cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.866t1g1nk
title: Potential for powered flight neared by most close avialan relatives but few crossed its thresholds

description: This dataset is the Supplementary Materials of the Pei, Pittman et al.
 (2020) study 'Potential for powered flight neared by most close
 avialan relatives but few crossed its thresholds' in Current Biology
 (https://doi.org/10.1016/j.cub.2020.06.105). In this study, a
 revised phylogeny of coelurosaurian theropod dinosaurs was used to
 reconstruct their potential for powered flight. It found that powered
 flight potential evolved at least three times (once in birds and twice in
 dromaeosaurids) and that many ancestors of close bird relatives neared
 thresholds of powered flight potential. The latter suggests that there was
 broad experimentation with wing-assisted locomotion before theropod flight
 evolved. This dataset contains an expanded version of
 the Theropod Working Group (TWiG) coelurosaurian
 theropod phylogenetic data matrix (revised after Brusatte et al. 2014).
 It also contains the script and results associated with
 an automated parsimony-based phylogenetic analysis of the data
 matrix. This dataset includes the wing loading and specific lift
 proxy data used to reconstruct flight potential in
 the pennaceous feathered pennaraptoran theropods listed
 in the taxon list as well as the results of the parsimony- and
 maximum-likelihood based mapping of these proxies over the reconstructed
 tree topology. Forelimb length [(humerus length + ulna length)/femoral
 length] and body size data are also included as well as the
 results of the parsimony- and maximum-likelihood based mapping of these
 parameters over the same tree topology. Please read the
 following files before navigating the dataset: README.pdf and
 Instructions for zip file use - please read this first.pdf
description: This dataset contains an expanded version of the Theropod Working
 Group (TWiG) coelurosaurian theropod phylogenetic data matrix (revised
 after Brusatte <em>et al</em>. 2014). It also contains the
 script and results associated with an automated parsimony-based
 phylogenetic analysis of the data matrix. This dataset includes the wing
 loading and specific lift proxy data used to reconstruct flight potential
 in the pennaceous feathered pennaraptoran theropods listed in the taxon
 list as well as the results of the parsimony- and maximum-likelihood based
 mapping of these proxies over the reconstructed tree topology. Forelimb
 length [(humerus length + ulna length)/femoral length] and body size data
 are also included as well as the results of the parsimony- and
 maximum-likelihood based mapping of these parameters over the same tree
 topology. 
description: This dataset contains all that is needed to replicate the results
 of the Pei, Pittman <em>et al</em>. study 'Potential for
 powered flight neared by most close avialan relatives but few crossed its
 thresholds'. Please read the following files before navigating the
 dataset: README.pdf and Instructions for zip file use - please read this
 first.pdf
DOI: 10.5061/dryad.mkkwh70wp
title: Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples

description: Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk
 specimen samples is a powerful tool in studies of biodiversity, diet and
 ecological interactions as its inherent labelling of amplicons allows
 sequencing of taxonomically informative genetic markers from many samples
 in parallel. However, the occurrence of so-called ‘tag-jumps’ can cause
 incorrect assignment of sequences to samples and artificially inflate
 diversity. Two steps during library preparation of pools of 5’
 nucleotide-tagged amplicons have been suggested to cause tag-jumps; i) T4
 DNA polymerase blunt-ending in the end-repair step and ii) post-ligation
 PCR amplification of amplicon libraries. The discovery of tag-jumps has
 led to recommendations to only carry out metabarcoding PCR amplifications
 with primers carrying twin-tags to ensure that tag-jumps cannot result in
 false assignments of sequences to samples. As this increases both cost and
 workload, a metabarcoding library preparation protocol which circumvents
 the two steps that causes tag-jumps is needed. Here, we demonstrate
 Tagsteady, a metabarcoding Illumina library preparation protocol for pools
 of nucleotide-tagged amplicons that enables efficient and cost-effective
 generation of metabarcoding data with virtually no tag-jumps. We use pools
 of twin-tagged amplicons to investigate the effect of T4 DNA polymerase
 blunt-ending and post-ligation PCR on the occurrence of tag-jumps. We
 demonstrate that both blunt-ending and post-ligation PCR, alone or
 together, can result in detrimental amounts of tag-jumps (here, up to ca.
 49% of total sequences), while leaving both steps out (the Tagsteady
 protocol) results in amounts of sequences carrying new combinations of
 used tags (tag-jumps) comparable to background contamination.
description: Please see the paper and associated supporting information.
description: Please see the data_overview.xlsx, the paper and its supporting
 information.
DOI: 10.5061/dryad.4tmpg4f6q
title: Supplementary material for: Phylogenomic analysis of ultraconserved elements reveals the recent evolutionary radiation of the fairy wrasses (Teleostei: Labridae: Cirrhilabrus)

description: The fairy wrasses (genus Cirrhilabrus) are among the most captivating and
 successful of the extant wrasse lineages (Teleostei: Labridae), with their
 61 species accounting for nearly 10% of the family. Although species
 complexes within the genus have been diagnosed on the basis of coloration
 patterns and synapomorphies, attempts to resolve the evolutionary
 relationships using molecular and morphological data have largely been
 unsuccessful. Here we use a phylogenomic analysis of 991 ultraconserved
 elements (UCEs) and mitochondrial COI to uncover the evolutionary history
 and patterns of temporal and spatial diversification of the fairy wrasses.
 We find that analyses of concatenated sequences confidently resolve the
 major relationships of Cirrhilabrus. Our analyses of phylogenetic signal
 suggest that extensive gene-tree incongruence is primarily caused by
 estimation error rather than incomplete lineage sorting, leading to poor
 phylogenetic resolution in a summary-coalescent analysis of the data. We
 determine the placements of species that were previously regarded as
 incertae sedis, and find evidence for the nesting of Conniella, an
 unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating
 analysis indicates that the major divergences within the genus occurred
 around the Miocene-Pliocene boundary, followed by extensive cladogenesis
 of species complexes. Biogeographic reconstruction suggests that the fairy
 wrasses emerged within the Coral Triangle, with episodic fluctuations of
 sea levels during glacial cycles coinciding with shallow divergence events
 but providing few opportunities for more sustained widespread dispersal.
 Our study demonstrates both the resolving power and limitations of UCEs
 across shallow timescales, where there is substantial estimation error in
 individual gene trees, in a phylogenetically recalcitrant group of fishes.
DOI: 10.15468/dl.qsx5rf
title: Occurrence Download

description: A dataset containing 79705 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mammalia",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 79705 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002349-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kwh70rz1m
title: Data from: Transcriptome sequencing reveals signatures of positive selection in the spot-tailed earless lizard

description: The continual loss of threatened biodiversity is occurring at an
 accelerated pace. High-throughput sequencing technologies are now
 providing opportunities to address this issue by aiding in the generation
 of molecular data for many understudied species of high conservation
 interest. Our overall goal of this study was to begin building the genomic
 resources to continue investigations and conservation of the Spot-Tailed
 Earless lizard. Here we leverage the power of high-throughput sequencing
 to generate the liver transcriptome for the Northern Spot-Tailed Earless
 Lizard (Holbrookia lacerata) and Southern Spot-Tailed Earless
 Lizard (Holbrookia subcaudalis), which have declined in abundance
 in the past decades, and their sister species, the Common Lesser Earless
 Lizard (Holbrookia maculata). Our efforts produced high quality and robust
 transcriptome assemblies validated by 1) quantifying the number
 of processed reads represented in the transcriptome assembly
 and 2) quantifying the number of highly conserved single-copy
 orthologs that are present in our transcript set using the BUSCO pipeline.
 We found 1,361 1-to-1 orthologs among the
 three Holbrookia species, Anolis carolinensis,
 and Sceloporus undulatus. We carried out dN/dS selection tests
 using a branch-sites model and identified a dozen genes that experienced
 positive selection in the Holbrookia lineage with
 functions in development, immunity, and metabolism. Our single-copy
 orthologous sequences additionally revealed significant pairwise sequence
 divergence (~.73%) between the Northern H. lacerata and
 Southern H. subcaudalis that further supports
 the recent elevation of the Southern Spot-Tailed Earless Lizard to full
 species.
description:
DOI: 10.5061/dryad.brv15dv6w
title: Data from: Sperm quality, aggressiveness and generation turnover can facilitate unidirectional Y chromosome introgression across the European house mouse hybrid zone

description: The widespread and locally massive introgression of Y chromosomes of the
 eastern house mouse (Mus musculus musculus) into the range of the western
 subspecies (M. m. domesticus) in Central Europe calls for an explanation
 of its underlying mechanisms. Given the paternal inheritance pattern,
 obvious candidates for traits mediating the introgression are characters
 associated with sperm quantity and quality. We can also expect traits such
 as size, aggression, or the length of generation cycles to facilitate the
 spread. We have created two consomic strains carrying the non-recombining
 region of the Y chromosome of the opposite subspecies, allowing us to
 study introgression in both directions, something impossible in nature due
 to the unidirectionality of introgression. We analysed several traits
 potentially related to male fitness. Transmission of the domesticus Y onto
 the musculus background had negative effects on all studied traits.
 Likewise , domesticus males possessing the musculus Y had, on average,
 smaller body and testes and lower sperm count than the parental strain.
 However, the same consomic males tended to produce less dissociated sperm
 heads, to win more dyadic encounters, and to have shorter generation
 cycles than pure domesticus males. These data suggest the domesticus Y is
 disadvantageous on the musculus background while introgression in the
 opposite direction can confer a recognizable, though not always
 significant, selective advantage. Our results are thus congruent with the
 unidirectional musculus→domesticus Y chromosome introgression in Central
 Europe. In addition to some previous studies, they show this to be a
 multifaceted phenomenon demanding a multidisciplinary approach.
DOI: 10.5281/zenodo.17783000
title: Automatic Composite Laying Dataset

description: This dataset supports research efforts in the field of anomaly detection and diagnosis. 

The system on which the data was recorded is the Multi-Layer in use at the Swinburne-CSIRO Industry 4.0 Testlab in Melbourne, Australia. It is composed of multiple laying head, each with their own dataset. The actlayer, layup and state files provide the metadata necessary to map the laying head data with the process status. The power consumption file records the entire power consumption of the system throughout the production operation.
DOI: 10.5281/zenodo.17783001
title: Automatic Composite Laying Dataset

description: This dataset supports research efforts in the field of anomaly detection and diagnosis. 

The system on which the data was recorded is the Multi-Layer in use at the Swinburne-CSIRO Industry 4.0 Testlab in Melbourne, Australia. It is composed of multiple laying head, each with their own dataset. The actlayer, layup and state files provide the metadata necessary to map the laying head data with the process status. The power consumption file records the entire power consumption of the system throughout the production operation.
DOI: 10.15468/dl.jn4szs
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ateleia apetala",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002390-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k98sf7m3z
title: Macroevolution of flower color patterning: biased transition rates and correlated evolution with flower size

description: Floral pigmentation patterns can both mediate plant-pollinator
 interactions and modify the abiotic environment of reproductive
 structures. To date there have been no inquiries into the rate and
 directionality of macroevolutionary transitions between patterned and
 non-patterned petals despite their ecological importance and ubiquity
 across angiosperms. Petals in the Potentilleae tribe (Rosaceae) display
 color patterns in the ultraviolet (UV) and human-visible spectrum, or can
 be uniform in color (i.e., patternless). Using a phylogeny of
 Potentilleae, I test whether evolutionary transition rates between
 patterned and non-patterned petals are biased in either direction. I then
 examine whether UV and human-visible patterns are phylogenetically
 correlated and test the prediction that color patterns will evolve in
 concert with larger flowers if they function as guides to orient
 pollinators to floral rewards. I found that transition rates were biased
 toward petals that were uniform in color. Transition rates from patterned
 to uniformly-colored petals were two and six times higher than the reverse
 for UV and human-visible pattern, respectively. The presence of UV and
 human-visible pattern evolved independently from one another. However, the
 evolution of human-visible pattern was associated with the evolution of
 larger flowers but the evolution of UV pattern was correlated with the
 evolution of smaller flowers. I posit that the transition bias towards
 non-patterned flowers may reflect developmental constraints on spatial
 regulation of pigments required to produce floral color patterning. The
 correlated evolution of larger flowers and human-visible pigmentation
 patterns support the hypothesis that nectar or pollen guides are more
 likely to evolve in larger-flowered species. This work provides insight
 into how transition rate bias and trait correlations can shape
 phylogenetic patterns of floral color pattern diversity.
description: The multiphylo object, R script, and data input are provided for
 comparative analyses associated with manuscript entitled,
 "Macroevolution of flower color patterning: biased transition rates
 and correlated evolution with flower size"
DOI: 10.5061/dryad.612jm641c
title: Integrating functional connectivity in designing networks of protected areas under climate change: a caribou case-study

description: Land-use change and climate change are recognized as two main drivers of
 the current biodiversity decline. Protected areas help safeguard the
 landscape from additional anthropogenic disturbances and, when properly
 designed, can help species cope with climate change impacts. When designed
 to protect the regional biodiversity rather than to conserve focal species
 or landscape elements, protected areas need to cover a representative
 sample of the regional biodiversity and be functionally connected,
 facilitating individual movements among protected areas in a network to
 maximize their effectiveness. We developed a methodology to define
 effective protected areas to implement in a regional network using
 ecological representativeness and functional connectivity as criteria. We
 illustrated this methodology in the Gaspésie region of Québec, Canada. We
 simulated movements for the endangered Atlantic-Gaspésie caribou
 population (Rangifer tarandus caribou), using an individual-based model,
 to determine functional connectivity based on this large mammal. We
 created multiple protected areas network scenarios and evaluated their
 ecological representativeness and functional connectivity for the current
 and future conditions. We selected a subset of the most effective network
 scenarios and extracted the protected areas included in them. There was a
 tradeoff between ecological representativeness and functional connectivity
 for the created networks. Only a few protected areas among those available
 were repeatedly chosen in the most effective networks. Protected areas
 maximizing both ecological representativeness and functional connectivity
 represented suitable areas to implement in an effective protected areas
 network. These areas ensured that a representative sample of the regional
 biodiversity was covered by the network, as well as maximizing the
 movement over time between and inside the protected areas for the focal
 population.
description: Starting from a published individual based model (Bauduin et al.
 2016; Ecological Modelling), we simulated movements for the endangered
 Atlantic-Gaspésie caribou population (<i>Rangifer tarandus
 caribou</i>) to determine functional connectivity based on this
 large mammal. We created multiple protected areas network scenarios and
 evaluated their ecological representativeness and functional connectivity
 for the current and future conditions. We selected a subset of the most
 effective network scenarios and extracted the protected areas included in
 them.
DOI: 10.5061/dryad.6q573n5wh
title: Data from: More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing

description: Non-invasive genotyping methods have become key elements of wildlife
 research over the last two decades, but their widespread adoption is
 limited by high costs, low success rates, and high error rates. The
 information lost when genotyping success is low may lead to decreased
 precision in animal population densities, which could misguide
 conservation and management actions. Single nucleotide polymorphisms
 (SNPs) provide a promising alternative to traditionally used
 microsatellites as SNPs allow amplification of shorter DNA fragments, are
 less prone to genotyping errors, and produce results that are easily
 shared among laboratories. Here, we outline a detailed protocol for
 cost-effective and accurate noninvasive SNP genotyping using multiplexed
 amplicon sequencing optimized for degraded DNA. We validated this method
 for individual identification by genotyping 216 scats, 18 hairs and 15
 tissues from coyotes (Canis latrans) using 26 SNPs. Our genotyping success
 rate for scat samples was 93%, and 100% for hair and tissue, representing
 a substantial increase compared to previous microsatellite-based studies
 while remaining at a low cost of under $5 per PCR replicate (excluding
 labor). The accuracy of the genotypes was further corroborated in that
 genotypes from scats matching known, GPS-collared coyotes were always
 located within the territory of the known individual. We also show that
 different levels of multiplexing produced similar results, but that PCR
 product cleanup strategies can have substantial effects on genotyping
 success. By making noninvasive genotyping more affordable, accurate, and
 efficient, this research may allow for a substantial increase in the use
 of noninvasive methods to monitor and conserve free-ranging wildlife
 populations.
DOI: 10.15468/dl.t7fcxd
title: Occurrence Download

description: A dataset containing 626 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Romania",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lucanus cervus"
 ]
}

 The dataset includes 626 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002392-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4paspg
title: Occurrence Download

description: A dataset containing 5276470 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((-82 30,-83 30,-83 29,-82 29,-82 30))",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 5276470 records from 609 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002370-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g79cnp5mx
title: Significant Differences in Ginkgotoxin among Nuts of 4 Ginkgo Cultivar Groups

description: 39 cultivars of ginkgo nuts were used to detect the content of
 ginkgotoxin, and were divided into 4 cultivar groups, including the main
 nut cultivars in China. The results showed that there was no significant
 correlation between different cultivars and ginkgotoxin content, however,
 there were significant differences between the 4 cultivar groups
 (P&lt;0.05). The ginkgotoxin content of 39 ginkgo cultivars ranged
 from 330.25 μg∙g-1 to 525.79 μg∙g-1. MPN accounts for most of the
 ginkgotoxin, from 54% to 95%. The ginkgotoxin content of 4 cultivar groups
 was ranked as Changzi, Fozhi, Zhongzi, Yuanzi. The correlation between
 ginkgotoxin and different cultivar groups was explored for the first time.
 Based on this finding, people can preliminarily determine the level of
 ginkgotoxin, which provides help and convenience for daily consumption.
description: The nuts of 39 ginkgo
 cultivars were collected from the National Ginkgo Seed Base of Pizhou,
 Xuzhou City, Jiangsu Province, China. Excellent cultivars of branches were
 collected from all parts of China and Japan, and rafted with 5-year-old
 seedlings 2-3 m high as rootstock in the 1990s. We selected a moderately
 growing tree from each cultivar to collect nuts in October 2019. The nuts
 coat was removed after morphology coefficient was measured. The endosperm
 was freeze-dried at -60 °C, crushed and ground, and then passed through a
 50-mesh sieve. We
 determined the ginkgotoxin content of nuts by HPLC with reference to the
 detection method of Liu, Y. et al. Took 0.5 g dry nuts powder, add 20 mL
 ultrapure water, shocked, 120 min, 10000 rꞏmin<sup>-1</sup>
 centrifugal supernatant on 10 min after collecting, repeat twice. The
 twice collected supernatant was passed through 0.22 microns filter
 membrane and then fixed volume to 50 mL for later use. Liquid
 chromatography mobile phase A: 5 mM potassium phosphate solution
 containing 5 mM sodium pentane sulfonate, pH was to 2.5 with phosphoric
 acid; mobile phase B: acetonitrile. The column temperature was 30 °C, the
 injection volume was 20 μL, the retention time was 40 min, and the flow
 rate was 1 mL·min<sup>-1</sup>. The detection conditions were:
 fluorescence emission wavelength 395 nm, excitation wavelength 295
 nm.