cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ft6r5
title: Data from: Fine mapping of dominant X-linked incompatibility alleles in Drosophila hybrids

description: Sex chromosomes have a large effect on reproductive isolation and play an
 important role in hybrid inviability. In Drosophila hybrids, X-linked
 genes have pronounced deleterious effects on fitness in male hybrids,
 which have only one X chromosome. Several studies have succeeded at
 locating and identifying recessive X-linked alleles involved in hybrid
 inviability. Nonetheless, the density of dominant X-linked alleles
 involved in interspecific hybrid viability remains largely unknown. In
 this report, we study the effects of a panel of small fragments of the D.
 melanogaster X-chromosome carried on the D. melanogaster Y-chromosome in
 three kinds of hybrid males: D. melanogaster/D. santomea, D.
 melanogaster/D. simulans and D. melanogaster/D. mauritiana. D. santomea
 and D. melanogaster diverged over 10 million years ago, while D. simulans
 (and D. mauritiana) diverged from D. melanogaster over 3 million years
 ago. We find that the X-chromosome from D. melanogaster carries dominant
 alleles that are lethal in mel/san, mel/sim, and mel/mau hybrids, and more
 of these alleles are revealed in the most divergent cross. We then compare
 these effects on hybrid viability with two D. melanogaster intraspecific
 crosses. Unlike the interspecific crosses, we found no X-linked alleles
 that cause lethality in intraspecific crosses. Our results reveal the
 existence of dominant alleles on the X-chromosome of D. melanogaster which
 cause lethality in three different interspecific hybrids. These alleles
 only cause inviability in hybrid males, yet have little effect in hybrid
 females. This suggests that X-linked elements that cause hybrid
 inviability in males might not do so in hybrid females due to differing
 sex chromosome interactions.
description: Raw data. Matute and
 Gavin-Smyth 2014This file includes all
 the raw data and the two R files required to generate all the results in
 Matute and Gavin-Smyth 2014. All statistical analyses are shown in the R
 files.DupMappingData
 2.zip
DOI: 10.5061/dryad.4781n
title: Data from: Plant spines deter herbivory by restricting caterpillar movement

description: The spines of flowering plants are thought to function primarily in
 defence against mammalian herbivores; however, we previously reported that
 feeding by Manduca sexta caterpillars on the leaves of horsenettle plants
 (Solanum carolinense) induces increased development of internode spines on
 new growth. To determine whether and how spines impact caterpillar
 feeding, we conducted assays with three Solanaceous plant species that
 vary in spine numbers (S. carolinense, S. atropurpureum and S.
 aethiopicum) and also manipulated spine numbers within each species. We
 found that M. sexta caterpillars located experimentally isolated target
 leaves much more quickly on plants with experimentally removed spines
 compared with plants with intact spines. Moreover, it took caterpillars
 longer to defoliate species with relatively high spine numbers (S.
 carolinense and particularly S. atropurpureum) compared with S.
 aethiopicum, which has fewer spines. These findings suggest that spines
 may play a significant role in defence against insect herbivores by
 restricting herbivore movement and increasing the time taken to access
 feeding sites, with possible consequences including longer developmental
 periods and increased vulnerability or apparency to predators.
description: SPINES AND CATERPILLAR
 MVMT_KARIYAT RAW DATAraw data used for
 analyses
DOI: 10.5061/dryad.bg77p
title: Data from: Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake

description: The fate of antibiotic resistance genes (ARGs) in environmental microbial
 communities is of primary concern as prodromal of a potential transfer to
 pathogenic bacteria. Although of diverse origin, the persistence of ARGs
 in aquatic environments is highly influenced by anthropic activities,
 allowing potential control actions in well-studied environments. However,
 knowledge of abundance and space–time distribution of ARGs in ecosystems
 is still scarce. Using quantitative real-time PCR, we investigated the
 presence and the abundance of twelve ARGs (against tetracyclines,
 β-lactams, aminoglycosides, quinolones and sulphonamides) at different
 sampling sites, depths and seasons, in Lake Maggiore, a large subalpine
 lake, and in the area of its watershed. We then evaluated the correlation
 between each ARG and a number of ecological parameters in the water column
 in the deepest part of the lake. Our results suggest the constitutive
 presence of at least four ARGs within the bacterial community with a high
 proportion of bacteria potentially resistant to tetracyclines and
 sulphonamides. The presence of these ARGs was independent of the total
 bacterial density and temperature. The dynamics of tet(A) and sulII genes
 were, however, positively correlated with dissolved oxygen and negatively
 to chlorophyll a, suggesting that the resistant microbes inhabit specific
 niches. These observations indicate that the lake is a reservoir of
 antibiotic resistances, highlighting the need of a deeper understanding of
 the sources of ARGs and the factors allowing their persistence in waters.
description: Data ms Di Cesare et al
 to Mol Ecol
DOI: 10.5061/dryad.b8649
title: Data from: Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea

description: The taxonomy of the mottled rabbitfish Siganus fuscescens species complex
 has long been challenging. In this study, we analyzed microsatellite
 genotypes, mitochondrial lineages, and morphometric data from 373 S.
 fuscescens individuals sampled from the northern Philippines and Hong Kong
 (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative
 species boundaries in samples comprising three co-occurring mitochondrial
 lineages previously reported to characterize S. fuscescens (Clade A and
 Clade B) or S. canaliculatus (Clade C). We report the existence of two
 cryptic species within S. fuscescens in the northeast region of the South
 China Sea and northern Philippine Sea, supported by genetic and
 morphological differences. Individual-based assignment methods recovered
 concordant groupings of individuals into two nuclear genotype clusters
 (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them
 (FST = 0.241; P &lt; 0.001); (2) low frequency of later-generation
 hybrids; (3) significant association with mitochondrial Clade A and Clade
 B, respectively; and (4) subtle yet significant body shape differences as
 inferred from geometric morphometric analysis. The divergence between
 mitochondrial Clade C and the two other clades was not matched by genetic
 differences at microsatellite marker loci. The occurrence of discordant
 mitonuclear combinations (20.5% of the total number of individuals) is
 thought to result from mitochondrial introgression, consistent with a
 scenario of demographic, and presumably spatial, post-Pleistocene
 expansion of populations from northern regions into a secondary contact
 zone in the South China Sea. Mitonuclear discordance due to introgression
 obscures phylogenetic relationships for recently-diverged lineages, and
 cautions against the use of mitochondrial markers alone for species
 identification within the mottled rabbitfish species complex in the South
 China Sea region.
description: Siganus
 fuscescens_Microsat_Genotypes_RRGotanco et al 2017Microsatellite genotype
 data in csv format. Data collected from 12 microsatellite loci for 343
 individuals. File description in the first row. Locus names are in the
 second row. Individual names are in the first column, followed by
 alleles.Alleles are coded as fragment sizes, in separate columns. Missing
 data are indicated by ‘?.’
DOI: 10.5061/dryad.s91h2
title: Data from: Consistency pays: sex differences and fitness consequences of behavioural specialisation in a wide ranging seabird

description: Specialists and generalists often coexist within a single population, but
 the biological drivers of individual strategies are not fully resolved.
 When sexes differ in their foraging strategy, this can lead them to
 different environmental conditions and stability across their habitat
 range. As such, sexual segregation, combined with dominance, may lead to
 varying levels of specialization between the sexes. Here, we examine
 spatial and temporal niche width (intraindividual variability in aspects
 of foraging behaviour) of male and female black-browed albatrosses
 (Thalassarche melanophrys), and its consequences for fitness. We show that
 females, where maximum foraging range is under fluctuating selection,
 exhibit more variable behaviours and appear more generalist than males,
 who are under directional selection to forage close to the colony. However
 within each sex, successful birds had a much narrower niche width across
 most behaviours, suggesting some specialization is adaptive in both sexes.
 These results demonstrate that while there are sex differences in niche
 width, the fitness benefit of specialization in spatial distribution is
 strong in this wide-ranging seabird.
description: Patrick and Weimerskirch
 Consistency Pays Biol Letts 2014
DOI: 10.5061/dryad.11j35
title: Data from: Complexity of the genetic basis of aging in nature revealed by a clinal study of lifespan and methuselah, a gene for aging, in Drosophila from eastern Australia.

description: Clinal studies are a powerful tool for understanding the genetic basis of
 climatic adaptation. However, while clines in quantitative traits and
 genetic polymorphisms have been observed within and across continents, few
 studies have attempted to demonstrate direct links between them. The gene
 methuselah in Drosophila has been shown to have a major effect on stress
 response and longevity phenotypes based largely on laboratory studies of
 induced mutations in the mth gene. Clinal patterns in the most common mth
 haplotype and for lifespan (both increasing with latitude) have been
 observed in North American populations of D. melanogaster, implicating
 climatic selection. While these clinal patterns have led some to suggest
 that mth influences ageing in natural populations, limited evidence on the
 association between the two has so far been collected. Here, we describe a
 significant cline in the mth haplotype in eastern Australian D.
 melanogaster populations that parallel the cline in North America. We also
 describe a cline in mth gene expression. These findings further support
 the idea that mth is itself under selection. In contrast, we show that
 lifespan has a strong nonlinear clinal pattern, increasing southwards from
 the tropics, but then decreasing again from mid-latitudes. Furthermore, in
 association studies, we find no evidence for a direct link between mth
 haplotype and lifespan. Thus, while our data support a role for mth
 variation being under natural selection, we found no link to naturally
 occurring variation in lifespan and ageing in Australian populations of D.
 melanogaster. Our results indicate that the mth locus likely has genetic
 background and environment-specific effects.
description: Sgro et al Mol
 EcolRTPCR raw Cp
 valuesmth_haplotype_2005_rawThe spreadsheet contains raw genotyping data of mth haplotypes from the 2005 clinal populations.mean lifespanMean lifespan for each clinal population
DOI: 10.5061/dryad.937s037
title: Data from: The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity

description: CRISPR-Cas immune systems are present in around half of bacterial genomes.
 Given the specificity and adaptability of this immune mechanism, it is
 perhaps surprising that they are not more widespread. Recent insights into
 the requirement for specific host factors for the function of some
 CRISPR-Cas subtypes, as well as the negative epistasis between CRISPR-Cas
 and other host genes, have shed light on potential reasons for the partial
 distribution of this immune strategy in bacteria. In this study, we
 examined how mutations in the bacterial mismatch repair system, which are
 frequently observed in natural and clinical isolates and cause elevated
 host mutation rates, influence the evolution of CRISPR-Cas–mediated
 immunity. We found that hosts with a high mutation rate very rarely
 evolved CRISPR-based immunity to phage compared to wild-type hosts. We
 explored the reason for this effect and found that the higher frequency at
 which surface mutants pre-exist in the mutator host background causes them
 to rapidly become the dominant phenotype under phage infection. These
 findings suggest that natural variation in bacterial mutation rates may,
 therefore, influence the distribution of CRISPR-Cas adaptive immune
 systems.
description: 2.Chevallereau_host
 mutation rate on the evolution of CRISPR-Cas adaptive
 immunity_dataData collected in the
 laboratory and used to make the figures shown in the
 manuscript.
DOI: 10.5061/dryad.rt8n4
title: Data from: Salinization triggers a trophic cascade in experimental freshwater communities with varying food-chain length

description: The application of road deicing salts in northern regions worldwide is
 changing the chemical environment of freshwater ecosystems. Chloride
 levels in many lakes, streams, and wetlands exceed the chronic and acute
 thresholds established by the United States and Canada for the protection
 of freshwater biota. Few studies have identified the impacts of deicing
 salts in stream and wetland communities and none have examined impacts in
 lake communities. We tested how relevant concentrations of road salt (15,
 100, 250, 500, and 1000 mg Cl− L−1) interacted with experimental
 communities containing two or three trophic levels (i.e. no fish vs.
 predatory fish). We hypothesized that road salt and fish would have a
 negative synergistic effect on zooplankton, which would then induce a
 trophic cascade. We tested this hypothesis in outdoor mesocosms containing
 filamentous algae, periphyton, phytoplankton, zooplankton, several
 macroinvertebrate species, and fish. We found that the presence of fish
 and high salt had a negative synergistic effect on the zooplankton
 community, which in turn caused an increase in phytoplankton. Contributing
 to the magnitude of this trophic cascade was a direct positive effect of
 high salinity on phytoplankton abundance. Cascading effects were limited
 with respect to impacts on the benthic food web. Periphyton and snail
 grazers were unaffected by the salt-induced trophic cascade, but the
 biomass of filamentous algae decreased as a result of shading effects from
 phytoplankton. We also found direct negative effects of high salinity on
 the biomass of filamentous algae and amphipods (Hyalella azteca) and the
 mortality of banded mystery snails (Viviparus georgianus) and fingernail
 clams (Sphaerium simile). Clam mortality was dependent on the presence of
 fish, suggesting a non-consumptive interactive effect with salt. Our
 results indicate that globally increasing concentrations of road salt can
 alter community structure via both direct and indirect effects.
description: Salt x Chain Data -
 Hintz et al. - Ecological ApplicationsExperimental data.
 Variable descriptions are included in the excel file.
DOI: 10.5061/dryad.1h5717p
title: Data from: Annual flower strips support pollinators and potentially enhance red clover seed yield

description: 1. Ecological intensification provides opportunity to increase
 agricultural productivity while minimizing negative environmental impacts,
 by supporting ecosystem services such as crop pollination and biological
 pest control. For this we need to develop targeted management solutions
 that provide critical resources to service-providing organisms at the
 right time and place. 2. We tested whether annual strips of early
 flowering phacelia Phacelia tanacetifolia support pollinators and natural
 enemies of seed weevils Protapion spp., by attracting and offering nectar
 and pollen before the crop flowers. This was expected to increase yield of
 red clover Trifolium pratense seed. 3. We monitored insect pollinators,
 pests, natural enemies and seed yields in a total of 50 clover fields
 along a landscape heterogeneity gradient, over two years and across two
 regions in southern Sweden. About half of the fields were sown with flower
 strips of 125 to 2000 m2. 4. The clover fields were pollinated by 60%
 bumble bees Bombus spp. and 40% honey bees Apis mellifera. The clover seed
 yield was negatively associated with weevil density, but was unrelated to
 bee species richness and density. 5. Flower strips enhanced bumble bees
 species richness in the clover fields, with the strongest influence in
 heterogeneous landscapes. There were few detectable differences between
 crop fields with and without flower strips. However, long tongued bumble
 bees were redistributed towards field interiors and during phacelia bloom
 honey bees towards field edges. Clover seed yield also increased with
 increasing size of the flower strip. 6. Synthesis and application. Annual
 flower strips of early flower resources can support bumble bee species
 richness and, if sufficiently large, possibly also increase crop yields.
 However, clover seed yield was mainly limited by weevil infestation, which
 was not influenced by the annual flower strips. A future goal should be to
 design targeted measures for pest control.
description: Main
 datasetMain dataset including
 data for the whole season and all sites - see the read me
 file.RundlofEtal2018EE_maindata.csvCo-flower datasetDataset including only data for sites where the phacelia and clover both flowered - see the read me file.RundlofEtal2018EE_coflowerdata.csv
DOI: 10.5061/dryad.qs3jn16
title: Data from: Enhanced cycle stability of a NiCo2S4 nanostructured electrode for supercapacitors fabricated by the alternate-dip-coating method

description: Nanostructured nickel cobalt sulfide (NiCo2S4) electrodes are successfully
 fabricated using a simple alternate-dip-coating method. The process
 involves dipping a TiO2 nanoparticles-covered substrate in a nickel/cobalt
 precursor solution and sulfur precursor solution alternately at room
 temperature. The fabricated bimetallic sulfide electrode exhibits a
 synergetic improvement compensating for the disadvantages of the two
 single metal sulfide electrodes, i.e. the poor cycle stability of the
 nickel sulfide electrode and the low specific capacitance (C) of the
 cobalt sulfide electrode. The two capacitive properties are optimized by
 adjusting the ratio of nickel and cobalt concentrations in the metal
 precursor solution, reaching a C of 516 F/g at a current density of 1
 mA/cm2 and its retention of 99.9 % even after 2000 galvanostatic
 charge-discharge cycles.
description: XRD measurements of
 metal sulfide-coated TiO2 nanoparticlesPeak position and full
 width at half maximum (FWHM) values of pristine, NiS, Co3S4 and
 NiCo2S4-coated TiO2 nanoparticles in x-ray diffraction
 measurementsXRD
 data.xlsxAreal capacitance values
 of nanostructured metal sulfide electrodesAreal capacitance values
 measured at various scan rates for the nanostructrued NiS, Co3S4 and
 NiCo2S4 electrodes fabricated by the alternate dip coating
 methodCareal at various scan
 rates.xlsxSpecific capacitance
 values measured at various current densitiesSpecific capacitance
 values measured at various current densities for the nanostructrued NiS,
 Co3S4 and NiCo2S4 electrodes fabricated by the alternate dip coating
 methodCsp
 at various current
 densities.xlsxCycle life of
 nanostructured metal sulfide electrodesSpecific capacitance
 values after various numbers of galvanostatic charge-discharge cycles for
 the nanostructrued NiS, Co3S4 and NiCo2S4 electrodes.Cycle
 life.xlsx
DOI: 10.15468/dl.m6c9gu
title: Occurrence Download

description: A dataset containing 226626 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Annonaceae",
 "Continent is one of (Africa, South America)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 226626 records from 1056 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001072-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15063940
title: QuiCAT: A Scalable and Flexible Framework for Mapping Synthetic Sequences

description: This Zenodo Entry contains the datasets generated for the quicat manuscript.
description:  

quicat_single_cell_data.tar.gz:

Contains the single cell data used in quicat manuscript.

Six bulk and five clonal primary pancreatic tumor mouse cell lines used for the single cell RNA-seq experiment. The five clonal cell lines were barcoded with Nuclear procode vector kit library (Addgene #1000000197) and isolated as single clones. All eleven cell lines were trypsinized and pooled together in equal amounts, then 5 million cells were fixed according to the protocol for Chromium Fixed RNA Profiling (10x). After fixation, a pool of 1 million cells was used for hybridization with probes, including custom probes, which lasted 19 h. For generation of GEM, 20000 cells were loaded on the chip and library was constructed as described in the guidelines (10x genomics,User guide CG000691). Quality and size analysis of cDNAs and libraries was performed on an Agilent Bioanalyzer 2100 using HS DNA Kit (Agilent). The sample was sequenced with Novaseq PE100 mode (Illumina) following the standard protocol.

Content of the archive:

Cellranger output files to reproduce single-cell analyses in quiCAT paper




barcodes.tsv.gz
whitelisted cells


sample_filtered_feature_bc_matrix.h5
count matrix 


sample_alignments.bam
bam alignment file


sample_alignments.bam.bai
bam alignment index




 

larry_dna.tar.gz:

Contains the DNA sequencing data for LARRY barcoded clonal cell lines used in quicat manuscript.

Unique lineage and RNA recovery (LARRY) DNA barcodes were generated using a modified LARRY barcoding system (Weinreb 2020; Addgene plasmid #140025). This modified construct includes the addition of a puromycin resistance marker, which is connected via a T2A self-cleaving peptide to the EGFP reporter containing a semi-random 16-mer in its 3’UTR. (sequence structure NNNNCTNNNNACNNNN).

Equal numbers of cells from each of the verified clones were pooled and immediately processed for barcode amplification.

Content of the archive:




single_clones directory
NGS sequencing data of single clones before pooling


pooled_clones directory
NGS sequencing data of pooled clones