cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nzs7h44t3
title: Data from: Darwin’s small and medium ground finches might have taste preferences, but not for human foods

description: Urbanization is rapidly changing ecological niches. On the inhabited
 Galapagos Islands, Darwin’s finches consume human-introduced foods
 preferentially; however, it remains unclear why. Here we presented pastry
 with flavour profiles typical of human foods (oily, salty, sweet) to small
 ground finches (Geospiza fuliginosa) and medium ground finches (Geospiza
 fortis) to test if latent taste preferences might drive selection of human
 foods. If human-food flavours were consumed more than a neutral or bitter
 control only at sites with human foods, then we predicted tastes were
 acquired after urbanization; however, if no site-differences were found
 then this would indicate latent taste preferences. Contrary to both
 predictions, we found little evidence that human-food flavours were
 preferred compared to control flavours at any site. Instead, finches
 showed a weak aversion to oily foods, but only at remote (no human foods
 present) sites. This was further supported by behavioural responses, with
 beak wiping occurring more often at remote sites after finches tasted
 flavours associated with human foods. Our results suggest, therefore, that
 while Darwin’s finches exposed to human foods might have acquired a
 tolerance human food flavours, latent taste preferences are unlikely to
 have played a major role in their dietary response to increased
 urbanization.
DOI: 10.5061/dryad.ht76hdrhh
title: A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae

description: Although studies of Saccharomyces cerevisiae have provided many insights
 into mutagenesis and DNA repair, most of this work has focused on a few
 laboratory strains. Much less is known about the phenotypic effects of
 natural variation within S. cerevisiae’s DNA repair pathways. Here, we use
 natural polymorphisms to detect historical mutation spectrum differences
 among several wild and domesticated S. cerevisiae strains. To determine
 whether these differences are likely caused by genetic mutation rate
 modifiers, we use a modified fluctuation assay with a CAN1 reporter to
 measure de novo mutation rates and spectra in 16 of the analyzed strains.
 We measure a 10-fold range of mutation rates and identify two strains with
 distinctive mutation spectra. These strains, known as AEQ and AAR, come
 from the panel’s ‘Mosaic beer’ clade and share an enrichment for C
 &gt; A mutations that is also observed in rare variation segregating
 throughout the genomes of several Mosaic beer and Mixed origin strains.
 Both AEQ and AAR are haploid derivatives of the diploid natural isolate
 CBS 1782, whose rare polymorphisms are enriched for C &gt; A as well,
 suggesting that the underlying mutator allele is likely active in nature.
 We use a plasmid complementation test to show that AAR and AEQ share a
 mutator allele in the DNA repair gene OGG1, which excises 8-oxoguanine
 lesions that can cause C &gt; A mutations if left unrepaired.
description: This includes some large files generated during data analysis
 process for the paper.  - sites from S.paradoxus that
 have been aligned to S.cerevisiae: Scer_para_consol_SNPs.txt
 - vcf file for the 1011 S.cerevisiae after filtering to count
 mutation spectra from polymorphisms: 
 1011_SNP_bi_mm0.8_GT_u_rm_final_no_close.vcf.gz
DOI: 10.5061/dryad.1ns1rn8vv
title: PAM-altering SNP-based allele-specific CRISPR-Cas9 therapeutic strategies for Huntington's disease

description: Huntington's disease (HD) is caused by an expanded CAG repeat in
 huntingtin (HTT). Since HD is dominant, and loss of HTT leads to
 neurological abnormalities, safe therapeutic strategies require selective
 inactivation of mutant HTT. Previously, we proposed a concept of
 CRISPR-Cas9 using mutant-specific PAM sites generated by SNPs to
 selectively inactivate mutant HTT. Aiming at revealing suitable targets
 for clinical development, we analyzed the largest HD genotype dataset to
 reveal target PAM-altering SNPs (PAS) and subsequently evaluated their
 allele specificities. The gRNAs based on the PAM sites generated by
 rs2857935, rs16843804, and rs16843836 showed high levels of allele
 specificity in patient-derived cells. Simultaneous use of two gRNAs based
 on rs2857935-rs16843804 or rs2857935-rs16843836 produced selective genomic
 deletions in mutant HTT and prevented the transcription of mutant HTT mRNA
 without impacting the expression of normal counterpart or re-integration
 of the excised fragment elsewhere in the genome. RNAseq and off-target
 analysis confirmed high levels of allele specificity and the lack of
 recurrent off-targeting. Approximately 60% of HD subjects are eligible for
 mutant-specific CRISPR-Cas9 strategies of targeting one of these 3 PAS in
 conjunction with one non-allele-specific site, supporting high
 applicability of PAS-based allele-specific CRISPR approaches in the HD
 patient population.
description: To fully characterize the molecular consequences of our
 mutant-specific CRISPR-Cas9 strategy, we performed RNAseq analysis. We
 transfected two HD iPSC lines (iPSC-A and iPSC-B) carrying adult onset CAG
 repeats with mutant-specific CRISPR-Cas9 (PX551 EFS vector expression
 SpCas9 and PX552 EFS plasmid expressing our test gRNA; experimental group;
 L4-R4 or L4-R6) or empty vector (PX551 EFS vector for SpCas9 and empty
 PX552 vector without gRNA; control group). Single cell clones were
 subsequently developed by limited dilution. Finally, 12 and 20 clonal
 lines were developed for the empty vector (EV) and TP-CRISPR group
 respectively. Clonal lines were further validated by Sanger sequencing and
 MiSeq analysis of genomic DNA. Then, genome-wide RNAseq analysis was
 performed by the Broad Institute. Sequence data were processed by STAR
 aligner as part of the Broad Institute's standard RNAseq analysis
 pipeline. For differential gene expression (DGE) analysis, we used
 transcripts per million (TPM) data computed by the TPMCalculator
 (https://github.com/ncbi/TPMCalculator). Expression levels in 20,260
 protein-coding genes based on Ensembl
 (ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/) were normalized;
 3,420 genes were excluded due to zero TPM values in at least one
 sample.
DOI: 10.5061/dryad.vq83bk3tp
title: Diatom biogeography in freshwaters – new insights from between-region comparisons and the role of unmeasured environmental factors

description: Diatom biogeography has attracted increased attention especially over the
 past two decades. However, due to covariance between space and
 environment, diatom biogeographical studies suffer from the fundamental
 problem of reliably evaluating the relative roles of dispersal processes
 versus local environment in shaping diatom distributions. Using
 between-region comparisons, we investigate whether diatom community
 differences stem partly from dispersal effects or are purely driven by the
 local environment. The data used comprise diatom presence-absence records
 and associated environmental-variable data from streams in Iceland and in
 northern Fennoscandia (Finland and Norway), and from ponds and lakes in
 Italy and northern Fennoscandia. We found that between-region differences
 were larger for diatom community composition than for local environmental
 variables, perhaps suggesting that biogeographical factors such as
 dispersal limitation or dispersal history influenced diatom communities
 causing their spatial segregation. We further discuss methods for
 disentangling the roles of spatial and environmental effects in shaping
 diatom communities. Finally, we highlight the possible role of unmeasured
 environmental factors in diatom biogeographical research.
description: Datasets were collected from streams and lakes in Northern
 Fennoscandia (Norway, Finland), Iceland and Italy. Diatoms were collected
 from benthic habitats using a toothbrush.
description: Please see Readme file for insructions for the dataset.
DOI: 10.5061/dryad.cz8w9gj4w
title: The impact of life stage and pigment source on the evolution of novel warning signal traits

description: Our understanding of how novel warning color traits evolve in natural
 populations is largely based on studies of reproductive stages and
 organisms with endogenously produced pigmentation. In these systems,
 genetic drift is often required for novel alleles to overcome strong
 purifying selection stemming from frequency-dependent predation and
 positive assortative mating. Here, we integrate data
 from field surveys, predation experiments, population genomics,
 and phenotypic correlations to explain the origin and maintenance
 of geographic variation in a diet-based larval pigmentation trait in the
 redheaded pine sawfly (Neodiprion lecontei), a pine-feeding hymenopteran.
 Although our experiments confirm that N. lecontei larvae
 are indeed aposematic—and
 therefore likely to experience frequency-dependent
 predation—our genomic data do not support a historical
 demographic scenario that would
 have facilitated the spread of an initially deleterious
 allele via drift. Additionally, significantly elevated differentiation at
 a known color locus suggests that geographic variation in larval color is
 currently maintained by selection. Together, these data suggest
 that the novel white morph likely spread via selection.
 However, white body color does not enhance aposematic
 displays, nor is it correlated with enhanced chemical defense or
 immune function. Instead, the derived white-bodied morph
 is disproportionately abundant on a pine species with a reduced carotenoid
 content relative to other pine hosts, suggesting that
 bottom-up selection via host plants may have driven divergence among
 populations. Overall, our results suggest that life stage and
 pigment source can have a substantial impact the evolution of novel
 warning signals, highlighting the need to investigate diverse aposematic
 taxa to develop a comprehensive understanding of color variation in
 nature.
DOI: 10.5061/dryad.jdfn2z3cb
title: Declining survival rates of red foxes (Vulpes vulpes) during the first outbreak of sarcoptic mange in Sweden

description: Rapid declines in red fox (Vulpes vulpes) populations have followed
 outbreaks of epizootic mange caused by the mite Sarcoptes scabiei. In
 Sweden, the first outbreak of sarcoptic mange started in 1977/78 and
 affected the whole country by 1984. Here we used data on number of
 harvested red foxes from Gävleborg county (18 199 km2) in Sweden between
 1970 and 1994. We used data on the prevalence of sarcoptic mange in
 harvested red foxes from 1974 to 1982. A rapid decline in harvested foxes
 occurred two to three years after the prevalence of sarcoptic mange first
 became evident. In the same period, Mark-Recovery data were used to
 estimate changes in survival rates, and the best model included an effect
 of age (young or adult) and period (annual) on the survival and recapture
 probabilities. The analysis was based data from 701 young foxes of which
 523 were recovered, and 133 adults of which 131 were recovered. Average
 annual survival was 0.55 (range=0.53-0.58) for adult and 0.36
 (range=0.32-0.39) for young foxes in the three years preceding the
 outbreak. During the outbreak and the remaining six years of the study,
 the average survival was reduced to 0.41 (range=0.30-0.48) for adult and
 to 0.25 (range=0.17-0.30) for young foxes. A population model, based on
 our results on survival and literature data on fecundity, was developed to
 project the decline of the fox population. The rate and magnitude of the
 reduction in the projected population and harvested foxes were similar,
 with both reduced by almost ninety percent. Harvest statistics indicate
 the fox population recovered to pre-mange densities in less than 10 years
 after the first detection of mange indicating a rapid development of
 resistance in the host. This study shows the importance of long-term
 population monitoring in combination with large-scale field-experiments to
 device alternative management options.
description: You will find the mark recovery data in the methods section,
 separate for adults and young. The second data set is the macroscopic
 prevalence of sarcoptic mange of collected foxes from hunter. It is
 uploaded as an excel file. See the published article and the supporting
 material for more information.
DOI: 10.5061/dryad.b2rbnzsgz
title: Whole genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot

description: 1. Biodiversity hotspots, such as the Caucasus mountains, provide
 unprecedented opportunities for understanding the evolutionary processes
 that shape species diversity and richness. Therefore, we investigated the
 evolution of Primula sect. Primula, a clade with a high degree of endemism
 in the Caucasus. 2. We performed phylogenetic and network analyses of
 whole-genome resequencing data from the entire nuclear genome, the entire
 chloroplast genome, and the entire heterostyly supergene. The different
 characteristics of the genomic partitions and the resulting phylogenetic
 incongruences enabled us to disentangle evolutionary histories resulting
 from tokogenetic versus cladogenetic processes. We provide the first
 phylogeny inferred from the heterostyly supergene that includes all
 species of Primula sect. Primula. 3. Our results identified recurrent
 admixture at deep nodes between lineages in the Caucasus as the cause of
 non-monophyly in Primula. Biogeographic analyses support the
 “out-of-the-Caucasus” hypothesis, emphasizing the importance of this
 hotspot as a cradle for biodiversity. 4. Our findings provide novel
 insights into causal processes of phylogenetic discordance, demonstrating
 that genome-wide analyses from partitions with contrasting genetic
 characteristics and broad geographic sampling are crucial for
 disentangling the diversification of species-rich clades in biodiversity
 hotspots.
description: Tree files and alignments (fastas) for
 <em>Primula</em> sect. <em>Primula</em> phylogeny.
 Includes complete nuclear, plastid, and s-locus alignments.
 All fastas were created from VCFs that were filtered. Variant
 calling was performed by BCFtools v.1.8 multiallelic caller and set to
 output only variant site. Repetitive sequence regions were masked based on
 the annotation from Potente et al. (2022). Filtering was performed using
 VCFtools v.0.1.14 and set to remove indels and include only single
 nucleotide polymorphisms (SNPs) occurring in at least 80% of individuals,
 with a minimum site quality of 30, and a mean site depth between 5x and
 60x. All fastas were output with heterozygous sites randomly
 resolved.  For information about phylogenies, please
 see the manuscript.
DOI: 10.5061/dryad.8pk0p2npg
title: Data from: The roles of growth regulation and appendage patterning genes in the morphogenesis of treehopper pronota

description: Treehoppers of the insect family Membracidae have evolved enlarged and
 elaborate pronotal structures, which is hypothesized to involve co-opted
 expression of genes that are shared with the wings. Here, we investigate
 the similarity between the pronotum and wings in relation to growth. We
 show that the ontogenetic allometry of the pronotum is similar to that of
 wings in Membracidae, but not the outgroup. Using transcriptomics, we find
 genes related to protein synthesis and translation are mutually
 upregulated. These genes are implicated in the eIF2, eIF4/p70S6K, and mTOR
 pathways, and have known roles in regulating cell growth and
 proliferation. We show that species-specific differential growth
 patterning of the pronotum begins as early as the third instar. This
 finding suggests that co-option of appendage patterning genes must occur
 before the metamorphic molt. We propose that a network related to growth
 and size determination is the more likely mechanism shared with wings.
 However, regulators upstream of the shared genes in the pronotum and wings
 need to be elucidated to substantiate whether co-option has occurred.
 Finally, we believe it will be helpful to distinguish the mechanisms
 leading to pronotal size from those regulating pronotal shape as we make
 sense of this spectacular evolutionary innovation.
DOI: 10.5281/zenodo.14892376
title: The SiliROck lithotheque: Geochemical Data of Scaglia Bianca Chert from Central Italy

description: The dataset shows part of the chert collection SiliROck, and the geochemical data acquired. It includes 110 chert samples from five different deposits, both primary and secondary, belonging to Scaglia Bianca Fm, located in the Abruzzo (1), Latium (3) and Umbria (1) regions. At least 15 samples per outcrop have been characterized.

The database is equipped with:



ID_sample: the identification code of the sample, composed by the GPS point name and the ID number of the sample

Region: the region where sampling was performed

Paleoenvironment: the depositional environment of the rock sample

Age: the age of the geological unit according to the geological literature (see relative paper)

Deposit: the type of source, whether primary or secondary (see relative paper)

Geochemistry: the geochemical data acquired through the pXRF analysis


The dataset is accompanied by a photographic archive where a selection of representative photomicrographs is shown. Chert fresh surfaces have been cleaned and immersed in water and photomicrographs have been acquired using a Leica EZ4W stereomicroscope with built-in LED illumination and CMOS camera.
DOI: 10.5281/zenodo.14892377
title: The SiliROck lithotheque: Geochemical Data of Scaglia Bianca Chert from Central Italy

description: The dataset shows part of the chert collection SiliROck, and the geochemical data acquired. It includes 110 chert samples from five different deposits, both primary and secondary, belonging to Scaglia Bianca Fm, located in the Abruzzo (1), Latium (3) and Umbria (1) regions. At least 15 samples per outcrop have been characterized.

The database is equipped with:



ID_sample: the identification code of the sample, composed by the GPS point name and the ID number of the sample

Region: the region where sampling was performed

Paleoenvironment: the depositional environment of the rock sample

Age: the age of the geological unit according to the geological literature (see relative paper)

Deposit: the type of source, whether primary or secondary (see relative paper)

Geochemistry: the geochemical data acquired through the pXRF analysis


The dataset is accompanied by a photographic archive where a selection of representative photomicrographs is shown. Chert fresh surfaces have been cleaned and immersed in water and photomicrographs have been acquired using a Leica EZ4W stereomicroscope with built-in LED illumination and CMOS camera.
DOI: 10.5061/dryad.05qfttf49
title: Tri-trophic interactions with avian predators: the effect of host plant species and herbivore-induced plant volatiles on recruiting avian predators

description: Herbivore-induced plant volatiles (HIPVs) are important signaling
 compounds released by plants upon wounding. These compounds have been
 shown to mediate tri-trophic interactions in recruiting insect predators
 and parasitoids. Recent work has begun to show that avian species, which
 were once thought to have a very limited sense of smell, can cue in on
 these HIPVs to find insect prey. Here, we test the ability for two general
 HIPVs, methyl jasmonate and methyl salicylate, to recruit avian predators.
 We test the recruitment efficacies of these HIPVs across 4 different host
 plant species (black walnut, red maple, cattail, and wheat) and use clay
 caterpillars to quantify predation by insectivorous birds. We found no
 significant differences in predation between treatment groups across any
 of our host plants. However, there was a nearly-significant effect of
 methyl salicylate in black-walnut trees. Interestingly, our results did
 show a significant effect of host plant species on predation levels. The
 two tree species, particularly black walnut, had higher levels of
 predation than the herbaceous species. We discuss the implications of
 these results and suggest a number of ideas and suggestions for future
 studies investigating the role of HIPVs in attracting insectivorous birds.
DOI: 10.5061/dryad.4mw6m90bx
title: Supporting CT Data for: Two exceptionally preserved juvenile specimens of Gorgosaurus libratus (Tyrannosauridae, Albertosaurinae) provide new insight into the timing of ontogenetic changes in tyrannosaurids

description: Known from dozens of specimens discovered since the early 20th century,
 Gorgosaurus libratus has arguably contributed more than any other taxon to
 our understanding of the life history of tyrannosaurids. However, juvenile
 material for this taxon is rare. Here, we describe two small, articulated
 Gorgosaurus specimens (skull lengths of ~500 mm) that help advance our
 knowledge of the anatomy and ontogeny of this taxon and of tyrannosaurids
 in general. The new specimens exhibit hallmark juvenile tyrannosaurid
 features, including long, low, and narrow skulls, large circular orbits,
 absent or incipient cranial ornamentation, ziphodont dentition, and an
 overall gracile skull frame. Comparison with other Gorgosaurus specimens
 of various ontogenetic stages allows for an examination of the timing of
 morphological changes that occurred through ontogeny in this taxon
 relative to other tyrannosaurids. Of particular note, Gorgosaurus and the
 larger Tyrannosaurus rex are found to have experienced similar ontogenetic
 transformations at similar percent skull length relative to the large
 known individuals for each respective taxon but at different absolute body
 sizes and biological ages, occurring at a larger size and older age in T.
 rex than in Gorgosaurus. These results suggest a dissociation between the
 timing of cranial development and body size in tyrannosaurids. Finally,
 the recognition of ontogenetically invariant characters in Gorgosaurus
 makes it possible to determine the taxonomic identity of previously
 misidentified specimens.
description: Data includes CT scans of the palate and medial mandible bones of
 juvenile Gorgosaurus specimens TMP 2009.12.14 and TMP 2016.14.1 and the
 alveolar region of the maxillae of TMP 1994.143.1. CT
 scan information: TMP 2016.14.1 was scanned at Mayfair
 Diagnostics, GE Discovery CT750 HD, 120 KVP, slice thickness 0.625mm
 (Z-dimension) for a total XYZ voxel dimensions of 0.841797 x 0.841797 x
 0.625mm. <br>    TMP 2009.12.14 was scanned at Drumheller Hospital,
 Toshiba Aquilion, 120 KVP, slice thickness 0.5mm (Z-dimension) for a total
 XYZ voxel dimensions of 0.595 x 0.595 x 0.5mm.<br>    TMP
 1994.143.1: Mayfair Diagnostics, GE Discovery CT750 HD, 120 KVP, slice
 thickness 0.625mm (Z-dimension) for a total XYZ voxel dimensions of
 0.746094 x 0.746094 x 0.625mm.