cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mw6m90635
title: Chlamydomonas cilia proteins

description: Axonemal dyneins are highly complex molecular motors that power ciliary
 motility. These multi-subunit enzymes are assembled at dedicated sites
 within the cytoplasm. At least nineteen cytosolic factors are specifically
 needed for the generation of dynein holoenzymes and/or their trafficking
 to the growing cilium. Many proteins are subject to N-terminal processing
 and acetylation which can generate degrons subject to the AcN-end rule and
 alter N-terminal electrostatics, generate new binding interfaces, and
 affect subunit stoichiometry through targeted degradation. Here we have
 used mass spectrometry of cilia samples and electrophoretically purified
 dynein heavy chains from Chlamydomonas to define their N-terminal
 processing; we also detail the N-terminal acetylase complexes present in
 this organism. We identify four classes of dynein heavy chain based on
 their processing pathways by two distinct acetylases one of which is
 dependent on methionine aminopeptidase activity. In addition, we find that
 one component of both the outer dynein arm intermediate/light chain
 subcomplex and the docking complex are processed to yield an unmodified
 Pro residue which may provide a setpoint to direct the cytosolic
 stoichiometry of other dynein complex subunits that contain N-terminal
 degrons. Thus, we identify an additional level of processing and
 complexity in the pathways leading to axonemal dynein formation in
 cytoplasm. 
description: These data were generated from whole cilia and
 electrophoretically purified dynein heavy chains digested with trypsin or
 Asp-N using an Orbitrap Eclipse mass spectrometer and positive mode
 electrospray ionization. Data were searched against the
 <em>Chlamydomonas</em> v.6.1 proteome. 
description: # Chlamydomonas cilia proteins
 [https://doi.org/10.5061/dryad.mw6m90635](https://doi.org/10.5061/dryad.mw6m90635) These are scaffold files that contain the proteomic data for whole cilia and electrophoretically purified axonemal dynein heavy chains from Chlamydomonas. ## Description of the data and file structure Four scaffold files are uploaded. 1. "Whole Cilia" - Chlamydomonas cilia digested with trypsin or endoproteinase AspN. 2. "Dynein Heavy Chains" - Electrophoretically purified wildtype Chlamydomonas axonemal dynein heavy chains digested with trypsin. 3. "Dynein Heavy Chains 2" - Electrophoretically purified wildtype Chlamydomonas axonemal dynein heavy chains digested with trypsin. 4. "AspN-digested Dynein Heavy Chains: - Electrophoretically purified wildtype and oda2 Chlamydomonas axonemal dynein heavy chains digested with endoproteinase AspN.
DOI: 10.5061/dryad.jm63xsjhh
title: List of 131 harlequin toad species (in alphabetical order) with information on occurence, population status 2004 and 2022, threats, IUCN Red List status and contributing experts

description: Biodiversity loss is extreme in amphibians. Despite ongoing conservation
 action, it is difficult to determine where we stand in overcoming their
 extinction crisis. Among the most threatened amphibians are the 131
 Neotropical harlequin toads. Many of them declined since the 1980s with
 several considered possibly extinct. Recently, more than 30 species have
 been rediscovered, raising hope for a reversing trend in the amphibian
 extinction crisis. We use past and present data available for harlequin
 toads (Atelopus), to examine whether the amphibian extinction crisis is
 still in an emergency state. Since 2004 no species has improved its
 population status, suggesting that recovery efforts have not been
 successful. Threats include habitat change, pathogen spread and climate
 change. More mitigation strategies need implementation, especially habitat
 protection and disease management, combined with captive conservation
 breeding. With harlequin toads serving as a model, it is clear that the
 amphibian extinction crisis is still underway.
description: Compilation of data from conservationists.
description: # Supplementary Table 1. List of 131 harlequin toad species (in
 alphabetical order) with information on occurence, population status 2004
 and 2022, threats, IUCN Red List status and contributing experts.
 [https://doi.org/10.5061/dryad.jm63xsjhh](https://doi.org/10.5061/dryad.jm63xsjhh) This table compiles information from experts on *Atelopus* population trends as in March 2004 and December 2022. ## Description of the data and file structure The table is a simple excel file. ## Sharing/Access information Not applicable. ## Code/Software Not applicable
DOI: 10.15468/dl.97x8nt
title: Occurrence Download

description: A dataset containing 560 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Polycarpaea nivea"
 ]
}

 The dataset includes 560 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003714-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u4eut3
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "OccurrenceStatus is Present",
 "TaxonKey is Polycarpaea robusta"
 ]
}

 The dataset includes 89 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003716-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ht76hdrng
title: Limnomysis benedeni ingestion rate in different prey

description: Understanding the diet preferences and food selection of invasive species
 is crucial to better predict their impact on community structure and
 ecosystem functioning. Limnomysis benedeni, a Ponto-Caspian
 invasive mysid shrimp, is one of the most successful invaders in numerous
 European river and lake ecosystems. While existing studies suggest
 potentially strong trophic impact due to high predation pressure on native
 plankton communities, little is known of its food selectivity between
 phyto- and zooplankton, under different food concentrations. Here, we
 therefore investigated the feeding selectivity
 of L. benedeni on two commonly occurring prey organisms
 in freshwaters, the small rotifer zooplankton Brachionus
 calyciflorus together with the
 microphytoplankton Cryptomonas sp. present in increasing
 densities. Our results demonstrated a clear shift in food selection,
 with L. benedeni switching
 from B. calyciflorus to Cryptomonas sp. already
 when the two prey species were provided in equal biomasses. Different
 functional responses were observed for the two food types, indicating
 somewhat different foraging mechanisms for each food type. These findings
 provide experimental evidence on the feeding flexibility of invasive mysid
 shrimps and potential implications for trophic interactions in invaded
 ecosystems.
description: # *Limnomysis benedeni* ingestion rate in different prey
 [https://doi.org/10.5061/dryad.ht76hdrng](https://doi.org/10.5061/dryad.ht76hdrng) The experiment was conducted at *21*°C temperature for a total duration of 14 hours in lab conditions using two different prey types and *Limnomysis benedeni* as predator. The aim of the study was to yield a better understanding of the impact of phytoplankton and zooplankton density on the diet preference of *L. benedeni.* To do this, we compared the ingestion rates of *L. benedeni* on food mixtures containing a rotifer and a microalga, across increasing algal biomass. The dataset has the algae number, rotifer number and the calculations for the ingestion rate of these prey types by *Limnomysis benedeni*. ## Description of the data and file structure No abbreviations have been used in the dataset. Columns A to AO are related to ingestion rate calculations and columns AQ to AW are related to Ivlev's selectivity coefficient.
DOI: 10.15468/dl.jkb94r
title: Occurrence Download

description: A dataset containing 612 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((0.258131873551685 46.12925514911446, 0.264461260546458 46.127823833488875, 0.263591860740393 46.12431229398505, 0.264934079679457 46.123849076334565, 0.261512006418888 46.121145474668296, 0.265785726759824 46.11978523207976, 0.262712967786314 46.11278315277209, 0.268311087119028 46.11254681296448, 0.267875358594336 46.109535900981925, 0.274752291594625 46.10889663919231, 0.270107842789102 46.10116502029881, 0.266435118440126 46.10237498121883, 0.266023287642558 46.100448570063016, 0.262250823851524 46.09825460244303, 0.274207299417868 46.09479961407109, 0.283415171830526 46.094649243860275, 0.285205904740993 46.093190104405615, 0.288449800916421 46.09529317674394, 0.291381691135925 46.093486386901084, 0.298765118525372 46.09803595805054, 0.305598745948761 46.09977161450413, 0.302957003460175 46.10226683188891, 0.301873685045942 46.106704705521615, 0.31298596564485 46.11825893059459, 0.312465969175168 46.12258137870779, 0.308641277693689 46.123234995448854, 0.301546938939794 46.12776896157621, 0.297054945314157 46.126752972029315, 0.288919167495543 46.1304865061445, 0.277208173765516 46.12958903731894, 0.268353483978635 46.13135137146303, 0.258131873551685 46.12925514911446))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 612 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003717-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x46z3c
title: Occurrence Download

description: A dataset containing 1344 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Plumeria rubra",
 "Year 1000-2026"
 ]
}

 The dataset includes 1344 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003715-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.p2ngf1vxm
title: Site entropy mapped to PB1 structure

description: The influenza virus polymerase is central to influenza virus evolution.
 Adaptive mutations within the polymerase are often a prerequisite for
 efficient spread of novel animal-derived viruses in human populations. The
 polymerase also determines fidelity, and therefore the rate at which the
 virus will acquire mutations that lead to host range expansion, drug
 resistance, or antigenic drift. Despite its importance to viral
 replication and evolution, our understanding of the mutational effects and
 associated constraints on the influenza RNA-dependent RNA polymerase
 (RdRp) is relatively limited. We performed deep mutational scanning of the
 A/WSN/1933(H1N1) PB1, generating a library of 95.4% of amino acid
 substitutions at 757 sites. After accuracy filters, we were able to
 measure replicative fitness for 13,354 (84%) of all possible amino acid
 substitutions, and 13 were validated by results from pairwise competition
 assays. Functional and structural constraints were better revealed by
 individual sites involved in RNA or protein interactions than by major
 subdomains defined by sequence conservation. Mutational tolerance, as
 defined by site entropy, was correlated with evolutionary potential, as
 captured by diversity in available H1N1 sequences. Of 29 beneficial sites,
 many have either been identified in the natural evolution of PB1 or shown
 experimentally to have important impacts on replication and adaptation.
 Accessibility of amino acid substitutions by single nucleotide mutation
 was a key factor in determining whether mutations appeared in natural PB1
 evolution. Our work provides a comprehensive map of mutational effects on
 a viral RdRp and a valuable resource for subsequent studies of influenza
 replication and evolution.
description: The deposited data is a .cxs file, which can be viewed on the
 UCSF Chimera structural analysis program. Details of the data and analysis
 are in the manuscript linked to this data.
description: # Site Entropy Mapped to PB1 Structure
 [https://doi.org/10.5061/dryad.p2ngf1vxm](https://doi.org/10.5061/dryad.p2ngf1vxm) This is a file that allow visualization of site entropy values on the PB1 structure in UCSF Chimera, as described in the accompanying paper
DOI: 10.5061/dryad.4f4qrfjjr
title: Whole genome sequence and annotation of Penstemon davidsonii

description: Penstemon is the most speciose flowering plant genus endemic to North
 America. Penstemon species' diverse morphology and adaptation to
 various environments have made them a valuable model system for studying
 evolution, but the absence of publicly available reference genomes limits
 possible research directions. Here we report the first reference genome
 assembly and annotation for Penstemon davidsonii. Using PacBio long-read
 sequencing and Hi-C scaffolding technology, we constructed a de novo
 reference genome of 437,568,744 bases, with a contig N50 of 40 Mb and L50
 of 5. The annotation includes 18,199 gene models, and both the genome and
 transcriptome assembly contain over 95% complete eudicot BUSCOs. This
 genome assembly will serve as a valuable reference for studying the
 evolutionary history and genetic diversity of the Penstemon genus.
description: # Whole genome sequence and annotation of Penstemon davidsonii
 These are files associated
 with the reference genome and annotation for *Penstemon davidsonii*. ##
 Description of the data and file structure There are 4 files included
 here: P_davidsonii_2022_v1.1.gff = annotation file
 P_davidsonii_2022_Trinity_transcriptome.fasta = transcriptome file
 P_davidsonii_2022_v1.1.fasta = genome reference file
 P_davidsonii_2022_v1.1.fasta.fai = genome reference index file For
 information about how the files were created, please read the manuscript.
 ## Sharing/Access
 information The raw sequencing data used to produce the above (PacBio WGS,
 Hi-C, & RNA-seq) have been deposited into the NCBI Sequence Read
 Archive under the accession number PRJNA1010203. ## Code/Software Note
 that the PATHs will need to be changed to run these scripts.
 P_davidsonii_2022_canu_clr.sh = Assembles genome used HiCanu v2.1
 P_davidsonii_2022_ccs.sh = Generates HiFi reads from the Pacbio
 subreads.bam P_davidsonii_2022_busco_slurm.sh = Assesses completeness of
 assembly using BUSCO P_davidsonii_2022_annotation_scripts.sh = Aligns
 RNA-seq to the genome, runs RepeatModeler and RepeatMasker, assembles
 transcriptome, and annotates the genome using Maker
DOI: 10.5061/dryad.fqz612jzh
title: Spontaneous quantity discrimination in Sleepy lizards

description: In this study, we tested 8 Sleepy-lizards (Tiliqua rugosa asper) on their
 ability to spontaneously choose the larger of two quantities based on
 continuous or discrete information. We recorded the lizards'
 identity, weight (g) and snout-vent length (mm). As we tested lizards in
 two batches (groups), we also recorded if they belonged to group A or B.
 In regards to the experiment, we recorded session (day), trial (1-12),
 stage (preference test or quantity discrimination), date of the test day
 and start time of the first trial, the test (continuous or discrete) and
 the comparison. We measured lizards' choice behaviour by recording
 the choice of the quantity as well as a binary version that represented
 the choice of the larger quantity as 1 and the smaller choice as 0.
 Finally, we also quantified the time it took lizards to make a choice from
 trial videos in seconds (latency). NA values indicate either no data or no
 choice. We analysed the choice behaviour using the binary choice data and
 also the latency to understand if lizards were able to discriminate
 quantities and if they showed a speed-accuracy trade-off. We provide
 trial-by-trial raw data in a horizontal format. How to transpose the data
 set into a vertical format and details regarding further calculations and
 statistical analyses can be found on OSF, doi: 10.17605/OSF.IO/PR46D
description: Data were collected in a Y-maze and the first choice of each
 individual recorded. Additionally, we also recorded the latency to choice
 from videos.
description: # Spontaneous quantity discrimination in Sleepy lizards
 [https://doi.org/10.5061/dryad.fqz612jzh](https://doi.org/10.5061/dryad.fqz612jzh) In this study, we tested 8 Sleepy-lizards (Tiliqua rugosa asper) on their ability to spontaneously choose the larger of two quantities either based on continuous our discrete information. ### Rugosa\_quantity\_discr\_raw.csv Raw data file with individual data for each trial performed in the experiment. Variables * Date – Variable for transposition (removed later) * session - Test session (1-17) * trial - Test trial given within a session (preference test: 13 trials, quantity discrimination test: 12 trials) * stage - pref = preference test, quantity = quantity discrimination test * ID – Individual identity * group - A or B, test batch * SVL - Lizard snout-vent length in mm * weight - Lizard weight in g * date - Date the session was conducted * start - Start time of the session for each lizard * test - Continuous or discrete * comp - Comparison tested in each trial (8 versus 2, 2 versus 6, 8 versus 4, 2 versus 4, 4 versus 6, 6 versus 8) * latency - Latency to choice in sec * binchoice - Preference test: 0 = left choice, 1 = right choice; quantity discrimination test:0 if the smaller quantity was chosen, 1 if the larger quantity was chosen * choice - Preference test: L = left choice, R = right choice; quantity discrimination test = actually quantity chosen in each trial
DOI: 10.5061/dryad.gtht76hst
title: The tolerance of a keystone ecosystem engineer to extreme heat stress is hampered by microplastic leachates

description: Plastic pollution and ongoing climatic changes exert considerable pressure
 on coastal ecosystems. Unraveling the combined effects of these two
 threats is essential to management and conservation actions to reduce the
 overall environmental risks. We assessed the capacity of a coastal
 ecosystem engineer, the blue mussel Mytilus edulis, to cope with various
 levels of aerial heat stress (20, 25, 30, and 35°C) after exposure to
 substances leached from beached and virgin low-density polyethylene
 pellets. Our results revealed a significant interaction between
 temperature and plastic leachates on mussel survival rates. Specifically,
 microplastic leachates had no effect on mussel survival at 20, 25 and
 30°C. In turn, mussel survival rates significantly decreased at 35°C, and
 this decrease was even more significant following exposure to leachates
 from beached pellets; these pellets had a higher concentration of
 additives compared to the virgin ones, potentially causing a bioenergetic
 imbalance. Our results stress the importance of adopting integrated
 approaches combining the effects of multiple environmental threats on key
 marine species to understand and mitigate their potential synergistic
 effects on ecosystem dynamics and resilience in the face of the changing
 environment.
description: # The tolerance of a keystone ecosystem engineer to extreme heat stress is
 hampered by microplastic leachates This file contains the data required to
 reproduce analyses and figures reported in the associated manuscript. ##
 File Description ### **S7\_Temperature\_Plastic\_data.xlsx:** This Excel
 file contains a dataset that results from 72h immersion-emersion
 experiments at 20°C with the second emersion where the mussels were
 exposed to the control temperature (20°C) or a low (25°C), moderate (30°C)
 or high (35°C) aerial heat stress event. It includes data for Control,
 virgin, and beached microplastic leachate (respectively, V-MPL and B-MPL)
 solutions. This file is used to produce the statistical analyses and
 figures in the manuscript and Supporting Information. Note that the
 experiment was designed to mimic the typical tidal cycle at the sampling
 site (i.e., 6 hours immersion/emersion). For each experimental treatment
 (temperature × solution), 20 mussels were used in triplicates. For more
 information see the Material and methods of the article. #### Variables *
 **Solution** = Treatment group: "Control" for Control,
 "V-MPL" for Virgin microplastic leachate treatment and
 "B-MPL" for Beached microplastic leachate treatment *
 **Temperature** = Second emersion temperature (°C) * **Replicate** =
 Replicate number * **Time** = Exposure time in hours *
 **Surviving_number** = Number of Surviving mussels * **Surviving_rate** =
 Proportion of surviving mussels (%)
DOI: 10.15468/dl.z53abc
title: Occurrence Download

description: A dataset containing 2720 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Crataegus",
 "OccurrenceStatus is Present",
 "Geometry POLYGON((8.4 44.6, 11.5 44.6, 11.5 46.7, 8.4 46.7, 8.4 44.6))"
 ]
}

 The dataset includes 2720 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003719-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n3wr32
title: Occurrence Download

description: A dataset containing 90 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Polycarpaea smithii"
 ]
}

 The dataset includes 90 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003718-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.