cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.v62z2t
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phalaris arundinacea",
 "Country is Chile",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035652-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tktfsu
title: Occurrence Download

description: A dataset containing 4076 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pycnanthemum incanum"
 ]
}

 The dataset includes 4076 records from 153 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035653-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7b9qfs
title: Occurrence Download

description: A dataset containing 48652 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ajuga chamaepitys"
 ]
}

 The dataset includes 48652 records from 807 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035651-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5cvh2s
title: Occurrence Download

description: A dataset containing 4366 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cygnus atratus",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4366 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035654-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.asnrm8
title: Occurrence Download

description: A dataset containing 50604 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lathyrus palustris"
 ]
}

 The dataset includes 50604 records from 636 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035539-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t23jw8
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cygnus atratus",
 "Country is Iceland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 29 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035655-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16933139
title: Extended data for :Single-cell RNA sequencing of cerebrospinal fluid reveals the expansion of innate lymphoid cells with upregulated transposable elements in multiple sclerosis

description: Fig.1: Single-cell analysis of cells from CSF samples of individuals with IIH patients as controls and MS patients

Fig.2: Bar plot summarizing the number of significantly upregulated TE subfamilies (logFC>0.5 and adj. p-value <0.05) in each cluster from IIH (a) and MS (b) patients

Fig.3: Cell type, GO molecular function, and KEGG pathway enrichment analysis for the list of TFs that probably could bind to the TE-enriched locations in the genome.

Supplementary  Tables    DescriptionTable S1                          Gene MarkerTable S2                          Differential expression analysis between all clusters in IIH populationTable S3                          Differential expression analysis between all clusters in MS populationTable S4                          Number of cells in each cluster of IIH samplesTable S5                          Number of cells in each cluster of MS samplesTable S6                          Retrotransposon-transcription factor associations
DOI: 10.5281/zenodo.16933140
title: Extended data for :Single-cell RNA sequencing of cerebrospinal fluid reveals the expansion of innate lymphoid cells with upregulated transposable elements in multiple sclerosis

description: Fig.1: Single-cell analysis of cells from CSF samples of individuals with IIH patients as controls and MS patients

Fig.2: Bar plot summarizing the number of significantly upregulated TE subfamilies (logFC>0.5 and adj. p-value <0.05) in each cluster from IIH (a) and MS (b) patients

Fig.3: Cell type, GO molecular function, and KEGG pathway enrichment analysis for the list of TFs that probably could bind to the TE-enriched locations in the genome.

Supplementary  Tables    DescriptionTable S1                          Gene MarkerTable S2                          Differential expression analysis between all clusters in IIH populationTable S3                          Differential expression analysis between all clusters in MS populationTable S4                          Number of cells in each cluster of IIH samplesTable S5                          Number of cells in each cluster of MS samplesTable S6                          Retrotransposon-transcription factor associations
DOI: 10.15468/dl.9326nj
title: Occurrence Download

description: A dataset containing 176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cygnus atratus",
 "Country is Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 176 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035659-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.utdj28
title: Occurrence Download

description: A dataset containing 4708 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pycnanthemum muticum"
 ]
}

 The dataset includes 4708 records from 164 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035656-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15485701
title: Rapid-E output for aerosolized fluorophores and Bacteria

description: Zip containing the compressed outputs of Rapid-E device after passing through different aerosolized fluorophores and bacteria. See https://github.com/AlFontal/lif-bacteria-aerosols-ms for more information.
DOI: 10.5281/zenodo.15485702
title: Rapid-E output for aerosolized fluorophores and Bacteria

description: Zip containing the compressed outputs of Rapid-E device after passing through different aerosolized fluorophores and bacteria. See https://github.com/AlFontal/lif-bacteria-aerosols-ms for more information.
DOI: 10.15468/dl.kcytsj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eubalaena glacialis (Müller, 1776)",
 "HasCoordinate is true",
 "Geometry POLYGON((-6.000000 30.000000, -6.000000 47.000000, 42.000000 47.000000, 42.000000 30.000000, -6.000000 30.000000))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002575-250426092105405/datasets/export for details.
DOI: 10.14288/1.0398076
title: Data from: Predator kairomones change food web structure and function, regardless of cues from consumed prey

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Predation risk in aquatic systems is often assessed by prey through chemical cues, either those released by prey or by the predator itself. Many studies on predation risk focus on simple pairwise interactions, with only a few studies examining community-level and ecosystem responses to predation risk in species-rich food webs. Further, of these few community-level studies, most assume that prey primarily assess predation risk through chemical cues from consumed prey, even heterospecific prey, rather than just those released by the predator. Here, we compared the effects of different predation cues (predator presence with or without consumed prey) on the structure and functioning of a speciose aquatic food web housed in tropical bromeliads. We found that the mere presence of the top predator (a damselfly) had a strong cascading effect on the food web, propagating down to nutrient cycling. This predation risk cue had no effect on the identity of colonizing species, but strongly reduced the abundance and biomass of the macroinvertebrate colonists. As a result, bacterial biomass and nitrogen cycling doubled, with a concomitant decrease in bacterial production, but CO2 flux was unaffected. These community and ecosystem effects of predator presence cues were not amplified by the addition of chemical cues from consumed prey. Our results show that some of the consequences of predation risk observed in controlled experiments with simplified food webs may be observed in a natural, species-rich food web.
DOI: 10.14288/1.0398077
title: Data from: Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Willows (Salix: Salicaceae) form a major ecological component of Holarctic floras, and consequently are an obvious target for a DNA-based identification system. We surveyed two to seven plastid genome regions (~3.8 kb; ~3% of the genome) from 71 Salix species across all five subgenera, to assess their performance as DNA barcode markers. Although Salix has a relatively high level of interspecific hybridization, this may not sufficiently explain the near complete failure of barcoding that we observed: only one species had a unique barcode. We recovered 39 unique haplotypes, from more than 500 specimens, that could be partitioned into six major haplotype groups. A unique variant of group I (haplotype 1*) was shared by 53 species in three of five Salix subgenera. This unusual pattern of haplotype sharing across infrageneric taxa is suggestive of either a massive non-random coalescence failure (incomplete lineage sorting), or of repeated plastid capture events, possibly including a historical selective sweep of haplotype 1* across taxonomic sections. The former is unlikely as molecular dating indicates that haplotype 1* originated recently, and is nested in the oldest major haplotype group in the genus. Further, we detected significant non-neutrality in the frequency spectrum of mutations in group I, but not outside group I, and demonstrated a striking absence of geographic structure to the haplotype distributions in this group. The most likely explanation for the patterns we observed involves recent repeated plastid capture events, aided by widespread hybridization and long-range seed dispersal, but primarily propelled by one or more trans-species selective sweeps.
DOI: 10.14288/1.0398078
title: Data from: Stabilizing selection, mutational bias and the evolution of sex

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Stabilizing selection around a fixed phenotypic optimum is expected to disfavor sexual reproduction, since asexually reproducing organisms can maintain a higher fitness at equilibrium, while sex disrupts combinations of compensatory mutations. This conclusion rests on the assumption that mutational effects on phenotypic traits are unbiased, that is, mutation does not tend to push phenotypes in any particular direction. In this paper, we consider a model of stabilizing selection acting on an arbitrary number of polygenic traits coded by bialellic loci, and show that mutational bias may greatly reduce the mean fitness of asexual populations compared with sexual ones in regimes where mutations have weak to moderate fitness effects. Indeed, mutation and drift tend to push the population mean phenotype away from the optimum, this effect being enhanced by the low effective population size of asexual populations. In a second part, we present results from individual-based simulations showing that positive rates of sex are favored when mutational bias is present, while the population evolves towards complete asexuality in the absence of bias. We also present analytical (QLE) approximations for the selective forces acting on sex in terms of the effect of sex on the mean and variance in fitness among offspring.
DOI: 10.14288/1.0398079
title: Data from: Shared genetic diversity across the global invasive range of the Monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;While genetic diversity is hypothesized to be an important factor explaining invasion success, there is no consensus yet on how variation in source populations or demographic processes affects invasiveness. We used mitochondrial DNA haplotypic and microsatellite genotypic data to investigate levels of genetic variation and reconstruct the history of replicate invasions on three continents in a globally invasive bird, the monk parakeet (Myiopsitta monachus). We evaluated whether genetic diversity at invasive sites could be explained by (i) the native source populations from which they were derived and (ii) demographic bottlenecks during introduction. Genetic data indicated a localized source area for most sampled invasive populations, with limited evidence for admixing of native source populations. This pattern largely coincides with historical data on pet trade exports. However, the invasive populations are genetically more similar than predicted from the export data alone. The extent of bottleneck effects varied among invasive populations. The observed low genetic diversity, evidence of demographic contraction and restricted source area do not support the hypothesis that invasion is favoured by the mixing and recombining of genetic variation from multiple source populations. Instead, they suggest that reduced genetic variation through random processes may not inhibit successful establishment and invasion in this species. However, convergent selection across invasive sites could also explain the observed patterns of reduction and similarity in genetic variation and/or the restricted source area. In general, the alternative explanation of intraspecific variation in invasive potential among genotypes or geographic areas is neglected, but warrants more attention as it could inform comparative studies and management of biological invaders.
DOI: 10.14288/1.0398080
title: Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.
DOI: 10.14288/1.0398081
title: Data from: Widespread genetic incompatibilities between first-step mutations during parallel adaptation of Saccharomyces cerevisiae to a common environment

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Independently evolving populations may adapt to similar selection pressures via different genetic changes. The interactions between such changes, such as in a hybrid individual, can inform us about what course adaptation may follow and allow us to determine whether gene flow would be facilitated or hampered following secondary contact. We used Saccharomyces cerevisiae to measure the genetic interactions between first-step mutations that independently evolved in the same biosynthetic pathway following exposure to the fungicide nystatin. We found that genetic interactions are prevalent and predominantly negative, with the majority of mutations causing lower growth when combined in a double mutant than when alone as a single mutant (sign epistasis). The prevalence of sign epistasis is surprising given the small number of mutations tested and runs counter to expectations for mutations arising in a single biosynthetic pathway in the face of a simple selective pressure. Furthermore, in one third of pairwise interactions, the double mutant grew less well than either single mutant (reciprocal sign epistasis). The observation of reciprocal sign epistasis among these first adaptive mutations arising in the same genetic background indicates that partial postzygotic reproductive isolation could evolve rapidly between populations under similar selective pressures, even with only a single genetic change in each. The nature of the epistatic relationships was sensitive, however, to the level of drug stress in the assay conditions, as many double mutants became fitter than the single mutants at higher concentrations of nystatin. We discuss the implications of these results both for our understanding of epistatic interactions among beneficial mutations in the same biochemical pathway and for speciation.
DOI: 10.14288/1.0398082
title: Data from: Relative importance of competition and plant-soil feedback, their synergy, context dependency and implications for coexistence

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Plants interact simultaneously with each other and with soil biota, yet the relative importance of competition versus plant soil feedback (PSF) on plant performance is poorly understood. Using a meta-analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter- vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide-treated soil) depended on treatments but were predominantly negative, broadly comparable in magnitude, and additive or synergistic. Stronger competitors experienced more negative PSF than weaker competitors when controlling for density (inter- to intraspecific competition), suggesting that PSF could prevent competitive dominance and promote coexistence. When competition was measured against plants growing singly, the strength of competition overwhelmed PSF, indicating that the relative importance of PSF may depend not only on neighbor identity but also density. We evaluate how competition and PSFs might interact across resource gradients; PSF will likely strengthen competitive interactions in high resource environments and enhance facilitative interactions in low resource environments. Finally, we provide a framework for filling key knowledge gaps and advancing our understanding of how these biotic interactions influence community structure.
DOI: 10.14288/1.0398084
title: Data from: Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high-throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors (RCFs) that account for multiple sources of bias and are applicable to field studies. RCFs will be most effective if they are not affected by input mass ratio or co-occurring species. In a model experiment involving three target fish species and a fixed control, we found RCFs did vary with input ratio but in a consistent fashion, and that 50/50 RCFs applied to DNA sequence counts from various mixtures of the target species still greatly improved relative abundance estimates (e.g. average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for corrected estimates). To demonstrate the use of correction factors in a field setting, we calculated 50/50 RCFs for 18 harbour seal (Phoca vitulina) prey species (RCFs ranging from 0.68 to 3.68). Applying these corrections to field-collected seal scats affected species percentages from individual samples (Δ 6.7 ± 6.6%) more than population-level species estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach is an effective tool for evaluating and correcting biases in DNA metabarcoding studies. The decision to apply correction factors will be influenced by the feasibility of creating tissue mixtures for the target species, and the level of accuracy needed to meet research objectives.
DOI: 10.14288/1.0398085
title: Data from: Physiological and genomic signatures of evolutionary thermal adaptation in redband trout from extreme climates

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Temperature is a master environmental factor that limits the geographical distribution of species, especially in ectotherms. To address challenges in biodiversity conservation under ongoing climate change, it is essential to characterize relevant functional limitations and adaptive genomic content at population and species levels. Here, we present evidence for adaptive divergence in cardiac function and genomic regions in redband trout (Oncorhynchus mykiss gairdneri) populations from desert and montane streams. Cardiac phenotypes of individual fish were measured in the field with a custom-built electrocardiogram apparatus. Maximum heart rate and its rate limiting temperature during acute warming were significantly higher in fish that have evolved in the extreme of a desert climate compared to a montane climate. Association mapping with 526,301 single nucleotide polymorphisms (SNPs) across the genome revealed signatures of thermal selection both within and among ecotypes. Among desert and montane populations, 413 SNPs were identified as putative outliers under natural selection and 20 of these loci showed significant association with average summer water temperatures among populations. Phenotypes for cardiac performance were variable within each ecotype and 207 genomic regions were strongly associated with either maximum heart rate or rate limiting temperatures among individuals. Annotation of significant loci provided candidate genes that underlie thermal adaptation, including pathways associated with cardiac function (IRX5, CASQ1, CAC1D and TITIN), neuroendocrine system (GPR17 and NOS) and stress response (SERPH). By integrating comparative physiology and population genomics, results here advance our knowledge on evolutionary processes of thermal adaptation in aquatic ectotherms.