cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s4mw6m94b
title: Sex-linked markers by genome-wide RAD sequencing to identify XX/XY Sex Chromosomes in the spiny frog (Quasipaa boulengeri)

description: We use genotyping by sequencing as an approach to identify sex-linked
 markers in the spiny frog Quasipaa boulengeri with 43 wild-collected
 adults from a single site. The GBS methodology identified 2 loci on sex
 differences in allele frequencies, 50 loci on sex differences in
 heterozygosity, and 523 loci on male-limited occurrence, altogether
 associated with males heterogamety, indicating an XX-XY system. The sex
 specificity of five markers was further validated by PCR amplification
 with a large number of additional individuals from 26 various populations
 in this species. A total of 27 sex linkage markers were matched to Dmrt1
 gene, a ubiquitous role in sex determination and differentiation from
 flies and nematodes to mammals. Chromosome 1, that harboring Dmrt1, has
 further been assigned to a highly potential candidate sex chromosome in
 anurans. Five sex-linked SNP makers explored 3 sex reversals out of 133
 individuals here, sparsely showing sex reversal detected in wild amphibian
 populations.
description: Genomic DNA of the 43 samples from a single site (DYYEC) was
 subjected to GBS by the Novogene. Clean Illumina reads were demultiplexed,
 trimmed, and filtered by the process_radtags function in STACKS [v 2.4]. e
 used RStudio 1.2.1335 to generate candidate alleles for each
 individual. 
description: <strong>catalog.fa.gz, catalog.tags.tsv.gz</strong> The files generated by the Stacks operation, by changing the parameters M (M controls the number of mismatches allowed between the two alleles of a heterozygote sample), m (m controls the number of identical reads required to initiate a new putative allele) and n (n controls the number of mismatches allowed between any two alleles of the population). Depending on the data set, gapped alignments may provide more loci for the analysis.  <strong>matches.zip</strong> Stacks will generate a matches file for each sample through operation comparison. By analyzing these matches files, you can find the depth of each site. <strong>populations.sumstats.tsv</strong> The populations program outputs a summary file for each site of the population. Can be grouped according to needs (such as male and female). <strong>Quasipaa_ boulengeri_Sex_linked_marker</strong> Sex-linked markers were screened with three approaches followed by Brelsford et al. (2017), respectively based on (i) sex differences in allele frequencies, (ii) sex differences in heterozygosity, and (iii) sex-limited occurrence. We used RStudio 1.2.1335 to generate candidate alleles for each individual. <strong>sequences.zip</strong> The primer design method was adopted for four sex-linked sites. After amplification in additional samples (10♀10♂) respectively from three populations, the PCR products were sequenced at Sangon Sequencing Center (Shanghai, China).
DOI: 10.21223/p3/tnnryw
title: Dataset for: Advanced clones of B3C0, group B3, population B in Comas-Peru

description: B3C0 is the initial cycle of recombination of group B3- Population B. This population has been derived from population A. R genes have been eliminated from this group and horizontal resistance has been retained. Currently, these clones are being used on the variety selection in developing countries. This group of clones were planted in a randomized complete block design (RCBD) with 2 replicates at Comas, located at 2400 to 2788 masl in Junin situated in the Central mountain ranges in Peru. The trials were established at Comas due to the high disease pressure of late blight present in the area and used to screen selected potato genotypes for resistance to this disease.
DOI: 10.5061/dryad.k0p2ngf5g
title: Land-use change erodes trophic redundancy in tropical forest streams: Evidence from amino acid stable isotope analysis

description: Studies have shown that food chain length is governed by interactions
 between species richness, ecosystem size, and resource availability. While
 redundant trophic links may buffer impacts of species loss on food chain
 length, higher extinction risks associated with predators may result in
 bottom-heavy food webs with shorter food chains. The lack of consensus in
 earlier empirical studies relating species richness and food chain length
 reflects the need to account robustly for the factors described above. In
 response to this, we conducted an empirical study to elucidate impacts of
 land-use change on food chain length in tropical forest streams of
 Southeast Asia. Despite species losses associated with forest loss at our
 study areas, results from amino acid isotope analyses showed that food
 chain length was not linked to land use, ecosystem size or resource
 availability. Correspondingly, species losses did not have a significant
 effect on occurrence likelihoods of all trophic guilds except herbivores.
 Impacts of species losses were likely buffered by high levels of initial
 trophic redundancy, which declined with canopy cover. Declines in trophic
 redundancy were most drastic amongst invertivorous fishes. Declines in
 redundancy across trophic guilds were also more pronounced in wider and
 more resource-rich streams. While our study found limited evidence for
 immediate land-use impacts on stream food chains, the potential loss of
 trophic redundancy in the longer term implies increasing vulnerability of
 streams to future perturbations, as long as land conversion continues
 unabated.
DOI: 10.5061/dryad.wh70rxwjv
title: Data from: TAS2R20 variants confer dietary adaptation to high-quercitrin bamboo leaves in Qinling giant pandas

description: Sensitivity to bitter tastes provides animals with an important means of
 interacting with their environment and thus, influences their dietary
 preferences. Genetic variants encoding functionally distinct receptor
 types contribute to variation in bitter taste sensitivity. Our previous
 study showed that two nonsynonymous sites, A52V and Q296H, in the TAS2R20
 gene are directionally selected in giant pandas from the Qinling
 Mountains, which are speculated to be the causative base-pair changes of
 Qinling pandas for the higher preference for bamboo leaves in comparison
 with other pandas. Here, we used functional expression in engineered cells
 to identify agonists of pTAS2R20 (i.e. giant panda’s TAS2R20) and
 interrogated the differences in perception in the in vitro responses of
 pTAS2R20 variants to the agonists. Our results show that pTAS2R20 is
 specifically activated by quercitrin and that pTAS2R20 variants exhibit
 differences in the sensitivity of their response to the agonist. Compared
 to pTAS2R20 in pandas from other areas, the receptor variant with A52V and
 Q296H, which is most commonly found in Qinling pandas, confers a
 significantly decreased sensitivity to quercitrin. We subsequently
 quantified the quercitrin content of the leaves of bamboo distributed in
 the Qinling Mountains, which was found to be significantly higher than
 that of the leaves of bamboo from panda habitats in other areas. Our
 results suggest that the decreased sensitivity to quercitrin in Qinling
 pandas results in higher-quercitrin-containing bamboo leaves to be tasting
 less bitter to them and thus, influences their dietary preference. This
 study illustrates the genetic adaptation of Qinling pandas to their
 environments and provides a fine example of the functional effects of
 directional selection in the giant panda.
description: We quantified the contents of quercitrin in the leaves of
 <i>B. fargesii </i>and<i> F.
 qinlingensis</i>,<i> </i>consumed in the diet of Qinling
 pandas, and in the leaves of <i>F. denudate </i>and<i>
 B. faberi</i>, consumed in the diet of pandas from other areas. The
 quercitrin content of <i>F.</i>
 <i>qinlingensis</i> leaves was the highest among the four
 examined bamboo species, reaching 222.3 ng/mg, followed by that of
 <i>B. fargesii </i>at<i> </i>143.7 ng/mg. In
 contrast, the quercitrin contents quantified in <i>F.
 denudata</i> and <i>B. faberi</i> leaves were 98.2 ng/mg
 and 66.4 ng/mg, respectively, which are much lower than those of the two
 bamboo species sampled in the Qinling Mountains (P &lt;
 0.05).
DOI: 10.5061/dryad.7wm37pvq4
title: Evolution of social organization: phylogenetic analyses of ecology and sexual selection in weavers

description: Crook published a landmark study on the
 social organization of weavers (or weaverbirds, family
 Ploceidae) that contributed to the emergence of sociobiology, behavioral
 ecology, and phylogenetic comparative methods. By comparing ecology,
 spatial distribution, and mating systems, Crook suggested that the spatial
 distribution of food resources and breeding habitats influence weaver
 aggregation, both during the breeding season (colonial vs solitary
 breeding) and non-breeding season (flocking vs solitary foraging), and
 the food resources distribution and breeding aggregation of
 individuals in turn impact mating systems and sexual selection.
 Although Crook’s study stimulated much follow-up research, his conclusions
 have not been scrutinized using phylogenetically
 controlled analyses. We revisited Crook’s hypotheses using modern
 phylogenetic comparative methods and an extended dataset of 107 weaver
 species. We showed that both diet
 and habitat type are associated with spatial
 distribution and the latter predicts mating
 system, consistent with Crook’s propositions. The best
 supported phylogenetic path model (PPA) also supported Crook’s arguments,
 and uncovered a direct relationship between non-breeding distribution and
 mating system. Taken together, our phylogenetically corrected
 analyses confirm Crook’s conjectures on the roles of ecology in social
 organizations of weavers; however, our analyses also uncovered an
 association between non-breeding distributions and mating systems, which
 was not envisaged by Crook.
DOI: 10.5061/dryad.3j9kd51dz
title: Data for: Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems

description: Advancements in the field of synthetic biology have been possible due to
 the development of genetic tools that are able to regulate gene
 expression. However, the current toolbox of gene regulatory tools for
 eukaryotic systems have been outpaced by those developed for simple,
 single-celled systems. Here, we engineered a set of gene regulatory tools
 by combining self-cleaving ribozymes with various upstream competing
 sequences that were designed to disrupt ribozyme self-cleavage. As a
 proof-of-concept, we were able to modulate GFP expression in mammalian
 cells, and then showed the feasibility of these tools in Drosophila
 embryos. For each system, the fold-reduction of gene expression was
 influenced by the location of the self-cleaving ribozyme/upstream
 competing sequence (i.e. 5′ vs. 3′ untranslated region) and the competing
 sequence used. Together, this work provides a set of genetic tools that
 can be used to tune gene expression across various eukaryotic systems.
description: Confocal microscopy
description: Refer to the manuscript (open access) for name designations.
DOI: 10.5281/zenodo.17193783
title: Repository of "Do 3D Dynamic Rupture Models Capture the Variability in Long-Period Velocity Pulses? Insights from the 2023 Mw 7.8 Kahramanmaraş Earthquake"

description: This Zenodo repository contains the SeisSol input files needed to reproduce the simulations presented in the paper "Do 3D Dynamic Rupture Models Capture the Variability in Long-Period Velocity Pulses? Insights from the 2023 Mw 7.8 Kahramanmaraş Earthquake", as well as the Shahi & Baker (2014) Pulse Extraction Algorithm used in this study, and the supplementary movies from this study.
DOI: 10.5281/zenodo.17193784
title: Repository of "Do 3D Dynamic Rupture Models Capture the Variability in Long-Period Velocity Pulses? Insights from the 2023 Mw 7.8 Kahramanmaraş Earthquake"

description: This Zenodo repository contains the SeisSol input files needed to reproduce the simulations presented in the paper "Do 3D Dynamic Rupture Models Capture the Variability in Long-Period Velocity Pulses? Insights from the 2023 Mw 7.8 Kahramanmaraş Earthquake", as well as the Shahi & Baker (2014) Pulse Extraction Algorithm used in this study, and the supplementary movies from this study.
DOI: 10.5061/dryad.fbg79cnrx
title: Data from: Black-capped chickadees (Poecile atricapillus) can identify individual females by their fee-bee songs

description: Individual recognition is a social behavior that occurs in many bird
 species. A bird’s ability to discriminate among familiar and unfamiliar
 conspecifics is critical to avoid wasting resources such as time and
 energy during social interactions. Black-capped Chickadees are able to
 discriminate individual female and male chick-a-dee calls, potentially
 male and female tseet calls, and male fee-bee songs. In the current study,
 we used an operant discrimination go/no-go paradigm to determine whether
 female and male chickadees could discriminate between fee-bee songs
 produced by individual female chickadees as well as test which song
 component(s) enable this discrimination. Birds trained on natural
 categories—the songs of different females—learned to respond to rewarded
 stimuli more quickly than birds trained on random groupings of female
 songs and were able to transfer this learning to new songs from the same
 categories. Chickadees were also able to generalize their responding when
 exposed to the bee note of the fee-bee song of rewarded individuals; they
 did not generalize to fee notes. Our results provide evidence that
 Black-capped Chickadees can use female-produced fee-bee songs for
 individual recognition. However, the acoustic features underlying
 individual recognition require further investigation.
description: The dataset was collected through custom operant
 conditing programming outputs into excel files and then processed through
 SPSS.
DOI: 10.15468/dl.rkf92d
title: Occurrence Download

description: A dataset containing 15313 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Butterfly distribution records for the UK from Butterfly Conservation, up to 2019",
 "TaxonKey is Riodinidae",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 15313 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002319-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18385846
title: RITHM Dataset : Robotic Inductive Tasks to monitor Human Mental state

description: This dataset contains multimodal recordings collected during a human–robot interaction experiment. Thirty participants took part in two experimental sessions, each involving two interaction tasks.

The dataset includes continuous physiological recordings (EEG, ECG, EDA, PPG), behavioral performance measures (response times, accuracy), and subjective ratings of mental effort.

Data were originally acquired using the Lab Streaming Layer (LSL) framework and recorded with LabRecorder. The recordings were subsequently converted to Brain Imaging Data Structure (BIDS)–compatible formats. EEG data are provided in EDF format, while peripheral physiological signals are provided in both EDF and tab-separated value (TSV) formats. Event markers corresponding to stimuli and participant responses are provided as TSV files.

The dataset is organized according to the BIDS specification and contains continuous, non-epoched recordings without filtering or artifact rejection. While BIDS standards are primarily defined for neural data (e.g., EEG), the same organizational principles were consistently extended to peripheral physiological signals to ensure coherence across modalities.

This dataset is intended to support research on cognitive effort during human–robot interaction, using both modality-specific and multimodal signal analyses. It is particularly suited for investigating inter-individual variability as well as differences across sessions and tasks.
DOI: 10.5281/zenodo.18385845
title: RITHM Dataset : Robotic Inductive Tasks to monitor Human Mental state

description: This dataset contains multimodal recordings collected during a human–robot interaction experiment. Thirty participants took part in two experimental sessions, each involving two interaction tasks.

The dataset includes continuous physiological recordings (EEG, ECG, EDA, PPG), behavioral performance measures (response times, accuracy), and subjective ratings of mental effort.

Data were originally acquired using the Lab Streaming Layer (LSL) framework and recorded with LabRecorder. The recordings were subsequently converted to Brain Imaging Data Structure (BIDS)–compatible formats. EEG data are provided in EDF format, while peripheral physiological signals are provided in both EDF and tab-separated value (TSV) formats. Event markers corresponding to stimuli and participant responses are provided as TSV files.

The dataset is organized according to the BIDS specification and contains continuous, non-epoched recordings without filtering or artifact rejection. While BIDS standards are primarily defined for neural data (e.g., EEG), the same organizational principles were consistently extended to peripheral physiological signals to ensure coherence across modalities.

This dataset is intended to support research on cognitive effort during human–robot interaction, using both modality-specific and multimodal signal analyses. It is particularly suited for investigating inter-individual variability as well as differences across sessions and tasks.
DOI: 10.5061/dryad.6hdr7sqxh
title: Data from: Threats to aquatic taxa in an arid landscape: knowledge gaps and areas of understanding for amphibians of the American Southwest

description: This dataset contains supporting information for WIREs
 Water Advanced Review: "Threats to aquatic taxa in an arid
 landscape: knowledge gaps and areas of understanding for amphibians of the
 American Southwest", by Mims et al., published in 2020
 (doi.org/10.1002/wat2.1449). Please see the original article for
 additional information, and contact Dr. Meryl Mims (mims@vt.edu) with
 questions or specific requests.
DOI: 10.5061/dryad.6q573n5w6
title: Data from: The functional roles of species in metacommunities, as revealed by metanetwork analyses of bird-plant frugivory networks

description: Understanding how biodiversity and interaction networks change across
 environmental gradients is a major challenge in ecology. We integrated
 metacommunity and metanetwork perspectives to test species’ functional
 roles in bird-plant frugivory interactions in a fragmented forest
 landscape in Southwest China, with consequences for seed dispersal.
 Availability of fruit resources both on and under trees created vertical
 feeding stratification for frugivorous birds. Bird-plant interactions
 involving birds feeding only on the tree or both on and under the tree
 (shared) had a higher centrality and contributed more to metanetwork
 organization than interactions involving birds feeding only under the
 tree. Moreover, bird-plant interactions associated with large-seeded
 plants disproportionately contributed to metanetwork organization and
 centrality. Consequently, on-the-tree and shared birds contributed more to
 metanetwork organization whereas under-the-tree birds were more involved
 in local processes. We would expect that species’ roles in the metanetwork
 will translate into different conservation values for maintaining
 functioning of seed-dispersal networks.
description: Across the 13 forest patches and 2 years, we recorded 47 bird
 species, involving 134 unique interactions with 19 plant
 species. - patch:
 patch ID - Higher level: Bird -
 Lower level: Plant - Animal: bird species
 Plant: plant species Mode:
 Frugivory freq: Total number of visits with frugivory
 interactions by a given bird
DOI: 10.6084/m9.figshare.31164520
title: ReCoVer 2/2

description: Pictures from <i>Acropora spathulata</i> colonies from New Caledonia and Coral Sea atolls collected within the project ReCoVer.Samples metadata can be accessed through GEOME portal: https://n2t.net/ark:/21547/R2650
DOI: 10.6084/m9.figshare.31164520.v1
title: ReCoVer 2/2

description: Pictures from <i>Acropora spathulata</i> colonies from New Caledonia and Coral Sea atolls collected within the project ReCoVer.Samples metadata can be accessed through GEOME portal: https://n2t.net/ark:/21547/R2650
DOI: 10.5061/dryad.qrfj6q5cb
title: Data from: Dynamic ice loss from the Greenland Ice Sheet driven by sustained glacier retreat

description: Here we share remotely-sensed Greenland outlet glacier data for 234
 individual glaciers. Data include observations of mena monthly discharge
 (ice volume flux exported by the glacier), front position changes,
 velocity, and ice thickness for the 1985-2018 period. Data will be
 periodically updated as needed.   The Greenland Ice Sheet is
 losing mass at accelerated rates in the 21st century, making it the
 largest single contributor to rising sea levels. Faster flow of outlet
 glaciers has substantially contributed to this loss, with the cause of
 speedup, and potential for future change, uncertain. Here we combine more
 than three decades of remotely sensed observational products of outlet
 glacier velocity, elevation, and front position changes over the full ice
 sheet. We compare decadal variability in discharge and calving front
 position and find that increased glacier discharge was due almost entirely
 to the retreat of glacier fronts, rather than inland ice sheet processes,
 with a remarkably consistent speedup of 4-5% per km of retreat across the
 ice sheet. We show that widespread retreat between 2000 and 2005 resulted
 in a step-increase in discharge and a switch to a new dynamic state of
 sustained mass loss that would persist even under a decline in surface
 melt.
description: Methods are described in the following open-access
 manuscript: King, M., <em>et
 al</em>. Dynamic ice loss from the Greenland Ice Sheet
 driven by sustained glacier retreat, <em>Nature Comms Earth and
 Environ., <strong>1</strong>, (2020).</em>
  
description: Please see the documentation in the readme.txt for
 usage. Contact Michalea King (michaleaking@gmail.com)
 for questions on usage or additional details. As a
 condition of using these data, you kindly ask you use the following
 citation: King, M., <em>et
 al</em>. Dynamic ice loss from the Greenland Ice Sheet
 driven by sustained glacier retreat, <em>Nature Comms Earth and
 Environ., <strong>1</strong>, (2020).</em>