cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3528sj6
title: Data from: Opening the door to the past: accessing phylogenetic, pathogen, and population data from museum curated bees

description: Tens of thousands of insects are deposited in collections every year as a
 result of survey-based studies that aim to investigate ecological
 questions. DNA-based techniques can expand the utility of these
 collections to explore their demographic and evolutionary history,
 temporal changes in their abundance, and pathogen dynamics. Using museum
 collections of the non-model bee species Eucera (Peponapis) pruinosa Say
 1837 (Hymenoptera: Apidae: Eucerini), we developed a standard
 minimally-destructive and budget-friendly protocol to extract DNA and
 amplify common gene-fragments for barcoding, phylogenetic analysis, and
 pathogens. We also generated genome-wide single nucleotide polymorphism
 (SNP) data from DNA sequencing (ddRADseq) libraries for population
 structure analyses. We systematically studied the effect of specimen age
 (≤10 years ago) and tissue type (whole bees vs. abdomen) on DNA quality,
 single gene-fragment amplification, and SNP calling. We found that all
 analyses were achievable with both tissue types, yet with variable levels
 of efficiency because of general DNA degradation. Specifically, we found
 that not all samples yielded satisfactory results for molecular studies;
 however, we did not find a systematic effect of specimen age on DNA
 quality which is encouraging for future studies involving historical
 specimens. We report the first evidence for the presence of the
 microsporidian pathogen Nosema spp. in squash bees, opening a window for
 the study of historical changes in disease pressure in this important
 agricultural pollinator. Our protocols can be used as a template for the
 design of future experiments that extract multiple pieces of information
 using DNA-based methods from insect museum stored specimens.
description: READMEddRAD sequences and
 metadata from Eucera (Peponapis) pruinosa (Hymenoptera: Apidae) males used
 in: Anthony D. Vaudo, Megan L. Fritz, and Margarita M. Lopez-Uribe (2018)
 Opening the door to the past: Accessing phylogenetic, pathogen, and
 population data from museum curated bees. Insect Systematics and
 DiversityEucera pruinosa museum
 specimen ddRAD readsThis file contains the
 demultiplexed, trimmed and quality filtered ddRAD reads from museum
 curated Eucera (Peponapis) pruinosa males. See README file for specific
 information about sample metadata.allmuseum_merged_edits.zip
DOI: 10.5061/dryad.4754j
title: Data from: Membrane potential dynamics of spontaneous and visually evoked gamma activity in V1 of awake mice

description: Cortical gamma activity (30–80 Hz) is believed to play important functions
 in neural computation and arises from the interplay of
 parvalbumin-expressing interneurons (PV) and pyramidal cells (PYRs).
 However, the subthreshold dynamics underlying its emergence in the cortex
 of awake animals remain unclear. Here, we characterized the intracellular
 dynamics of PVs and PYRs during spontaneous and visually evoked gamma
 activity in layers 2/3 of V1 of awake mice using targeted patch-clamp
 recordings and synchronous local field potentials (LFPs). Strong gamma
 activity patterned in short bouts (one to three cycles), occurred when PVs
 and PYRs were depolarizing and entrained their membrane potential dynamics
 regardless of the presence of visual stimulation. PV firing phase locked
 unconditionally to gamma activity. However, PYRs only phase locked to
 visually evoked gamma bouts. Taken together, our results indicate that
 gamma activity corresponds to short pulses of correlated background
 synaptic activity synchronizing the output of cortical neurons depending
 on external sensory drive.
description: PV_ICData1Current-clamp data for PV cells (Set 1 of 3)PV_ICData2Current-clamp data for PV cells (Set 1 of 3)PV_ICData3Current-clamp data for PV cells (Set 3 of 3)PV_IC_SubthresholdCurrent-clamp Subthreshold data for PV cellsPV_VC+10DataVoltage-Clamp Data at +10mV for PV cellsPV_VC-80DataVoltage-Clamp Data at -80mV for PV cellsPYR_ICCurrent-Clamp Data for PYR cellsFig1-4Analyses and Scripts used to compute and generate results from Fig1-4Fig5-6Analyses and Scripts used to compute and generate results from Fig5-6SupFig1-3Analyses and Scripts used to compute and generate results from SupFig1-3SupFig4-6Analyses and Scripts used to compute and generate results from SupFig4-6UtilitiesMatlab Scripts written and used for the analysisReadMeInformation File describing each of the above files and how to use the scripts correctly
DOI: 10.5061/dryad.m57sd
title: Data from: Testing sensory evidence against mnemonic templates

description: Most perceptual decisions require comparisons between current input and an
 internal template. Classic studies propose that templates are encoded in
 sustained activity of sensory neurons. However, stimulus encoding is
 itself dynamic, tracing a complex trajectory through activity space. Which
 part of this trajectory is pre-activated to reflect the template? Here we
 recorded magneto- and electroencephalography during a visual
 target-detection task, and used pattern analyses to decode template,
 stimulus, and decision-variable representation. Our findings ran counter
 to the dominant model of sustained pre-activation. Instead, template
 information emerged transiently around stimulus onset and quickly
 subsided. Cross-generalization between stimulus and template coding,
 indicating a shared neural representation, occurred only briefly. Our
 results are compatible with the proposal that template representation
 relies on a matched filter, transforming input into task-appropriate
 output. This proposal was consistent with a signed difference response at
 the perceptual decision stage, which can be explained by a simple neural
 model.
description: S01_EEGSubject 1. Data from one session (MEG+EEG)S01_MEGSubject 1. Data from one session (MEG only)S02_EEGSubject 2. Data from one session (MEG+EEG).S02_MEGSubject 2. Data from one session (MEG only).S03_EEGSubject 3. Data from one session (MEG+EEG).S03_MEGSubject 3. Data from one session (MEG only).S04_EEGSubject 4. Data from one session (MEG+EEG).S04_MEGSubject 4. Data from one session (MEG only).S05_EEGSubject 5. Data from one session (MEG+EEG).S05_MEGSubject 5. Data from one session (MEG only).S06_EEGSubject 6. Data from one session (MEG+EEG).S06_MEGSubject 6. Data from one session (MEG only).S07_EEGSubject 7. Data from one session (MEG+EEG).S07_MEGSubject 7. Data from one session (MEG only).S08_EEGSubject 8. Data from one session (MEG+EEG).S08_MEGSubject 8. Data from one session (MEG only).S09_EEGSubject 9. Data from one session (MEG+EEG).S09_MEGSubject 9. Data from one session (MEG only).S10_EEGSubject 10. Data from one session (MEG+EEG).S10_MEGSubject 10. Data from one session (MEG only).Behaviorbehavior.mat
DOI: 10.5061/dryad.p7c77
title: Data from: Drosophila simulans: a species with improved resolution in evolve and resequence studies

description: The combination of experimental evolution with high-throughput sequencing
 of pooled individuals—i.e., evolve and resequence (E&R)—is a
 powerful approach to study adaptation from standing genetic variation
 under controlled, replicated conditions. Nevertheless, E&R studies
 in Drosophila melanogaster have frequently resulted in inordinate numbers
 of candidate SNPs, particularly for complex traits. Here, we contrast the
 genomic signature of adaptation following ∼60 generations in a novel hot
 environment for D. melanogaster and D. simulans. For D. simulans, the
 regions carrying putatively selected loci were far more distinct, and thus
 harbored fewer false positives, than those in D. melanogaster. We propose
 that species without segregating inversions and higher recombination
 rates, such as D. simulans, are better suited for E&R studies that
 aim to characterize the genetic variants underlying the adaptive response.
description: Dsim_3reps_F0F60_majorChr_downsampledSync file of allele coverage for Drosophila simulans SNPs in major chromosome arms (X, 2L, 2R, 3L, 3R). Columns in this sync file correspond to chromosome, position, base, Dsim_A_F0, Dsim_B_F0, Dsim_C_F0, Dsim_A_F60_Hot, Dsim_B_F60_Hot, Dsim_C_F60_Hot. Nomenclature of the samples is as follows: e.g. species_replicate_generation_selection regime. Species: Dsim (Drosophila simulans), replicate: letters (A-Z), generation: F#, # indicating the number of generations, and selection regime: Hot. Format specification of sync file is described in Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011;27:3435-3436. See main publication for additional information about data processing, SNP calling and filtering.Dsim_baseF60_rep1-3-5_bam.sorted.rmdup.filter.mpileup.Q20.polymorphic_repeatIndelmaskedmincov5_Ytranslocremoved_majorChr_downsampled.syncDmel_3reps_F0F59_majorChr_downsampledSync file of allele coverage for Drosophila melanogaster SNPs in major chromosome arms (X, 2L, 2R, 3L, 3R). Columns in this sync file correspond to chromosome, position, base, Dmel _A_F0, Dmel _B_F0, Dmel _C_F0, Dmel _A_F59_Hot, Dmel _B_F59_Hot, Dmel _C_F59_Hot. Nomenclature of the samples is as follows: e.g. species_replicate_generation_selection regime. Species: Dmel (Drosophila melanogaster), replicate: letters (A-Z), generation: F#, # indicating the number of generations, and selection regime: Hot. Format specification of sync file is described in Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011;27:3435-3436. See main publication for additional information about data processing, SNP calling and filtering.Dmel_base_F59_reps_1_4_5_downsampled.mpileup.Q20.polymorphic_majorChr.sync
DOI: 10.5061/dryad.hq68q
title: Data from: Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms

description: Inherited genetic variation affects local gene expression and DNA
 methylation in humans. Most expression quantitative trait loci (cis-eQTLs)
 occur at the same genomic location as methylation QTLs (cis-meQTLs),
 suggesting a common causal variant and shared mechanism. Using DNA and RNA
 from peripheral blood of Bangladeshi individuals, here we use
 co-localization methods to identify eQTL-meQTL pairs likely to share a
 causal variant. We use partial correlation and mediation analyses to
 identify &gt;400 of these pairs showing evidence of a causal
 relationship between expression and methylation (i.e., shared mechanism)
 with many additional pairs we are underpowered to detect. These
 co-localized pairs are enriched for SNPs showing opposite associations
 with expression and methylation, although a many SNPs affect multiple CpGs
 in opposite directions. This work demonstrates the pervasiveness of
 co-regulated expression and methylation in the human genome. Applying this
 approach to other types of molecular QTLs can enhance our understanding of
 regulatory mechanisms.
description: ciseQTL_results_for_colocThis file contains complete eQTL results for all eQTLs used in co-localization analyses. Summary results for all SNPs within 250 kb of the lead eSNP are provided.sort_all_ciseQTL_wind250k_for_coloc.zipcismeQTL_results_for_colocThis file contains complete meQTL results for all meQTLs used in co-localization analyses. Summary results for all SNPs included in the eQTL results file are included here (except SNPs &gt;500 kb away from the target CpG site, as these were not included in cis-meQTL analyses).sort_all_cismQTL_wind500k_for_coloc.zipGenome-wide cis-eQTL results (SNPs with P&lt;0.05)genome_wide_cis_eQTL_p_ltp05.zipGenome-wide cis-meQTL results (SNPs with P&lt;0.05)genome_wide_cis_mQTL_p_ltp05.zip
DOI: 10.5061/dryad.mh67v
title: Data from: The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

description: Although genome scans have become a popular approach towards understanding
 the genetic basis of local adaptation, the field still does not have a
 firm grasp on how sampling design and demographic history affect the
 performance of genome scans on complex landscapes. To explore these
 issues, we compared 20 different sampling designs in equilibrium (i.e.
 island model and isolation by distance) and nonequilibrium (i.e. range
 expansion from one or two refugia) demographic histories in spatially
 heterogeneous environments. We simulated spatially complex landscapes,
 which allowed us to exploit local maxima and minima in the environment in
 ‘pair’ and ‘transect’ sampling strategies. We compared FST outlier and
 genetic–environment association (GEA) methods for each of two approaches
 that control for population structure: with a covariance matrix or with
 latent factors. We show that while the relative power of two methods in
 the same category (FST or GEA) depended largely on the number of
 individuals sampled, overall GEA tests had higher power in the island
 model and FST had higher power under isolation by distance. In the refugia
 models, however, these methods varied in their power to detect local
 adaptation at weakly selected loci. At weakly selected loci, paired
 sampling designs had equal or higher power than transect or random designs
 to detect local adaptation. Our results can inform sampling designs for
 studies of local adaptation and have important implications for the
 interpretation of genome scans based on landscape data.
description: Zip file containing
 datasets and resultsSee the README
 file.dryad.zip
DOI: 10.5061/dryad.43bv0
title: Data from: Matching seed to site by climate similarity: Techniques to prioritize plant materials development and use in restoration

description: Land management agencies are increasing the use of native plant materials
 for vegetation treatments to restore ecosystem function and maintain
 natural ecological integrity. This shift towards the use of natives has
 highlighted a need to increase the diversity of materials available. A key
 problem is agreeing on how many, and which, new accessions should be
 developed. Here we describe new methods that address this problem. Our
 methods use climate data to calculate a climate similarity index between
 two points in a defined extent. This index can be used to predict relative
 performance of available accessions at a target site. In addition, the
 index can be used in combination with standard cluster analysis algorithms
 to quantify and maximize climate coverage (mean climate similarity), given
 a modeled range extent and a specified number of accessions. We
 demonstrate the utility of this latter feature by applying it to the
 extents of 11 Western North American species with proven or potential use
 in restoration. First, a species-specific seed transfer map can be readily
 generated for a species by predicting performance for accessions currently
 available; this map can be readily updated to accommodate new accessions.
 Next, the increase in climate coverage achieved by adding successive
 accessions can be explored, yielding information that managers can use to
 balance ecologic and economic considerations in determining how many
 accessions to develop. This approach identifies sampling sites, referred
 to as climate centers, which contribute unique, complementary climate
 coverage to accessions on hand, thus providing explicit sampling guidance
 for both germplasm preservation and research. We examine how these, and
 other, features of our approach add to existing methods used to guide
 plant materials development and use. Finally, we discuss how these new
 methods provide a framework that could be used to coordinate native plant
 materials development, evaluation, and use across agencies, regions, and
 research groups.
description: Climate Similarity
 Support ScriptsThis compressed file
 contains scripts and supporting data necessary to reproduce the analyses
 and products associated with Doherty et al. (2017), “Matching seed to site
 by climate similarity: Techniques to prioritize plant materials
 development and use in restoration.”Climate Similarity
 Scripts.zip
DOI: 10.5061/dryad.jq285
title: Data from: Evolution of the snake body form reveals homoplasy in amniote Hox gene function

description: Hox genes regulate regionalization of the axial skeleton in vertebrates,
 and changes in their expression have been proposed to be a fundamental
 mechanism driving the evolution of new body forms. The origin of the
 snake-like body form, with its deregionalized pre-cloacal axial skeleton,
 has been explained as either homogenization of Hox gene expression
 domains9, or retention of standard vertebrate Hox domains with alteration
 of downstream expression that suppresses development of distinct regions.
 Both models assume a highly regionalized ancestor, but the extent of
 deregionalization of the primaxial domain (vertebrae, dorsal ribs) of the
 skeleton in snake-like body forms has never been analysed. Here we combine
 geometric morphometrics and maximum-likelihood analysis to show that the
 pre-cloacal primaxial domain of elongate, limb-reduced lizards and snakes
 is not deregionalized compared with limbed taxa, and that the phylogenetic
 structure of primaxial morphology in reptiles does not support a loss of
 regionalization in the evolution of snakes. We demonstrate that
 morphometric regional boundaries correspond to mapped gene expression
 domains in snakes, suggesting that their primaxial domain is patterned by
 a normally functional Hox code. Comparison of primaxial osteology in
 fossil and modern amniotes with Hox gene distributions within Amniota
 indicates that a functional, sequentially expressed Hox code patterned a
 subtle morphological gradient along the anterior–posterior axis in stem
 members of amniote clades and extant lizards, including snakes. The highly
 regionalized skeletons of extant archosaurs and mammals result from
 independent evolution in the Hox code and do not represent ancestral
 conditions for clades with snake-like body forms. The developmental origin
 of snakes is best explained by decoupling of the primaxial and abaxial
 domains and by increases in somite number, not by changes in the function
 of primaxial Hox genes.
description: Morphometric
 dataMorphometric data files
 for Alligator, Mus, and squamatesArchive.zip
DOI: 10.5061/dryad.2gp4g
title: Data from: Distinct BOLD fMRI responses of capsaicin-induced thermal sensation reveal pain-related brain activation in nonhuman primates

description: Background: Approximately 20% of the adult population suffer from chronic
 pain that is not adequately treated by current therapies, highlighting a
 great need for improved treatment options. To develop effective
 analgesics, experimental human and animal models of pain are critical.
 Topically/intra-dermally applied capsaicin induces hyperalgesia and
 allodynia to thermal and tactile stimuli that mimics chronic pain and is a
 useful translation from preclinical research to clinical investigation.
 Many behavioral and self-report studies of pain have exploited the use of
 the capsaicin pain model, but objective biomarker correlates of the
 capsaicin augmented nociceptive response in nonhuman primates remains to
 be explored. Methodology: Here we establish an aversive capsaicin-induced
 fMRI model using non-noxious heat stimuli in Cynomolgus monkeys (n = 8).
 BOLD fMRI data were collected during thermal challenge (ON:20 s/42°C;
 OFF:40 s/35°C, 4-cycle) at baseline and 30 min post-capsaicin (0.1 mg,
 topical, forearm) application. Tail withdrawal behavioral studies were
 also conducted in the same animals using 42°C or 48°C water bath pre- and
 post- capsaicin application (0.1 mg, subcutaneous, tail). Principal
 Findings: Group comparisons between pre- and post-capsaicin application
 revealed significant BOLD signal increases in brain regions associated
 with the ‘pain matrix’, including somatosensory, frontal, and cingulate
 cortices, as well as the cerebellum (paired t-test, p&lt;0.02, n = 8),
 while no significant change was found after the vehicle application. The
 tail withdrawal behavioral study demonstrated a significant main effect of
 temperature and a trend towards capsaicin induced reduction of latency at
 both temperatures. Conclusions: These findings provide insights into the
 specific brain regions involved with aversive, ‘pain-like’, responses in a
 nonhuman primate model. Future studies may employ both behavioral and fMRI
 measures as translational biomarkers to gain deeper understanding of pain
 processing and evaluate the preclinical efficacy of novel analgesics.
description: Raw
 DataImage raw epi data,
 group activation map, activation volume, PSC,Tail withdrawal
 dataData.zip
DOI: 10.5061/dryad.n726pq6
title: Data from: Compensatory conservation measures for an endangered caribou population under climate change

description: Future human land use and climate change may disrupt movement behaviors of
 terrestrial animals, thereby altering the ability of individuals to move
 across a landscape. Some of the expected changes result from processes
 whose effects will be difficult to alter, such as global climate change.
 We present a novel framework in which we use models to (1) identify the
 ecological changes from these difficult-to-alter processes, as well as (2)
 the potential conservation measures that are best able to compensate for
 these changes. We illustrated this framework with the case of an
 endangered caribou population in Québec, Canada. We coupled a spatially
 explicit individual-based movement model with a range of landscape
 scenarios to assess the impacts of varying degrees of climate change, and
 the ability of conservation actions to compensate for such impacts on
 caribou movement behaviors. We found that (1) climate change impacts
 reduced movement potential, and that (2) the complete restoration of
 secondary roads inside protected areas was able to fully offset this
 reduction, suggesting that road restoration would be an effective
 compensatory conservation action. By evaluating conservation actions via
 landscape use simulated by an individual-based model, we were able to
 identify compensatory conservation options for an endangered species
 facing climate change.
description: Habitat Quality Maps for
 caribou movement modelsArchive of 24 tifs of
 seasonal (winter&summef) habitat quality maps for 12
 management/climate change scenarios, as detailed in the manuscript and
 supplementary material.rasterMapsScenarios.rar