cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zs7h44jn5
title: Supplemental data for: Type genomics: a framework for integrating genomic data into biodiversity and taxonomic research

description: Name-bearing type specimens have a fundamental role in characterising
 biodiversity, as these objects represent the physical link between a
 scientific name and the biological organism. Type specimens are usually
 deposited in natural history collections, which provide key infrastructure
 for research on essential biological structures and processes, while
 preserving records of biodiversity for future generations. Modern
 systematics increasingly depends on genetic and genomic data to
 differentiate and characterise species. While the results of genome
 sequencing are often connected to a physical voucher specimen, they are
 rarely derived from the ultimate taxonomic reference for a species, i.e.,
 the name-bearing type specimens. This is a known but under-appreciated
 problem for ensuring the replicability of findings, especially those that
 affect the interpretation of biodiversity distributions and phylogenetic
 relationships. Destructive sampling of museum specimens, particularly of
 type material, often carries a high risk of sequencing failure, and thus
 the cost of damage to the specimen may outweigh the resulting benefit.
 Both taxonomic work and genome sequencing require specialist skills and
 there are often communication gaps between the respective experts. A new,
 harmonised approach, maximising information extraction while minimising
 risk to type specimens, is a critical step forward toward linking
 disciplines across biodiversity research and promoting a better taxonomic
 and systematic understanding of eukaryotic diversity. The genetic make-up
 of a type specimen is a fundamental part of its biological information,
 which can and should be made freely and digitally available through type
 genomics. Here we describe guidelines for the use of nomenclatural types
 in genome sequencing approaches considering different kinds of types in
 different stages of preservation and different data types.
description: # Supplemental data for: Type genomics: a framework for integrating
 genomic data into biodiversity and taxonomic research ### Files and
 variables #### File: Supplement_S1.pdf **Description:** Table S1: hDNA and
 aDNA extraction protocols used for type specimens ## Access information
 Other publicly accessible locations of the data: *
 [https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syaf040/8138649](https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syaf040/8138649)
DOI: 10.5061/dryad.f4qrfj779
title: Data from: Spatiotemporal variation in selection on floral traits related to abortion rate, predispersal seed predation, and fitness variance

description: Spatiotemporal variation in phenotypic selection is important for
 understanding the potential consequences of selection. Variable selection
 on floral traits is common, yet connecting the variation to potential
 drivers of selection is less so. Here, we estimated selection on six
 floral traits of Penstemon digitalis for four populations, with two over
 four years. We also tested whether an extreme year (2012) with an early
 spring affected selection on floral traits. For traits that showed
 evidence of spatiotemporal variation (three), we asked whether variation
 was related to three aspects of their ecology: flower/fruit abortion,
 predispersal seed predation and/or opportunity for selection. Attached
 data includes phenotypic fitness measures used in the main analyses for
 the paper.
description: # Dryad dataset Dataset DOI:
 [10.5061/dryad.f4qrfj779](10.5061/dryad.f4qrfj779) ## Description of the
 data and file structure Phenotypic traits and fitness measures were done
 in four populations of *Penstemon digitalis* (BB, NR TH, WF) in 1-4 years.
 ### Files and variables Single file with all data
 "PhenoData.dryad.csv". Missing values are left blank. year =
 collection year population = one of four values, see publication for
 location details gape.width = width of floral tube opening (mm)
 petal.width = width of centre lower petal at widest point (mm)
 constriction. width = width of the constriction of floral tube near
 nectary at the narrowest point (mm) (not included in publication)
 tube.length = length of floral tube (mm) lines = number of purple lines in
 the corolla tube colour = intensity of colour based on a 4 point ordinal
 scale (0 = no lines, 1 = light, 2 = medium, 3 = dark) pigment =
 lines*colour (estimate used in paper) height = total plant height measured
 at end of season (cm) flowers= total flowers produced fruit = number of
 fruit aborted = number of aborted flowers/fruit damage = number of fruits
 with predispersal seed predator damage fitness = sum of undamaged fruit
 diameter + 1/2 the sum of undamaged fruit diameter as an estimate of
 successful seed production based on the positive correlation between fruit
 diameter and seed number
DOI: 10.15468/dl.az3s5n
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Conocyema polymorpha",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004403-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.51c59zwmc
title: Beyond the surface: Untangling molecular complexity in organic residue analysis of coated archaeological ceramics

description: Mixed molecular and isotopic signals are readily encountered in organic
 residue analysis (ORA) of archaeological ceramics, which can impact our
 ability to identify the contents/use of the vessel. One reason for these
 mixed signals that is rarely considered, is the mixture of organic
 products used to coat vessels and the organic products that were later
 contained in the ceramic vessel. Here, we apply a multi-faceted ORA
 approach to experimental cooking vessels that were coated with a range of
 organic products during post-firing treatment and then used to cook a
 variety of organic contents. Our results show that the visibility of the
 coating agent or cooking commodity varies depending on the type of
 extraction or analytical method applied. We show that it is important to
 use a combination of extraction methods (acidified methanol and solvent
 extraction) and that both molecular and isotopic data must be considered.
 For the first time, we have also shown that thermal transformation markers
 could reflect the post-firing coating as opposed to cooking. We call on
 organic residue analysis specialists to carefully consider the impact of
 post-firing coating before interpreting residues from archaeological
 ceramics and to implement a multi-faceted ORA approach to aid their
 detection.
description: # Beyond the surface: Untangling molecular complexity in organic residue
 analysis of coated archaeological ceramics Dataset DOI:
 [10.5061/dryad.51c59zwmc](10.5061/dryad.51c59zwmc) ## Description of the
 data and file structure This data set is comprised of data files produced
 by Gas Chromatography-Mass Spectrometry (GC-MS) of lipids extracted using
 acid extraction method and solvent extraction methods as described in
 Supplementary Information S2 of the journal article.  These data are
 linked to the published journal where methods of extraction, the context
 of pottery and the interpretation of data are fully described.  Each file
 corresponds to the sample name as recorded in S3 data and the extraction
 method used (Acid extraction- AE or Solvent extraction- TLE) and contains
 a usable mzML. file. which can be opened and converted as necessary in
 open MS software.  To note, the result of the paper are formed from a
 multifaceted analysis. These TIC's are raw TICs to give examples of
 the compounds acquired using GC-MS and HTGC-MS. Specific compounds were
 analysed using selective ion monitoring methods and TAG distributions were
 calculated using FID chromatograms not reported here. Some samples may
 have been diluted and/or re-run for analysis.
DOI: 10.5061/dryad.573n5tbm9
title: Evaluation of federal habitat stewardship projects for aquatic species at risk in Canada: The province of Ontario as a case study

description: The Habitat Stewardship Program (HSP) is a major pillar in Canada’s
 National Strategy for the Protection of Species at Risk that supports
 projects assisting the recovery of species at risk (SAR). To assess
 long-term and biological outcomes and evaluate taxonomic and geographic
 coverage of HSP-funded projects using Ontario as a case study, 95
 HSP-funded projects for aquatic SAR (2006-2017), were evaluated. Fifteen
 million CAD was allocated to 66 habitat stewardship projects targeting
 aquatic SAR. Twenty-nine fish and mussel SAR were targeted in 12
 watersheds located primarily in southwestern Ontario. Greater funding was
 allocated to multi-year projects targeting higher numbers of SAR. Future
 funding should target geographically widespread SAR and SAR-rich
 watersheds in southwestern Ontario. To align stewardship actions with
 aquatic SAR recovery priorities, proposals and reports must identify the
 threats being addressed by stewardship actions. Standardized pre- and
 post-activity monitoring should be required to ensure measurable
 conservation benefits and to enable assessment of the effectiveness of
 habitat stewardship actions. Similar analyses should be undertaken in
 other Canadian provinces and territories to evaluate the HSP nationwide.
description: # Dryad dataset Dataset DOI:
 [10.5061/dryad.573n5tbm9](10.5061/dryad.573n5tbm9) ## Description of the
 data and file structure ### Files and variables #### File:
 cjfas-2025-distribution-data.xls **Description:** Distribution of
 COSEWIC-assessed and SARA-listed Species at Risk in tertiary watersheds of
 Ontario. A value of zero indicates the species is absent, and a value of
 one indicates the species is present. ##### Variables * Common Name:
 Common name of fish and mussel species * Scientific Name: Scientific name
 of fish and mussel species * Watershed code: Four-digit tertiary watershed
 code from the Ontario Watershed Boundaries collection ## Access
 information Data was derived from the following sources: * The dataset was
 created by cross-referencing unpublished data from Nicholas Mandrak with
 current distributions in species-specific COSEWIC and SARA reports.
DOI: 10.5061/dryad.v6wwpzh7q
title: Data from: Macroevolutionary patterns and drivers of skull shape in the global radiation of true toads

description: True toads (Bufonidae) are a highly diverse group of amphibians that have
 dispersed across the globe. This makes them well-suited to exploring
 deep-time patterns of phenotypic evolution on a global scale. However,
 most true toads (former genus Bufo) have long been considered
 morphologically conserved and the adaptive nature of their radiation has
 previously yielded mixed results. We investigated the macroevolutionary
 patterns of the skull in true toads using micro-computed tomography data,
 geometric morphometrics, and comparative methods, and assessed the
 relationship between skull shape and geographical range, as well as
 phylogeny, body size, and habitat, which have previously been suggested as
 important drivers of amphibian cranial evolution. Body size and
 geographical range are identified as key factors influencing skull shape
 in true toads. The assumption that true toads formerly in the genus Bufo
 have highly conserved skulls is challenged by the fact that different
 groups occupy distinct morphospace domains. Early in the evolution of
 large true toads, prior to their global expansion, high morphological
 change and relatively high evolutionary rates resulted in increased
 disparity, which are signs of adaptive radiation.
description: GENERAL INFORMATION 1. Data from: Macroevolutionary patterns and drivers
 of skull shape in the global radiation of true toads By: Tomás Ventura
 & Raúl O. Gómez Proceedings of the Royal Society B
 DOI:10.1098/rspb.2025.2323 SHARING/ACCESS INFORMATION 1.
 Licenses/restrictions placed on the data: None: CC0 1.0 Universal (CC0
 1.0) Public Domain DATA & FILE OVERVIEW 1. File List: A) coords.tps:
 3D coordinates of skull shape in 72 species of true toads in TPS format.
 B) classifiers.csv: species data including ID, species in tree, species,
 group memberships (Group_5; Group_2), geographic range (Area in deg^2^),
 maximum body size category (in mm), body size (in mm), and microhabitat.
 C) PEA23_Bufonidae.phy: phylogenetic tree used in the analyses. D)
 links.csv: links file to be used in the making of transformation grids. E)
 RSCRIPT_PRSB.R: R script used to perform all the analyses. F)
 Ventura_Gomez_tables_figures_ESM.pdf: PDF compiling species data and
 results including Table S1. Micro-CT data of true toads Figure S1.
 Phylogeny of true toads Table S2. Group, geographical rngae, body size,
 and microhabitat data of true toads Table S3. Summary of variance in PCs
 1–5 Table S4. Scores of PCs 1–5 Table S5. Loadings of PCs 1–5 Figure S2.
 Phylomorphospaces of skull shape coloured by group Table S6. Results of
 the Procrustes ANOVA Table S7. Results of the phylogenetic ANOVA Figure
 S3. Phylomorphospaces of skull shape coloured by body size category Table
 S8. Procrustes distances along PC1, branch times, and evolutionary rates
DOI: 10.5061/dryad.hmgqnk9wh
title: Loss of the starvation-and-light fruitbody formation trigger in the myxomycete Physarum roseum

description: Myxomycetes are unicellular amoebozoans that form fruiting bodies to
 reproduce, a process known as sporulation. In the model species Physarum
 polycephalum, plasmodia form fruiting bodies only after several days of
 starvation followed by light exposure. It has long been assumed that the
 same starvation-plus-light trigger applies to the genus Physarum. Recent
 observations of congeners that fail to sporulate under the same conditions
 have raised doubts about this assumption and prompted tentative taxonomic
 reconsideration. Because comparable starvation　and light tests are rare
 for other species of Physarum, their phenotypes and molecular
 mechanisms remain unclear.Consequently, we investigated Physarum rigidum
 and Physarum roseum under starvation and light conditions. Four of the six
 *P. rigidum *plasmodia sporulated by day 6,
 whereas P. roseum did not sporulate within seven days. RNA‑seq
 of P. roseum across nutrient‑rich/starved and
 dark/light conditions revealed differential expression was driven chiefly
 by nutrition; light caused only minor changes and did not elicit the
 transcriptional program characteristic
 of P. polycephalum sporulation. The
 photoreceptor genes that drive sporulation
 in P. polycephalum were not detected
 in P. roseum, and 92 candidate photoreceptor genes
 showed no significant regulation. These findings suggest that P. roseum
 responds only minimally to light stimulation and that the
 starvation‑plus‑light trigger is not universally retained within the genus
 Physarum.
description: # Loss of the starvation-and-light fruitbody formation trigger in the
 myxomycete Physarum roseum Dataset DOI:
 [10.5061/dryad.hmgqnk9wh](10.5061/dryad.hmgqnk9wh) ## Description of the
 data and file structure Spectrum of light under “light conditions” in the
 experimental environment. The photon flux density (PFD) under the
 sporulation-inducing conditions (indirect sunlight through a translucent
 panel with ambient LED room lighting) was measured using a Nippon Medical
 & Chemical Instruments Co., Ltd. Light Analyzer LA-105. The
 measurements were performed by placing the instrument at the exact
 location where plasmodium was positioned for sporulation induction. PFD
 values correspond to the wavelength range 380–780 nm. ### Files and
 variables #### File: ESM_2_light_condition.pdf
 **Description:** Supplementary figure S1. Spectrum of light under “light
 conditions” in the experimental environment. #### File: ESM2.jpeg
 **Description:** Original image data for the spectrum of light under
 “light conditions” in the experimental environment.
DOI: 10.5061/dryad.5tb2rbpg9
title: Data from: Hitting rock bottom: exaptation, ecological filtering and the benthopelagic divergence of Percid fishes

description: Ecological filtering and exaptation are related concepts in which prior
 traits and adaptations facilitate transitions to new habitats or niches,
 sometimes by being co-opted for a new function. I investigated possible
 ecological filtering/exaptation in Percidae, a family of freshwater fishes
 that shows its highest species richness in small benthic fishes living in
 creeks and small streams. I hypothesize that traits associated with
 transitions to benthic living subsequently facilitated the colonization of
 small river habitats. Using phylogenetic comparative approaches, I found
 that transitions in river size were dependent on presence or absence of a
 gas bladder, and long-term residency in small rivers in particular was
 associated with transitions to benthic living. Based on body size and 3D
 whole body shape datasets, I found that selection towards smaller bodies
 and longer caudal peduncles in benthic species in large rivers appears to
 have enabled transitions to small rivers, while also slowing rates of
 shape and size evolution; this may explain the high proportion of small,
 benthic darters. Contrasting selective pressures from habitat exaptation
 and trophic adaptations in small rivers may constrain ecomorphological
 diversification. Overall, ecological filtering and/or exaptation may
 impact both the biodiversity and phylogenetic composition of fish
 assemblages in small streams.
description: # Data from: Hitting rock bottom: exaptation, ecological filtering and the
 benthopelagic divergence of Percid fishes (published in the journal
 Evolution) Authors: Jessica H. Arbour correspondence: Jessica H. Arbour;
 [[jessica.arbour@mtsu.edu](mailto:jessica.arbour@mtsu.edu)] The associated
 dryad repository contains two files: (1) a xlsx file that contains the
 supporting data used for the analyses in the manuscript This file contains
 two tables. "ecological and body size data" includes data on the
 presence/absence of gas bladders, the categorization of large and small
 river habitats, and the maximum observed body size (maximum TL - total
 length - in cm) per species. The second table "geomorph landmark
 data" contains average coordinate data for each species, with
 landmark x, y and z coordinates given in order for each landmark (sensu
 two.d.array from the R package geomorph). (2) a phylogenetic tree file
 corresponding to the taxa in this study. Tree from Arbour and Stanchak
 (2021) "The little fishes that could".
DOI: 10.15468/dl.xzjrhv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Microcyema vespa",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004406-260126135527185/datasets/export for details.
DOI: 10.15468/dl.by92hj
title: Occurrence Download

description: A dataset containing 1636 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lestidae)",
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Continent is North America",
 "Country is one of (United States of America, Canada)",
 "GadmGid is one of (USA.23_1)",
 "OccurrenceStatus is Present",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 1636 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004405-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zsd6gx
title: Occurrence Download

description: A dataset containing 696 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Castilleja litoralis"
 ]
}

 The dataset includes 696 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004407-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5mkkwh7hp
title: The impact of cognitive ability on multitalker speech perception in neurodivergent individuals

description: This is a behavioral dataset obtained from 49 human participants from 3
 different groups: autism, fetal alcohol spectrum disorder, age- and
 sex-matched comparison group. The datafile contains multitalker speech
 perception thresholds across 4 separate runs, as well as performance on
 the Wescler Abbreviated Scale of Intelligence, 2nd Edition.
description: # The impact of cognitive ability on multitalker speech perception in
 neurodivergent individuals Dataset DOI:
 [10.5061/dryad.5mkkwh7hp](10.5061/dryad.5mkkwh7hp) ## Description of the
 data and file structure In this study, we investigated the relationship
 between intellectual ability and speech perception under noisy
 multi-talker conditions. We tested individuals with autism, fetal alcohol
 spectrum disorder, and an age- and sex-matched comparison group, all with
 typical hearing. We found a strong positive correlation between IQ and
 multitalker speech perception thresholds. This data file contains speech
 perception thresholds across 4 runs as well as performance on the Wechsler
 Abbreviated Scale of Intelligence, 2nd Edition.  Please contact Bonnie
 Lau, [blau@uw.edu](mailto:blau@uw.edu) for further information.  ### Files
 and variables #### File: Lau_etal_2025_CRMSentences_datafile.csv
 **Description:**  ##### Variables * Sex * Group * Age at testing reported
 in age bins * Speech Perception Threshold Run 1 * Speech Perception
 Threshold Run 2 * Speech Perception Threshold Run 3 * Speech Perception
 Threshold Run 4 * WASI-II Full Scale IQ -4 * WASI-II Verbal Comprehension
 Index * WASI-II Perceptual Reasoning Index * WASI-II Block Design T-Score
 * WASI-II Vocabulary T-Score * WASI-II Matrix Design T-Score * WASI-II
 Similarities T-Score * ADHD Status - 1 = Has ADHD, 0 = Does not have ADHD,
 -999 - unknown ## Code/software CSV file ## Human subjects data Consent
 from participants was obtained to publish de-identified data in the public
 domain. All names and direct identifiers have been removed from the data
 file.