cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tqjq2bvwk
title: Nonrandom missing data can bias PCA inference of population genetic structure

description: Population genetic studies in non-model systems increasingly use
 next-generation sequencing to obtain more loci, but such methods also
 generate more missing data that may affect downstream analyses. Here we
 focus on the Principal Component Analysis (PCA) which has been widely used
 to explore and visualize population structure with mean-imputed missing
 data. We simulated data of different population models with various total
 missingness (1%, 10%, 20%) introduced either randomly or biased among
 individuals or populations. We found that individuals biased with missing
 data would be dragged away from their real population clusters to the
 origin of PCA plots, making them indistinguishable from true admixed
 individuals and potentially leading to misinterpreted population
 structure. We also generated empirical data of the big brown bat
 (Eptesicus fuscus) using restriction site-associated DNA sequencing
 (RADseq). We filtered three data sets with 19.12%, 9.87%, and 1.35% total
 missingness, all showing nonrandom missing data with biased individuals
 dragged towards the PCA origin, consistent with results from simulations.
 We highlight the importance of considering missing data effects on PCA in
 non-model systems where nonrandom missing data are common due to varying
 sample quality. To help detect missing data effects, we suggest to 1) plot
 PCA with a color gradient showing per sample missingness, 2) interpret
 samples close to the PCA origin with extra caution, 3) explore filtering
 parameters with and without the missingness-biased samples, and
 4) use complementary analyses (e.g., model-based methods) to
 cross-validate PCA results and help interpret population structure.
description: These are the filtered vcf data sets (bat1, bat10, bat20) used
 for empirical analyses in this study. The corresponding sample information
 (including museum catalogues) are provided in Table S1 of the
 journal's online supplementary material.
DOI: 10.5061/dryad.h70rxwdgj
title: QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient

description: Local adaptation is the process by which natural selection drives adaptive
 phenotypic divergence across environmental gradients. Theory suggests that
 local adaptation results from genetic trade-offs at individual genetic
 loci, where adaptation to one set of environmental conditions results in a
 cost to fitness in alternative environments. However, the degree to which
 there are costs associated with local adaptation is poorly understood
 because most of these experiments rely on two-site reciprocal transplant
 experiments. Here, we quantify the benefits and costs of locally adaptive
 loci across 17° of latitude in a four-grandparent outbred mapping
 population in outcrossing switchgrass (Panicum virgatumL.), an emerging
 biofuel crop and dominant tallgrass species. We conducted quantitative
 trait locus (QTL) mapping across 10 sites, ranging from Texas to South
 Dakota. This analysis revealed that beneficial biomass (fitness) QTL
 generally incur minimal costs when transplanted to other field sites
 distributed over a large climatic gradient over the 2 y of our study.
 Therefore, locally advantageous alleles could potentially be combined
 across multiple loci through breeding to create high-yielding regionally
 adapted cultivars.
description: This is the phenotype and genotype files for the quantitative
 trait locus (QTL) mapping that was conducted in the study. The input files
 are formatted for anlysis in the program Genstat (VSN
 International, Genstat for Windows (VSN International,
 Hemel Hempstead,
 UK, ed.
 19, 2017)<em>)</em>, which is how they were analyzed in our study.
DOI: 10.5068/d16h37
title: The start sites of sequences of 18S and 25S rRNA found to be exonuclease resistant as indicated by oligo attachment

description: Abstract   Background We have previously reported 18S and 25S
 ribosomal RNA molecules in Candida albicans resistant to processive 5´→3´
 exonuclease, appearing as cells approached stationary growth phase.
 Initial analysis pointed to extra phosphate(s) at their 5’- end raising
 the possibility that they were newly transcribed. Here we report on
 additional experiments exploring this possibility and try to establish
 which of the RNA polymerases may be transcribing them. Results
 Oligo-ligation and primer extension again showed the presence of extra
 phosphate at 5’-end at or near the reported processing sites for both 18S
 and 25S ribosomal RNA components. Inhibition of Pol I with BMH-21
 increased the presence of the molecules.  Quantitation with an
 Agilent Bioanalyzer showed that resistant 18S and 25S molecules are
 primarily produced in the nucleus.  Utilizing an RNA cap specific
 antibody, a signal could be detected on these molecules via
 immunoblotting; such signal could be eliminated by decapping reaction.
 Both the cap specific antibody and eIF4E cap-binding protein, increased
 fold enrichment upon quantitative amplification. Antibodies specific for
 the RNA Polymerase II c-terminal domain and TFIIB initiator factor showed
 the presence of Pol II on DNA sequences for both 18S and 25S molecules in
 chromatin precipitation and qPCR assays.  Rapamycin inhibition of
 TOR complex also resulted in an increase of resistant 18S and 25S
 molecules. Conclusions These data raise the possibility of a role for RNA
 Polymerase II in the production of 18S and 25S molecules and indicate that
 efforts for more direct proof may be worthwhile.  If definitively
 proven it will establish an additional role for RNA Polymerase II in
 ribosomal production.  
description: Sequences were obtained from various RNA samples (extracted from
 <em>C. albicans</em> at stationary growth phase) using
 distinct primers specifically designed for either 18S or 25S rRNAs. 
 Several sequences are included and each one is highlighted where the oligo
 has been attached,
DOI: 10.5281/zenodo.15658546
title: Dataset for Linear Ubiquitination of NMDA Receptor GluN2A Subunit Facilitates the GluN2B-to-GluN2A Switch and Synaptic Maturation

description: This Zenodo deposit provides the blot scans, image analysis macros, and quantification data generated for the study published in Proceedings of the National Academy of Sciences of the United States of America (PNAS), “Linear ubiquitination of the NMDA receptor GluN2A subunit facilitates the GluN2B-to-GluN2A switch and synaptic maturation” (DOI: 10.1073/pnas.2515389123), by Yuanyuan Chu, Yiwen Xu, Maoqing Huang, Xueying Fang, Xinying Huang, Zhengwei Yao, Jian Wu, Ning Zhou, Kaiwen He, Yanfen Liu, and Tong Wang;

 The record includes two ZIP files: ZIP 1 contains the image analysis macros, and ZIP 2 contains the original blot scans and the corresponding quantification data.
DOI: 10.6086/d1wq1r
title: Supplement 1: Challenges Faced by Neurology Trainees in a Neuro-Intervention Career Track

description: Introduction: The widespread adoption of endovascular therapy (EVT) for
 emergent large vessel occlusion (LVO) has led to increased nationwide
 demand for neuro-interventionalists, heightened interest among Neurology
 residents to pursue neuro-intervention (NI) as a career, and increased
 importance of NI exposure for all Neurologists who care for patients with
 AIS. Currently, exposure to NI and its career path are not well-defined
 for Neurology trainees. Methods: The Society for Vascular and
 Interventional Neurology (SVIN) Education Committee conducted a
 multi-center electronic survey directed towards Neurology residents,
 Vascular Neurology (VN), Neuro-critical care (NCC) and NI fellows in June
 2018. 250 programs were invited to participate; 76 trainees completed the
 survey. Results: Respondents self-identified as 22% PGY-2, 40% PGY-3/4,
 30% VN fellows, and 8% NI or NCC fellows. 87% of trainees had greater than
 2 months exposure to VN during residency, 41% to NCC and only 3% to NI.
 68% of respondents had no exposure to NI during residency. While 72% felt
 that a background in Neurology was good preparation for NI, only 41%
 agreed that fellowship training pathway in NI is well structured for
 Neurology residents when compared to other sub-specialties. Conclusion: In
 this survey, respondents identified lack of exposure to NI and a
 well-defined training pathway as obstacles towards pursuing NI as a
 career. These obstacles must be addressed for the continued development of
 NI as a sub-specialty of Neurology.
description: This dataset was collected as a SurveyMonkey sent out to
 Neurology residents and fellows in June 2018.
DOI: 10.5061/dryad.v9s4mw6st
title: Data from: An assessment of sampling designs using SCR analyses to estimate abundance of boreal caribou

description: Accurately estimating abundance is a critical component of monitoring and
 recovery of rare and elusive species. Spatial capture-recapture (SCR)
 models are an increasingly popular method for robust estimation of
 ecological parameters. We provide an analytical framework to assess
 results from empirical studies to inform SCR sampling design, using both
 simulated and empirical data from non-invasive genetic sampling of seven
 boreal caribou populations (Rangifer tarandus caribou) which varied in
 range size and estimated population density. We use simulated population
 data with varying levels of clustered distributions to quantify the impact
 of non-independence of detections on density estimates, and empirical
 datasets to explore the influence of varied sampling intensity on the
 relative bias and precision of density estimates.  Simulations
 revealed that clustered distributions of detections did not significantly
 impact relative bias or precision of density estimates. The genotyping
 success rate of our empirical dataset (n = 7,210 samples) was 95.1%, and
 1,755 unique individuals were identified. Analysis of the empirical data
 indicated that reduced sampling intensity had a greater impact on density
 estimates in smaller ranges. The number of captures and spatial recaptures
 were strongly correlated with precision, but not absolute relative bias.
 The best sampling designs did not differ with estimated population density
 but differed between large and small ranges. We provide an efficient
 framework implemented in R to estimate the detection parameters required
 when designing SCR studies. The framework can be used when designing a
 monitoring program to minimize effort and cost while maximizing
 effectiveness, which is critical for informing wildlife management and
 conservation.
description: Text files and R scripts for SCR analysis.  Read attached README
 text file<strong> </strong>for additional
 information.  This dataset is only available to the public at a summary resolution for the following reason. The spatial information held within this dataset relates to a species at risk, that is highly sensitive.  Provision of precise locations would subject the species to threats such as disturbance and lethal exploitation. Data are supplied to the public with the geo-reference denatured to 0.1 degrees (~10 km grid). Depending on stated need, data may be supplied at finer scales upon request to the Government of Alberta under provisions of a data sharing agreement.
DOI: 10.5061/dryad.866t1g1ns
title: Experimental evolution of ancestrally reconstructed BCL2 family proteins

description: The roles of chance, contingency, and necessity in evolution is
 unresolved, because they have never been assessed in a single system or on
 timescales relevant to historical evolution. We combined ancestral protein
 reconstruction and a new continuous evolution technology to mutate and
 select B-cell-lymphoma-2-family proteins to acquire
 protein-protein-interaction specificities that occurred during animal
 evolution. By replicating evolutionary trajectories from multiple
 ancestral proteins, we found that contingency generated over long
 historical timescales steadily erased necessity and overwhelmed chance as
 the primary cause of acquired sequence variation; trajectories launched
 from phylogenetically distant proteins yielded virtually no common
 mutations, even under strong and identical selection pressures. Chance
 arose because many sets of mutations could alter specificity at any
 timepoint; contingency arose because historical substitutions changed
 these sets. Our results suggest that patterns of variation in BCL-2
 sequences – and likely other proteins, too – are idiosyncratic products of
 a particular, unpredictable course of historical events.
description: Illumina sequencing yielded 22
 million total and 13 million identified reads. The number of reads for
 each library are listed in Supplemental Table 13. We used Trim Galore to trim the primary
 sequences (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). BBMerge was then used to merge the paired sequences (https://sourceforge.net/projects/bbmap/). Next, we used the Clumpify script in the BBMap package to remove repeated sequences. After this, Seal was used to separate the three fragments of each library based on the library sequences. Finally, we used BBDuk to remove the sequence of the library construction primers. Reads were then binned by experiment and aligned to the appropriate WT sequence using Geneious (low Sensitivity, 5 iterations, gaps allowed). Sequences were then processed in R to remove sequences containing Ns or that were not full length. Insertions found in less than 1% of the population and sites that extended outside of the coding region were also removed from all sequences. Remaining gaps were then standardized among replicates and within an experiment. Finally, allele frequencies were calculated for each site and amino acid, as well as remaining insertions and deletions.
DOI: 10.5061/dryad.sxksn0314
title: Modeling cannabinoids from a large-scale sample of Cannabis sativa chemotypes

description: The widespread legalization of Cannabis has opened the industry to using
 contemporary analytical techniques for chemotype analysis. Chemotypic data
 has been collected on a large variety of oil profiles inherent to the
 cultivars that are commercially available. The unknown gene regulation and
 pharmacokinetics of dozens of cannabinoids offer opportunities of high
 interest in pharmacology research.  Retailers in many medical and
 recreational jurisdictions are typically required to report chemical
 concentrations of at least some cannabinoids. Commercial cannabis
 laboratories have collected large chemotype datasets of diverse Cannabis
 cultivars. In this work a data set of 17,600 cultivars tested by Steep
 Hill Inc., is examined using machine learning techniques to interpolate
 missing chemotype observations and cluster cultivars into groups based on
 chemotype similarity.   The results indicate cultivars
 cluster based on their chemotypes, and that some imputation methods work
 better than others at grouping these cultivars based on chemotypic
 identity. Due to the missing data and to the low signal to noise ratio for
 some less common cannabinoids, their behavior could not be accurately
 predicted. These findings have implications for characterizing complex
 interactions in cannabinoid biosynthesis and improving phenotypical
 classification of Cannabis cultivars.
DOI: 10.5061/dryad.b5mkkwh9z
title: Data from: Density-dependent sex-biased development of macroptery in a water strider

description: In wing-polymorphic insects, wing morphs differ not only in dispersal
 capability but also in life history traits because of trade-offs between
 flight capability and reproduction. When the fitness benefits and costs of
 producing wings differ between males and females, sex-specific trade-offs
 can result in sex differences in the frequency of long-winged individuals.
 Furthermore, the social environment during development affects sex
 differences in wing development, but few empirical tests of this
 phenomenon have been performed to date. Here, I used the wing-dimorphic
 water strider Tenagogerris euphrosyne to test how rearing density and sex
 ratio affect the sex-specific development of long-winged dispersing morphs
 (i.e., sex-specific macroptery). I also used a full-sib, split-family
 breeding design to assess genetic effects on density-dependent,
 sex-specific macroptery. I reared water strider nymphs at either high or
 low densities and measured their wing development. I found that
 long-winged morphs developed more frequently in males than in females when
 individuals were reared in a high-density environment. However, the
 frequency of long-winged morphs was not biased according to sex when
 individuals were reared in a low-density environment. In addition,
 full-sib males and females showed similar macroptery incidence rates at
 low nymphal density, whereas the macroptery incidence rates differed
 between full-sib males and females at high nymphal density. Thus complex
 gene-by-environment-by-sex interactions may explain the density-specific
 levels of sex bias in macroptery, although this interpretation should be
 treated with some caution. Overall, my study provides empirical evidence
 for density-specific, sex-biased wing development. My findings suggest
 that social factors as well as abiotic factors can be important in
 determining sex-biased wing development in insects.
DOI: 10.5061/dryad.b5mkkwhb0
title: Data from: Morphometrics and redescription of Aphyllon fasciculatum and Aphyllon franciscanum (Orobanchaceae), two widespread but previously conflated species in western North America

description: We continue the taxonomic reevaluation of Aphyllon sect. Aphyllon by
 describing a widespread species throughout Western North America
 previously recognized within a polyphyletic A. fasciculatum. To support
 our description and revised key, we analyzed fifteen continuous and
 discrete characters across 156 herbarium specimens and iNaturalist
 observations sampled from across the geographic range. Principal component
 and multiple correspondence analyses reveal clear variation in floral
 characters. Discriminant analyses show that floral color, the calyx cup to
 calyx lobe ratio, calyx lobe length, and degree of bend in the corolla
 tube are useful distinguishing features, but not diagnostic in every case.
description: Aphyllon_master_data.xlsx All measurement
 and observation data used in this study, including georeferencing,
 herbarium voucher accession numbers, and iNaturalist observation URLs.
 (Excel format with 3 sheets).
 Aphyllon_analyses.R Annotated R scripts for
 linear discriminant analysis, multiple correspondence analysis, and
 discriminant correspondence analysis.
 MCA_all.csv Input data file for multiple
 correspondence analysis in R (comma separated value format).
 MCA_confirmed_host.csv Subset of MCA_all.csv
 that includes only samples with known hosts.for multiple correspondence
 analysis in R (comma separated value format).
 PCA_normalized_data.csv Input (normalized)
 data file for principal components analysis in python and linear
 discriminant analysis in R (comma separated value format).
 MCA_by_Host.pdf Multiple correspondence
 analysis dimensions 1 and 2 showing categorical data sampled from 50
 iNaturalist observations of parasites <i>Aphyllon
 fasciculatum</i> and <i>A. franciscanum</i>, colored by
 host genus. Triangles indicate the correlation between each character
 state and each MCA dimension. See Figure 4 of Schneider and Benton 2021.
 (portable document format).
DOI: 10.5061/dryad.n5tb2rbt2
title: Data set for 'Lunge filter feeding biomechanics constrain rorqual foraging ecology across scale'...

description: Fundamental scaling relationships influence the physiology of vital rates,
 which in turn shape the ecology and evolution of organisms. For diving
 mammals, benefits conferred by large body size include reduced transport
 costs and enhanced breath-holding capacity, thereby increasing overall
 foraging efficiency. Rorqual whales feed by engulfing a large mass of
 prey-laden water at high speed and filter it through baleen plates.
 However, as engulfment capacity increases with body length across species
 (Engulfment Volume ∝ Body Length 3.57), the surface area of the baleen
 filter does not increase proportionally (Baleen Area ∝ Body Length1.82),
 and thus the filtration time of larger rorquals predictably increases
 because the baleen surface area must filter a disproportionally large
 amount of water. We predicted that filtration time should scale with body
 length to the power of 1.75 (Filter Time ∝ Body Length1.75). We tested
 this hypothesis on four rorqual species using multi-sensor tags with
 corresponding unoccupied aerial systems (UAS) -based body length
 estimates. We found that filter time scales with body length to the power
 of 1.79 (95% CI: 1.61 - 1.97). This result highlights a scale-dependent
 trade-off between engulfment capacity and baleen area that creates a
 biomechanical constraint to foraging through increased filtration time.
 Consequently, larger whales must target high density prey patches
 commensurate to the gulp size to meet their increased energetic demands.
 If these optimal patches are absent, larger rorquals may experience
 reduced foraging efficiency compared to smaller whales if they do not
 match engulfment capacity to the size of targeted prey aggregations.
description: The morphometric data for engulfment capacity measurements was
 collected from the Discovery Reports (Mackintosh, 1929; Mackintosh, 1942;
 Matthews, 1937; Matthews, 1938). The baleen area data was collected from
 Werth et al., 2018. The tag data was collected from 21
 blue whales (Monterey Bay), three fin whales (Eastern Greenland and
 Monterey Bay), nine humpback whales (Antarctic Peninsula and Monterey
 Bay), and nine Antarctic minke whales (Antarctic Peninsula) between 2017
 and 2019 using motion-sensing suction-cup attached tags. Whale body length
 measurements were taken from high-resolution aerial images using
 unoccupied aerial systems. Data was processed using
 MATLAB, R, MorphoMetriX, and CollatriX.
DOI: 10.5061/dryad.d7wm37pzs
title: Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

description: The cloning of agriculturally important genes is often complicated by
 haplotype variation across crop cultivars. Access to pan-genome
 information greatly facilitates the assessment of structural variations
 and rapid candidate gene identification. Here, we identified the red glume
 1 (Rg-B1) gene using association genetics and haplotype analyses in ten
 reference-grade wheat genomes. Glume color is an important trait to
 characterize wheat cultivars. Red glumes are frequent among Central
 European spelt, a dominant wheat subspecies in Europe before the 20th
 century. We used genotyping-by-sequencing to characterize a global
 diversity panel of 267 spelt accessions, which provided evidence for two
 independent introductions of spelt into Europe. A single region at the
 Rg-B1 locus on chromosome 1BS was associated with glume color in the
 diversity panel. Haplotype comparisons across ten high-quality wheat
 genomes revealed a MYB transcription factor as candidate gene. We found
 extensive haplotype variation across the ten cultivars, with a particular
 group of MYB alleles that was conserved in red glume wheat cultivars.
 Genetic mapping and transient infiltration experiments allowed us to
 validate this particular MYB transcription factor variants. Our study
 demonstrates the value of multiple high-quality genomes to rapidly resolve
 copy number and haplotype variations in regions controlling agriculturally
 important traits.