cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vq275
title: Data from: Evaluation of TagSeq, a reliable low-cost alternative for RNAseq

description: RNAseq is a relatively new tool for ecological genetics that offers
 researchers insight into changes in gene expression in response to a
 myriad of natural or experimental conditions. However, standard RNAseq
 methods (e.g., Illumina TruSeq® or NEBNext®) can be cost prohibitive,
 especially when study designs require large sample sizes. Consequently,
 RNAseq is often underused as a method, or is applied to small sample sizes
 that confer poor statistical power. Low cost RNAseq methods could
 therefore enable far greater and more powerful applications of
 transcriptomics in ecological genetics and beyond. Standard mRNAseq is
 costly partly because one sequences portions of the full length of all
 transcripts. Such whole-mRNA data is redundant for estimates of relative
 gene expression. TagSeq is an alternative method that focuses sequencing
 effort on mRNAs’ 3’ end, reducing the necessary sequencing depth per
 sample, and thus cost. We present a revised TagSeq library construction
 procedure, and compare its performance against NEBNext®, the
 “gold-standard” whole mRNAseq method. We built both TagSeq and NEBNext®
 libraries from the same biological samples, each spiked with control RNAs.
 We found that TagSeq measured the control RNA distribution more accurately
 than NEBNext®, for a fraction of the cost per sample (~10%). The higher
 accuracy of TagSeq was particularly apparent for transcripts of moderate
 to low abundance. Technical replicates of TagSeq libraries are highly
 correlated, and were correlated with NEBNext® results. Overall, we show
 that our modified TagSeq protocol is an efficient alternative to
 traditional whole mRNAseq, offering researchers comparable data at greatly
 reduced cost.
description: Lohman et al Evaluation
 of TagSeqAll necessary raw data
 and code (raw sequences deposited on Corral)
DOI: 10.5061/dryad.nv0p1
title: Data from: Modeling the influence of genetic and environmental variation on the expression of plant life cycles across landscapes

description: Organisms develop through multiple life stages that differ in
 environmental tolerances. The seasonal timing, or phenology, of life-stage
 transitions determines the environmental conditions to which each life
 stage is exposed and the length of time required to complete a generation.
 Both environmental and genetic factors contribute to phenological
 variation, yet predicting their combined effect on life cycles across a
 geographic range remains a challenge. We linked submodels of the
 plasticity of individual life stages to create an integrated model that
 predicts life-cycle phenology in complex environments. We parameterized
 the model for Arabidopsis thaliana and simulated life cycles in four
 locations. We compared multiple “genotypes” by varying two parameters
 associated with natural genetic variation in phenology: seed dormancy and
 floral repression. The model predicted variation in life cycles across
 locations that qualitatively matches observed natural phenology. Seed
 dormancy had larger effects on life-cycle length than floral repression,
 and results suggest that a genetic cline in dormancy maintains a
 life-cycle length of 1 year across the geographic range of this species.
 By integrating across life stages, this approach demonstrates how genetic
 variation in one transition can influence subsequent transitions and the
 geographic distribution of life cycles more generally.
description: Environmental data,
 source code, and summarized resultsThis package contains
 the necessary environmental data (.csv) and R source code (.R) to recreate
 the life cycle results for six genotypes in four European locations
 highlighted in the paper "Modeling the influence of genetic and
 environmental variation on the expression of plant life cycles across
 landscapes". We also provide the summarized results for each of these
 24 genotype x environment combinations so you do not actually have to run
 all the simulations to explore the results (.Rdata).Dryad
 package.zip
DOI: 10.5061/dryad.8s544
title: Data from: Enhancing the efficiency of planar heterojunction perovskite solar cells via interfacial engineering with 3-aminopropyl trimethoxy silane hydrolysate

description: The interfacial compatibility between compact TiO2 and perovskite layers
 is critical for the performance of planar heterojunction perovskite solar
 cells (PSCs). A compact TiO2 film employed as an electron-transport layer
 (ETL) was modified using 3-aminopropyl trimethoxy silane (APMS)
 hydrolysate. The power conversion efficiency (PCE) of PSCs composed of an
 APMS-hydrolysate-modified TiO2 layer increased from 13.45 to 15.79%, which
 was associated with a significant enhancement in the fill factor (FF) from
 62.23 to 68.04%. The results indicate that APMS hydrolysate can enhance
 the wettability of γ-butyrolactone (GBL) on the TiO2 surface, form a
 perfect CH3NH3PbI3 film, and increase the recombination resistance at the
 interface. This work demonstrates a simple but efficient method to improve
 the TiO2/perovskite interface that can be greatly beneficial for
 developing high-performance PSCs.
description: Data for manuscript and
 supplementary informationData.zip
DOI: 10.5061/dryad.88n4d54
title: Data from: Infant CPAP for low-income countries: an experimental comparison of standard bubble CPAP and the Pumani system

description: Introduction: Access to inexpensive respiratory support to newborn infants
 improves survival in low-income countries. Standard bubble continuous
 positive airway pressure (CPAP) has been extensively used worldwide for
 more than 30 years. One project aimed at providing affordable CPAP is the
 Pumani system developed by Rice 360. Compared to standard bubble CPAP the
 system has an unconventional design. The aim was to compare the Pumani
 system with two traditional bubble CPAP systems, focusing on in-vitro
 performance and safety. Methods: The Pumani system was compared to
 traditional bubble CPAP from Fisher & Paykel (Auckland, New
 Zealand) and Diamedica (Devon, United Kingdom). The systems were tested
 using static flow resistance and simulated breathing for a range of fresh
 gas flows and submersion levels. Results: There were large differences
 between the Pumani CPAP and the conventional bubble CPAP systems. The
 Pumani system was not pressure stable, had high resistance and high
 imposed work of breathing. It was not possible to use submersion depth to
 adjust CPAP without accounting for fresh gas flow. Discussion: The Pumani
 design is novel and not similar to any previously described CPAP system.
 The main mechanism for CPAP generation was resistance, not submersion
 depth. The system should therefore not be referred to as bubble CPAP. The
 clinical consequences of its pressure instability and high imposed work of
 breathing are not known and trials on outcome and safety are needed.
description: Fig3Fig4Fig5Fig6Fig7Fig8Readme
DOI: 10.5061/dryad.rd24d
title: Data from: Booming far: the long-range vocal strategy of a lekking bird

description: The pressures of selection acting on transmission of information by
 acoustic signals are particularly high in long-distance communication
 networks. Males of the North African houbara bustard (Chlamydotis undulata
 undulata) produce extremely low-frequency vocalizations called
 'booms' as a component of their courtship displays. These
 displays are performed on sites separated by a distance of on average
 550 m, constituting exploded leks. Here, we investigate the acoustic
 features of booms involved in species-specific identity. We first assessed
 the modifications of acoustic parameters during boom transmission at long
 range within the natural habitat of the species, finding that the
 frequency content of booms was reliably transmitted up to 600 m.
 Additionally, by testing males' behavioural responses to playbacks of
 modified signals, we found that the presence of the second harmonic and
 the frequency modulation are the key parameters for species
 identification, and also that a sequence of booms elicited stronger
 responses than a single boom. Thus, the coding-decoding process relies on
 redundant and propagation-resistant features, making the booms
 particularly well adapted for the long-range transmission of information
 between males. Moreover, by experimentally disentangling the presentation
 of visual and acoustic signals, we showed that during the booming phase of
 courtship, the two sensory modalities act in synergy. The acoustic
 component is dominant in the context of intra-sexual competition. While
 the visual component is not necessary to induce agonistic response, it
 acts as an amplifier and reduces the time of detection of the signaller.
 The utilization of these adaptive strategies allows houbara males to
 maximize the active space of vocalizations emitted in exploded leks.
description: DataRaw_Cornec_etal_BoomingFarDataRaw_Cornec_et_al_BoomingFar.rar
DOI: 10.15468/84bz7j
title: Houston Museum of Natural Science, Ornithology Collection

description: The ornithology collection of the Houston Museum of Natural Science has an emphasis on the birds of Texas, with a focus on the Gulf Coast. The collection also includes species from Africa, Asia, South and Central America, and Australia.
DOI: 10.5061/dryad.9gp8g
title: Data from: Landscape genomics reveals altered genome wide diversity within revegetated stands of Eucalyptus microcarpa (Grey Box)

description: In order to contribute to evolutionary resilience and adaptive potential
 in highly modified landscapes, revegetated areas should ideally reflect
 levels of genetic diversity within and across natural stands. Landscape
 genomic analyses enable such diversity patterns to be characterized at
 genome and chromosomal levels. Landscape-wide patterns of genomic
 diversity were assessed in Eucalyptus microcarpa, a dominant tree species
 widely used in revegetation in Southeastern Australia. Trees from small
 and large patches within large remnants, small isolated remnants and
 revegetation sites were assessed across the now highly fragmented
 distribution of this species using the DArTseq genomic approach. Genomic
 diversity was similar within all three types of remnant patches analysed,
 although often significantly but only slightly lower in revegetation sites
 compared with natural remnants. Differences in diversity between stand
 types varied across chromosomes. Genomic differentiation was higher
 between small, isolated remnants, and among revegetated sites compared
 with natural stands. We conclude that small remnants and revegetated sites
 of our E. microcarpa samples largely but not completely capture patterns
 in genomic diversity across the landscape. Genomic approaches provide a
 powerful tool for assessing restoration efforts across the landscape.
description: "Globally"
 filtered SNPsVCF file containing 6490
 "globally filtered" SNPs for all Eucalyptus microcarpa
 samplesglobal-filter.vcf.gz"Population-level" filtered SNPsVCF file containing 13,113 "population-level filtered" SNPs for Eucalyptus microcarpa samples excluding outlier samplespopulation-filter.vcf.gzMetadata for Eucalyptus microcarpa samplesAdditional data regarding locations and samples belonging to each siteEmicrocarpa_metadata.xlsxREADME fileREADME file for Eucalyptus microcarpa data
DOI: 10.5061/dryad.s279c
title: Data from: Comparative genomics of the mimicry switch in Papilio dardanus

description: The African Mocker Swallowtail, Papilio dardanus, is a textbook example in
 evolutionary genetics. Classical breeding experiments have shown that wing
 pattern variation in this polymorphic Batesian mimic is determined by the
 polyallelic H locus that controls a set of distinct mimetic phenotypes.
 Using bacterial artificial chromosome (BAC) sequencing, recombination
 analyses and comparative genomics, we show that H co-segregates with an
 interval of less than 500 kb that is collinear with two other Lepidoptera
 genomes and contains 24 genes, including the transcription factor genes
 engrailed (en) and invected (inv). H is located in a region of conserved
 gene order, which argues against any role for genomic translocations in
 the evolution of a hypothesized multi-gene mimicry locus. Natural
 populations of P. dardanus show significant associations of specific
 morphs with single nucleotide polymorphisms (SNPs), centred on en. In
 addition, SNP variation in the H region reveals evidence of non-neutral
 molecular evolution in the en gene alone. We find evidence for a
 duplication potentially driving physical constraints on recombination in
 the lamborni morph. Absence of perfect linkage disequilibrium between
 different genes in the other morphs suggests that H is limited to
 nucleotide positions in the regulatory and coding regions of en. Our
 results therefore support the hypothesis that a single gene underlies wing
 pattern variation in P. dardanus.
description: 454 sequence data
 obtained for P. dardanus f. lamborniThe extent of a
 duplicated fragment in Papilio dardanus f. lamborni was investigated using
 long-range PCR. PCR amplicons were shotgun sequenced with 454
 pyrosequencing technology. Reads were mapped onto a subfragment of the BAC
 tile path using BWA. The file is a sorted bam file.846920_NHM12_QC.sorted.bamConcatanatedBAC_Orange_CTDcontig71.fastaMasked reference file for bam file
DOI: 10.5061/dryad.j02mk45
title: Data from: Encroachment of shrubs into subalpine grasslands in the Pyrenees modifies the structure of soil fungal communities and soil properties.

description: The encroachment of shrubs into grasslands is common in terrestrial
 ecosystems dominated by grass. Land abandonment and favourable climatic
 trends in recent decades have favoured the expansion of shrubs into
 subalpine grasslands in many mountainous regions across Europe. The
 advance of the succession from grassland to shrubland is expected to have
 a major impact on ecosystem functioning. We used DNA metabarcoding to
 assess whether the structure of soil fungal communities varied along the
 succession from subalpine grassland to shrubland in the Pyrenees, and
 investigated whether shrub encroachment was associated with changes in
 soil properties. The expansion of shrubs increased the soil C:N ratio
 and/or reduced the N, P, or K contents. Plant-driven changes in soil
 properties were strongly associated with the compositional turnover of
 fungi, including arbuscular mycorrhizal, ectomycorrhizal, ericoid, root
 endophytic, saprotrophic, lichenised, and pathogenic fungi. Total richness
 and the richness of most functional groups were correlated with soil P, N,
 and the C:N or N:P ratios. We show that the interplay between abiotic
 factors (changes in soil properties) and biotic factors (occurrence and
 identity of shrubs) played a key role in the structure and uniqueness of
 soil fungal communities along the succession.
description: Oriol_fasta_files_for_submissionOriol fasta files for submission.zip
DOI: 10.5061/dryad.5hh54
title: Data from: Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator

description: During hibernation, animals cycle between torpor and arousal. These cycles
 involve dramatic but poorly understood mechanisms of dynamic physiological
 regulation at the level of gene expression. Each cycle, Brown Adipose
 Tissue (BAT) drives periodic arousal from torpor by generating essential
 heat. We applied digital transcriptome analysis to precisely timed samples
 to identify molecular pathways that underlie the intense activity cycles
 of hibernator BAT. A cohort of transcripts increased during torpor,
 paradoxical because transcription effectively ceases at these low
 temperatures. We show that this increase occurs not by elevated
 transcription but rather by enhanced stabilization associated with
 maintenance and/or extension of long poly(A) tails. Mathematical modeling
 further supports a temperature-sensitive mechanism to protect a subset of
 transcripts from ongoing bulk degradation instead of increased
 transcription. This subset was enriched in a C-rich motif and genes
 required for BAT activation, suggesting a model and mechanism to
 prioritize translation of key proteins for thermogenesis.
description: Supplementary File
 3EDGE-tag
 dataGrabek_eLIFE_Supplementary_File3_010715.xlsx
DOI: 10.5061/dryad.6f576
title: Data from: Evolution of sexual traits influencing vectorial capacity in anopheline mosquitoes

description: The availability of genome sequences from 16 anopheline species provides
 unprecedented opportunities to study the evolution of reproductive traits
 relevant for malaria transmission. In Anopheles gambiae, a likely
 candidate for sexual selection is male 20-hydroxyecdysone (20E). Sexual
 transfer of this steroid hormone as part of a mating plug dramatically
 changes female physiological processes intimately tied to vectorial
 capacity. By combining phenotypic studies with ancestral state
 reconstructions and phylogenetic analyses, we show that mating plug
 transfer and male 20E synthesis are both derived characters that have
 coevolved in anophelines, driving the adaptation of a female
 20E-interacting protein that promotes oogenesis via mechanisms also
 favoring Plasmodium survival. Our data reveal coevolutionary dynamics of
 reproductive traits between the sexes likely to have shaped the ability of
 anophelines to transmit malaria.
description: Fig S1 Species phylogeny
 based on single copy orthologs_protein sequence
 alignmentThe concatenated protein
 sequence alignments of nine anopheline and two outgroup dipteran species
 (created using MUSCLE and trimmed with trimAl) of 4,829 relaxed
 single-copy orthologs (a maximum of three paralogs allowed in no more than
 two species, longest protein selected) determined by OrthoDB orthology
 delineation (available at http://cegg.unige.ch/orthodbmoz2), which
 resulted in 3,400,861 amino acid columns (with 906,126 distinct alignment
 patterns).Fig 4 Phylogenetic
 analysis of MISO and AGAP002621_protein sequence
 alignmentMISO and AGAP002621
 alignment of orthologous protein sequences from nine anopheline and two
 outgroup dipteran species retrieved from VectorBase
 (https://www.vectorbase.org). For each species, MISO andAGAP002621
 orthologs were identified via BLAST/Translated blat search in VectorBase.
 However in some instances the gene models of MISO and AGAP002621 were
 fused and as a result were manually resolved using Apollo Genome
 Annotation and Curation Tool, Version 1.11.8. Gene identifiers for MISO
 and 2621 orthologs respectively are listed below with single identifiers
 corresponding to fused gene models: A. arabiensis (AARA004231); A.
 stephensi (ASTE005249); A. funestus (AFUN011077); A. dirus (ADIR010237);
 A. farauti (AFAF007180, AFAF018121); A. sinensis (ASIS013552, ASIS009594);
 A. atroparvus (AATE003240, AATE008584); A. albimanus (AALB003668); A.
 aegypti (AAEL003936, AAEL017464); D. melanogaster (FBgn0003065, no
 AGAP002621 ortholog present).
DOI: 10.5061/dryad.g3q80
title: Data from: Facile fabrication of microfluidic surface-enhanced raman scattering devices via lift-up lithography

description: We describe a facile and low-cost approach for flexible integration
 surface-enhanced Raman scattering (SERS) substrate in microfluidic chips.
 Briefly, a SERS substrate was fabricated by electrostatic assembly of gold
 nanoparticles, and shaped into designed patterns by the subsequent lift-up
 soft lithography. The SERS micropattern could be further integrated within
 microfluidic channels conveniently. The resulting microfluidic SERS chip
 allows one to ultrasensitively in-situ SERS monitor from the transparent
 glass window. With its advantages in simplicity, functionality, and
 cost-effectivity, this method can be readily expanded in optical
 microfluidic fabrication for biochemical applications.
description: data for microfluidics
 SERSdata.rar
DOI: 10.5061/dryad.qb5j6
title: Data from: Three-dimensional analysis of the fast-start escape response of the least killifish, Heterandria formosa

description: Fish make C-starts to evade predator strikes. Double-bend (DB) C-starts
 consist of three stages: Stage 1, in which the fish rapidly bends into a
 C-shape; Stage 2, in which the fish bends in the opposite direction; and a
 variable Stage 3. In single-bend (SB) C-starts, the fish immediately
 straightens after Stage 1. Despite fish moving in 3D space, fast-start
 responses of adult fish have mainly been studied in a horizontal plane.
 Using automated 3D tracking of multi-camera high-speed video sequences, we
 show that both SB and DB fast-starts by adult female least killifish
 (Heterandria formosa) often contain a significant vertical velocity
 component, and large changes in pitch (DB: up to 43 deg) and roll (DB: up
 to 77 deg) angles. Upwards and downwards elevation changes are correlated
 with changes in pitch angle of the head; movement in the horizontal plane
 is correlated with changes in yaw angle of the head. With respect to the
 stimulus, escape heading correlates with the elevation of the fish at the
 onset of motion. Irrespective of the initial orientation, fish can escape
 in any horizontal direction. In many cases, the centre of mass barely
 accelerates during Stage 1. However, it does accelerate in the final
 direction of the escape in other instances, indicating that Stage 1 can
 serve a propulsive role in addition to its preparatory role for Stage 2.
 Our findings highlight the importance of large-scale 3D analyses of
 fast-start manoeuvres of adult fish in uncovering the versatility of fish
 escape repertoire.
description: MATLAB_FS_Movie_Database.zip package containing .mat files with all the tracking data and derivatives - for all high-speed movies analyzed using the FishTracker. See the included Readme files for further details.Derived_data_angles_headingsExcel-file that contains the derived data from the Fishtracker MATLAB program (Voesenek et al., 2016). See the included Readme files for further details.
DOI: 10.5061/dryad.pc762
title: Data from: Genomic evidence that sexual selection impedes adaptation to a novel environment

description: Sexual selection is widely appreciated for generating remarkable
 phenotypic diversity, but its contribution to adaptation and the purging
 of deleterious mutations is unresolved. To provide insight into the impact
 of sexual selection on naturally segregating polymorphisms across the
 genome, we previously evolved 12 populations of Drosophila serrata in a
 novel environment employing a factorial manipulation of the opportunities
 for natural and sexual selection. Here, we genotype more than 1,400 SNPs
 in the evolved populations and reveal that sexual selection affected many
 of the same genomic regions as natural selection, aligning with it as
 often as opposing it. Intriguingly, more than half of the 80 SNPs showing
 treatment effects revealed an interaction between natural and sexual
 selection. For these SNPs, while sexual selection alone often caused a
 change in allele frequency in the same direction as natural selection
 alone, when natural and sexual selection occurred together, changes in
 allele frequency were greatly reduced or even reversed. This suggests an
 antagonism between natural and sexual selection arising from male-induced
 harm to females. Behavioral experiments showed that males preferentially
 courted and mated with high-fitness females, and that the harm associated
 with this increased male attention eliminated the female fitness
 advantage. During our experiment, females carrying otherwise adaptive
 alleles may therefore have disproportionally suffered male-induced harm
 due to their increased sexual attractiveness. These results suggest that a
 class of otherwise adaptive mutations may not contribute to adaptation
 when mating systems involve sexual conflict and male mate preferences.
description: harassmentSee ReadMe fileproductivitySee ReadMe file.reference_scaffolds.fastaPlease see Readme file.survivalPlease see ReadMe file.