotype for
 this species. This comprehensive taxonomic synopsis, supported by both
 phylogenomic and morphological analyses, provides a robust foundation for
 future taxonomic and evolutionary studies of the Shandong hawthorn.
description: [https://doi.org/10.5061/dryad.z612jm6nc](https://doi.org/10.5061/dryad.z612jm6nc) ## Description of the data and file structure # Data from: Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of *Crataegus shandongensis* (Rosaceae, Maleae) ### Files and variables #### File: Crataegus_whole_plastomes_IQTREE.treefile **Description:** Whole plastome-based phylogenetic backbone of *Crataegus* estimated through maximum likelihood analysis using IQ-TREE2. #### File: Crataegus_whole_plastomes_RAxML.tre **Description:** Whole plastome-based phylogenetic backbone of *Crataegus* estimated through maximum likelihood analysis using RAxML. #### File: Crataegus_whole_plastomes_Mrbayes.tre **Description:** Whole plastome-based phylogenetic backbone of *Crataegus* estimated through Bayesian Inference analysis using MrBayes. #### File: Crataegus.mafft.trimal.fasta **Description:** Alignment of *Crataegus* and outgroups.
DOI: 10.5061/dryad.g79cnp612
title: Nanopore sequencing genomic DNA from Stentor pyriformis and its endosymbiont, Chlorella variabilis

description: Stentor pyriformis are giant, unicellular ciliates that harbor an
 algal endosymbiont that we have identified as Chlorella variabilis. These
 organisms are a new model system for mixotrophy in ciliates, which has
 primarily been studied in Paramecium bursaria and its
 endosymbiont, also Chlorella variabilis. Understanding the similarities
 and differences between the genomes in these endosymbioses will ultimately
 aid our understanding of the evolution of mixotrophy, endosymbiosis, and
 organelle fixation. 
description: Samples were sequenced with an Oxford Nanopore MinION or GridION.
 Draft assemblies and annotation information can be found at https://stentor.ciliate.org/, and are described in the associated preprint.  
description: # Nanopore sequencing genomic DNA from Stentor pyriformis and its
 endosymbiont, Chlorella variabilis
 [https://doi.org/10.5061/dryad.g79cnp612](https://doi.org/10.5061/dryad.g79cnp612) ## Description of the data and file structure *Stentor pyriformis* are an emerging model for studying mixotrophy in ciliates, which is primarily studied in *Paramecium bursaria*. Sequencing and annotating the genomes of both *S. pyriformis,* and its endosymbiont, which we identified as *Chlorella variabilis* (see related work), is important for our understanding of the relationship between these two species.  ### Files #### File: stentor\_DNA.guppy4.2.2\_hac.fastq.gz **Description:** Nanopore DNA sequencing data from Stentor pyriformis #### File: stentor.RNA.guppy4.2.2\_hac.fastq.gz **Description:** Nanopore RNA sequencing data from Stentor pyriformis #### File: chlorella.rna.gridion\_hac.fastq.gz **Description:** Nanopore RNA sequencing data from Chlorella variabilis (endosymbiont of S. pyriformis)  #### File: chlorella.dna.gridion\_hac.fastq.gz **Description:** Nanopore DNA sequencing data from Chlorella variabilis (endosymbiont of S. pyriformis)
DOI: 10.5061/dryad.7sqv9s536
title: Sexual differences in defensive strategies: Investigating chemical defences and visual signals in a wasp moth Amata nigriceps

description: Aposematic animals use conspicuous warning signals to advertise their
 chemical defences to predators. Selection from predators can favour
 conspicuousness and large pattern elements, which enhance predator
 avoidance learning. In aposematic species, conspicuousness often varies
 among individuals. This variation can be explained if conspicuousness
 reflects the levels of chemical defences, if signal production or defence
 acquisition is costly, and if physiological trade-offs and opposing
 selection pressures impose constraints. To understand the link between
 conspicuousness and chemical defences, we must quantify the variability in
 warning signals and identify the chemical compounds involved. Here, we
 examined the warning signal variability and chemical composition of the
 red-necked wasp moth (Amata nigriceps). We photographed the wings of male
 and female moths and analysed their chemical composition using
 ultra-performance liquid chromatography. Females displayed more orange on
 their wings, a trait known to enhance protection against predators. While
 we ruled out the presence of pyrrolizidine alkaloids in adult moths, an
 untargeted metabolomics approach suggests that they sequester other
 compounds, such as steroidal alkaloids and alkylbenzenes, which may serve
 as chemical defences. Females had higher concentrations of these compounds
 than males but ecotoxicology assays with Daphnia showed that male and
 female moths exhibited similar levels of toxicity. 
description: # Sexual differences in defensive strategies: Investigating chemical
 defences and visual signals in a wasp moth Amata nigriceps
 [https://doi.org/10.5061/dryad.7sqv9s536](https://doi.org/10.5061/dryad.7sqv9s536) ## Description of the data and file structure Data and R code for 'Sexual differences in defensive strategies: investigating chemical defences and visual signals in a wasp moth Amata nigriceps' by Binns et al. This research was done using three main methods: analysing morphological (and warning signals) data to compare sexes, comparing targeted and untargeted metabolomics analysis of male and female moths, and using ecotoxicology assays to determine differences between sexes. ### Files and variables #### File: Amata\_sex\_diffs\_analysis\_20241211.zip **Description:** This directory contains three folders for different analyses for this research: Image analysis, Metabolomics analysis and Ecotoxicology analysis. The Image analysis folder contains a database CSV file, the data analysis code and a README.txt explaining code. The Metabolomics analysis folder contains 2 analysis results CSV files, 1 analysis XLSB file, the data analysis code and a README.txt explaining code and analysis files. The Ecotoxicology analysis folder contains 2 database CSV file, the data analysis code and a README.txt explaining code. ## Code/software All code can be run through R. Packages needed to run code are described in each R code file.
DOI: 10.5061/dryad.08kprr5d0
title: Data from: New evidence for the earliest ornithischian dinosaurs from Asia

description: The Early Jurassic ornithischian dinosaurs in Laurasia are dominated by
 armored dinosaurs, with other early ornithischian groups being rare. Here,
 a new taxon, Archaeocursor asiaticus gen. et sp. nov., is reported from
 the Lower Jurassic of southwestern China. Phylogenetic analysis places
 Archaeocursor asiaticus as the earliest-diverging ornithischian dinosaur
 yet discovered in Asia, albeit with weak support. Osteohistological
 analysis of the femoral cross-section suggests that Archaeocursor
 asiaticus was a young adult at the time of death, indicating a small body
 size of approximately 1 meter in body length. This discovery extends the
 known presence of ornithischian dinosaurs in East Asia to the
 Pliensbachian or even late Sinemurian stages. Additionally, it points to
 an earlier dispersal event of Early Jurassic ornithischian dinosaurs from
 Gondwana to Laurasia, including East Asia, which appears to be independent
 of, and possibly earlier than, the dispersal of armored dinosaurs.
description: These files include a data matrix for phylogenetic analysis used
 in the paper, and the supplementary information detailing the collecting
 and analysis of the data set. It also includes additional comparison with
 other ornithischian dinosaurs. 
description: # New evidence for the earliest ornithischian dinosaurs from Asia We have
 submitted the data matrix used for our phylogenetic analysis (Dataset S1.
 tnt), and supplemental information (Supplemental information.docx) for our
 paper. #### Descriptions of the data and file structure **Dataset S1**
 This is a typical TNT file used in our phylogenetic analysis. It includes
 383 morphological characters extracted from 73 taxa (mostly ornithischian
 dinosaurs and a few outgroups). **Supplemental information** This file
 includes supplementing content used to support the conclusion of our
 paper, but which is not suitable for the main context. It includes
 additional comparison with Heterodontosauridae and Silesauridae. Some
 technical details concerning the phylogenetic analyses are also included
 in this file. Software TNT 1.1 is required to run Dataset S1; the
 supplemetal information was created using Microsoft Word.
DOI: 10.15468/dl.h7nwpb
title: Occurrence Download

description: A dataset containing 2742 records in GBIF matching the query:
SELECT
 '504' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 51.21395264452012
 AND decimalLatitude &lt;= 56.135291543055025
 AND decimalLongitude &gt;= -64.759591695172
 AND decimalLongitude &lt;= -53.451504131127514
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 2742 records were derived from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004214-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pugazm
title: Occurrence Download

description: A dataset containing 515 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Herpailurus yaguarondi"
 ]
}

 The dataset includes 515 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004222-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5gk3ya
title: Occurrence Download

description: A dataset containing 11784 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-83.12506 42.10856,-93.05419 41.62289,-96.29196 41.38006,-95.5095 34.14906,-86.63263 31.20809,-81.04749 39.3025,-83.12506 42.10856))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lithobates catesbeianus"
 ]
}

 The dataset includes 11784 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004223-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18407587
title: 3230-temporal-keys covers B-C
DOI: 10.5281/zenodo.18407588
title: 3230-temporal-keys covers B-C
DOI: 10.5061/dryad.wm37pvmz0
title: Nutribloods: Novel synthetic lepidopteran haemolymphs for understanding insect-microbe nutritional interactions in vitro

description: Understanding the role of nutrients in microbial population dynamics
 relies on a sound appreciation of their nutritional environment and how
 this may vary in different habitats. For microbial pathogens and
 commensals, this can be especially challenging because the microbe may
 share nutritional resources with its host. Here we design a series of 20
 synthetic cell-free haemolymphs (nutribloods) that mimic haemolymph
 nutrient profiles of caterpillars fed on one of 20 chemically-defined
 diets, that vary in their protein:carbohydrate (P:C) ratio and caloric
 density. Using these, we are able to simulate the range of nutritional
 conditions that insect blood pathogens might face, providing a model
 system for understanding the role of nutrition in microbial growth. We
 tested this using the entomopathogen, Xenorhabdus nematophila, a
 gram-negative extracellular bacterium of insect hosts. This revealed that
 whilst bacterial fitness peaked in nutriblood nutrient space that was high
 in carbohydrates and low in proteins, levels of amino acids in the
 nutribloods also appear to be an important driving force for bacterial
 growth. Using synthetic haemolymphs that had average levels of all
 nutrients other than carbohydrate, protein or amino acids, we also
 established that bacterial growth is generally enhanced by carbohydrate
 and amino acids but reduced by proteins. Here, we have established a
 tractable model system for examining the role that nutrition plays in the
 growth of an entomopathogenic bacterium. In future work, this model
 host-pathogen system can be used to test a range of nutritionally-driven
 processes, including competition during co-infection and interactions with
 the host microbiome, as well as comparative studies of other
 entomopathogens.
description: All data were collected in a laboratory setting
description: # Nutribloods: Novel synthetic lepidopteran haemolymphs for understanding
 insect-microbe nutritional interactions *in vitro*
 [https://doi.org/10.5061/dryad.wm37pvmz0](https://doi.org/10.5061/dryad.wm37pvmz0) ## Description of the data and file structure These data were generated from experiments designed to establish how bacterial growth (*Xenorhabdus nematophila*) varies in 20 synthetic haemolymphs that differ in their nutritional properties ### Files and variables #### File: dat2\_archive.xlsx **Description:** Bacterial growth in 20 synthetic haemolymphs varying in their nutritional properties. ##### Variables * data are described in a 'Key' sheet in the Excel file #### File: dat10\_archive.xlsx **Description:** Bacterial growth in synthetic haemolymphs in which all nutrients are constant across all haemolymphs except for one nutrient, carbohydrate, protein or amino acids. ##### Variables * data are described in a 'Key' sheet in the Excel file ## Code/software All data are in Excel files ## Access information Other publicly accessible locations of the data: * n/a Data was derived from the following sources: * n/a
DOI: 10.5061/dryad.dr7sqvb7z
title: Data from: Promoting human-carnivore coexistence through outreach in Namibia’s eastern communal conservancies

description: Education and community outreach are fundamental to raising conservation
 awareness in rural communities for alleviating human wildlife conflict
 (HWC). Evaluating the impacts of programs aimed at reducing HWC is
 necessary to justify the effectiveness of mitigation strategies, and to
 provide feedback for designing sustainable conservation initiatives at the
 community level. We examined the impacts of an outreach program in four
 eastern communal conservancies in Namibia using questionnaire surveys
 administered to outreach workshop participants. Most participants
 experienced livestock losses (91.7%), which were caused primarily by
 predators and droughts. Following workshop attendance, significant
 declines in livestock losses were observed and perceptions regarding the
 abundances of predators in the area reflected the reality on the ground
 more accurately. These results suggest that workshops can be effective in
 teaching communities about predator ecology and mitigating depredation
 losses of livestock. Therefore, workshops can be used as an important
 strategy to promote conservation and sustainable livelihoods.
description: The dataset herein was used in an article published in
 <em>Wildlife Biology</em> and was collected through
 questionnaire surveys carried out by the Cheetah Conservation Fund during
 workshops with rural communities in Namibian communal
 conservancies.
description: # Promoting Human-Carnivore Coexistence through Outreach in Namibia’s
 Eastern Communal Conservancies - Supporting DATASET
 [https://doi.org/10.5061/dryad.dr7sqvb7z](https://doi.org/10.5061/dryad.dr7sqvb7z) ## Description of the data and file structure The data represent responses from farmers to questions administered as part of questionnaire surveys carried out by the Cheetah Conservation Fund. The column headings in the MS Excel spreadsheet are self-explanatory. ### Files and variables #### File: CCF\_data\_HWC\_workshops\_121224.xlsx **Description:**  ##### **This is a data file with text (string), date, numeric and Yes/No fields. All data are self-explanatory based on column headings.** ## Code/software The data can be visualized in MS Excel or in R statistical software. ## Access information The data are accessible solely herein on Dryad.