cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2z34tmpps
title: Transformed crane data from: Balancing structural complexity with ecological insight in spatio-temporal species distribution models

description: The potential for statistical complexity in species distribution models
 (SDMs) has greatly increased with advances in computational power.
 Structurally complex models provide the flexibility to analyse intricate
 ecological systems and realistically messy data, but can be difficult to
 interpret, reducing their practical impact. Founding model complexity in
 ecological theory can improve insight gained from SDMs.  Here, we
 evaluate a marked point process approach, which uses multiple Gaussian
 random fields to represent population dynamics of the Eurasian crane (Grus
 grus) in a spatio-temporal species distribution model. We discuss the role
 of model components and their impacts on predictions, in comparison with a
 simpler binomial presence/absence approach. Inference is carried out using
 Integrated Nested Laplace Approximation (INLA) with inlabru, an accessible
 and computationally efficient approach for Bayesian hierarchical
 modelling, which is not yet widely used in SDMs.  Using the
 marked point process approach, crane distribution was predicted to be
 dependent on the density of suitable habitat patches, as well as close to
 observations of the existing population. This demonstrates the advantage
 of complex model components in accounting for spatio-temporal population
 dynamics (such as habitat preferences and dispersal limitations) that are
 not explained by environmental variables. However, including an AR1
 temporal correlation structure in the models resulted in unrealistic
 predictions of species distribution; highlighting the need for careful
 consideration when determining the level of model complexity. Increasing
 model complexity, with careful evaluation of the effects of additional
 model components, can provide a more realistic representation of a system,
 which is of particular importance for a practical and impact-focused
 discipline such as ecology (though these methods extend to applications
 for a wide range of systems). Founding complexity in contextual theory is
 not only fundamental to maintaining model interpretability, but can be a
 useful approach to improving insight gained from model outputs. 
description: A transformed version of the data used in "Balancing
 Structural Complexity with Ecological Insight in Spatio-temporal Species
 Distribution Models". These data have been randomly transformed to
 prevent an exact identification of nest locations and avoid potential
 disturbance to cranes during the breeding period.
DOI: 10.15468/dl.876nr8
title: Occurrence Download

description: A dataset containing 141616 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lycopodium",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 141616 records from 1176 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003165-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g79cnp5sc
title: Thermal physiology of Drosophila tripunctata across an urbanization gradient

description: In Drosophila spp., their often high number of annual generations, large
 population sizes, and large amounts of standing genetic variation should
 predispose them to undergo contemporary adaptation to climatic warming.
 However, a number of laboratory experimental evolution studies in this
 group of organisms suggest strong limits on the rate and magnitude of
 contemporary thermal adaptation. Here we explore this discrepancy by
 examining the potential for rapid evolutionary divergence between wild
 populations of Drosophila tripunctata (Loew 1962) from rural and urban
 sites. We performed a multi-generation common garden study and found
 evidence for the evolution of higher heat tolerance (critical thermal
 maximum) in urban population flies. We also detected evolutionary
 divergence in cold resistance (chill coma recovery time) with diminished
 cold resistance in urban population flies, though the effect was weaker
 than the shift in heat tolerance. Although our study provides evidence of
 contemporary urban thermal adaptation, the magnitude of phenotypic change
 lagged behind the magnitude of environmental temperature change across the
 urbanization gradient, suggesting potential limits on the evolution of
 urban thermal physiology.
DOI: 10.5061/dryad.qfttdz0ks
title: Predictors of genomic diversity within North American squamates

description: Comparisons of intraspecific genetic diversity across species can reveal
 the roles of geography, ecology, and life history in shaping biodiversity.
 The wide availability of mitochondrial DNA (mtDNA) sequences in
 open-access databases makes this marker practical for conducting analyses
 across several species in a common framework, but patterns may not be
 representative of overall species diversity. Here, we gather new and
 existing mtDNA sequences and genome-wide nuclear data
 (genotyping-by-sequencing; GBS) for 30 North American squamate species
 sampled in the Southeastern and Southwestern United States. We estimated
 mtDNA nucleotide diversity for two mtDNA genes, COI (22 species
 alignments; average 16 sequences) and cytb (22 species; average 58
 sequences), as well as nuclear heterozygosity and nucleotide diversity
 from GBS data for 118 individuals (30 species; four individuals and
 6,820–44,309 loci per species). We showed that nuclear genomic diversity
 estimates were highly consistent across individuals for some species,
 while other species showed large differences depending on the locality
 sampled. Range size was positively correlated with both cytb diversity
 (Phylogenetically Independent Contrasts: R2 = 0.31, p = 0.007) and GBS
 diversity (R2 = 0.21; p = 0.006), while other predictors differed across
 the top models for each dataset. Mitochondrial and nuclear diversity
 estimates were not correlated within species, although sampling
 differences in the data available made these datasets difficult to
 compare. Further study of mtDNA and nuclear diversity sampled across
 species’ ranges is needed to evaluate the roles of geography and life
 history in structuring diversity across a variety of taxonomic groups.
description: The datasets consist of mitochondrial and
 genotyping-by-sequencing data and trait data for 30 squamate species. New
 genetic data for 12 species were collected and previously published data
 for 18 species were combined for analysis. Two mitochondrial genes (COI
 and cytb) were sequenced via Sanger sequencing and assembled in Geneious;
 published GenBank sequences were downloaded and aligned for each species.
 Genetic diversity metrics were generated using the 'pegas' R
 package. Genotyping-by-sequencing (GBS) data were collected for 12 species
 and analyzed along with previously published data for 18 species. Data
 were assembled in ipyrad v. 0.7.28 and genetic diversity metrics were
 estimated using the R packages 'PopGenome' and
 'adegenet'. Trait data were obtained from previously published
 work. Additional details are provided in the associated
 manuscript.
description: R/RStudio
DOI: 10.5281/zenodo.18397040
title: Molecular data for: Evaluating the conservation effectiveness of Ammopiptanthus nanus under different ex situ strategies

description: This dataset contains all molecular data supporting the findings of the manuscript titled “Evaluating the conservation effectiveness of Ammopiptanthus nanus (Fabaceae) under different Ex Situ strategies through Multi-Molecular marker analysis“ (Manuscript #: PJS_2_169174).

The data were generated from 114 samples of Ammopiptanthus nanus collected from four ex situ conservation populations to assess genetic diversity and conservation efficacy. It includes the following files: 1) A_nanus_EST-SSR_RawGenotypes.csv: Raw genotype data from Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) markers; 2) A_nanus_ITS_Sequences.fasta: Nuclear ribosomal Internal Transcribed Spacer (ITS) sequences; 3) psbA-trnH.fasta, trnL-trnF.fasta, trnS-trnG.fasta: Chloroplast DNA (cpDNA) intergenic spacer sequences. Detailed laboratory protocols and analytical methods are described in the associated manuscript.

If you use this dataset in your work, please cite both the resulting data publication (this DOI) and the related research article.
DOI: 10.5281/zenodo.18397039
title: Molecular data for: Evaluating the conservation effectiveness of Ammopiptanthus nanus under different ex situ strategies

description: This dataset contains all molecular data supporting the findings of the manuscript titled “Evaluating the conservation effectiveness of Ammopiptanthus nanus (Fabaceae) under different Ex Situ strategies through Multi-Molecular marker analysis“ (Manuscript #: PJS_2_169174).

The data were generated from 114 samples of Ammopiptanthus nanus collected from four ex situ conservation populations to assess genetic diversity and conservation efficacy. It includes the following files: 1) A_nanus_EST-SSR_RawGenotypes.csv: Raw genotype data from Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) markers; 2) A_nanus_ITS_Sequences.fasta: Nuclear ribosomal Internal Transcribed Spacer (ITS) sequences; 3) psbA-trnH.fasta, trnL-trnF.fasta, trnS-trnG.fasta: Chloroplast DNA (cpDNA) intergenic spacer sequences. Detailed laboratory protocols and analytical methods are described in the associated manuscript.

If you use this dataset in your work, please cite both the resulting data publication (this DOI) and the related research article.
DOI: 10.5061/dryad.p5hqbzkrv
title: Data for: Cholinergic activity during probabilistic Pavlovian conditioning in mice

description: Cholinergic activity was monitored while mice performed a probabilistic
 Pavlovian conditioning task. Mice were headfixed and listened to auditory
 stimuli of different frequency, which signaled either likely reward and
 unlikely punishment, or likely punishment and unlikely reward. Cholinergic
 activity was measured in two ways. First, bulk calcium imaging of
 cholinergic neurons was performed by fiber photometry. Second,
 extracellular electrophysiology recordings were performed and optogenetic
 tagging was used to identify cholinergic neurons in task-performing mice.
 This dataset contains fiber photometry data, electrophysiology data and
 behavioral data of mice.
description: Behavioral training was performed as previously described
 (Hegedus et al., 2021, Training protocol for probabilistic Pavlovian
 conditioning in mice using an open-source head-fixed setup). Briefly, mice
 were habituated to a headfixation apparatus and were trained to listen to
 tones and collect water rewards in a headfixed setup. Two tones of
 different frequency were associated with likely reward / unlikely
 punishment or unlikely reward/likely punishment (12 kHz tone predicted 80%
 water reward, 10% air-puff punishment, 10% omission; 4 kHz tone predicted
 25% water reward, 65% air-puff punishment, 10% omission).
 Bulk calcium imaging of cholinergic neurons was performed by
 fiber photometry (dual fiber photometry setup, Doric Neuroscience) and
 visualized online with Doric Studio Software. Two LED light sources (465
 nm, 405 nm) were channeled into fluorescent Mini Cubes (iFMC4, Doric
 Neuroscience). Light was amplitude-modulated by the command voltage of the
 two-channel LED driver (LEDD_2, Doric Neuroscience, the 465 nm wavelength
 light was modulated at 208 Hz and 405 nm wavelength was modulated at 572
 Hz). Light was channeled into 400 µm diameter patch cord fibers and was
 connected to optical fiber implants during training sessions. The same
 optical fibers were used to collect the bilateral emitted fluorescence
 signal, which were detected with 500-550 nm fluorescent detectors
 integrated in the Mini Cubes. Emitted signals were sampled at 12 kHz,
 decoded in silico and saved in a *.csv format. Chronic
 extracellular electrophysiology recordings were performed using tetrode
 electrodes, as described in Hegedus et al, 2021, Differential recruitment
 of ventral pallidal e-types by behaviorally salient stimuli during
 Pavlovian conditioning. We performed optogenetic tagging of cholinergic
 neurons in ChAT-Cre mice, as detailed in Hangya et al., 2015, Central
 Cholinergic Neurons Are Rapidly Recruited by Reinforcement
 Feedback.
description: Associated code located at
 https://github.com/hangyabalazs/cholinergic_Pavlovian_analysis.
DOI: 10.5061/dryad.2fqz612rw
title: Data for: NFATc1 marks articular cartilage progenitors and negatively determines articular chondrocyte differentiation

description: The origin and differentiation mechanism of articular chondrocytes remain
 poorly understood. Broadly, the difference in developmental mechanisms of
 articular and growth-plate cartilage is still less elucidated. Here, we
 identified that the nuclear factor of activated T-cells cytoplasmic 1
 (NFATc1) is a crucial regulator of articular, but not growth-plate,
 chondrocyte differentiation during development. At the early stage of
 mouse knee development (embryonic day 13.5), NFATc1-expressing cells were
 mainly located in the flanking region of the joint interzone. With
 development, NFATc1-expressing cells generated almost all articular
 chondrocytes, but not chondrocytes in limb growth-plate primordium.
 NFATc1-expressing cells displayed prominent capacities for colony
 formation and multipotent differentiation. Transcriptome analyses revealed
 a set of characteristic genes in NFATc1-enriched articular cartilage
 progenitors. Strikingly, the expression of NFATc1 was diminished with
 articular chondrocyte differentiation and suppressing NFATc1 expression in
 articular cartilage progenitors was sufficient to induce spontaneous
 chondrogenesis while overexpressing NFATc1 suppresses chondrogenesis.
 Mechanistically, NFATc1 negatively regulated the transcriptional activity
 of the Col2a1 gene. Thus, our results reveal that NFATc1
 characterizes articular, but not growth-plate, cartilage progenitors
 during development and negatively determines articular chondrocyte
 differentiation at least partly through regulating COL2A1 gene
 transcription.
DOI: 10.25349/d9991t
title: The relative strength of selection on modifiers of genetic architecture under migration load

description: Gene flow between populations adapting to differing local environmental
 conditions creates a "migration load" because individuals might
 disperse to habitats where their survival is low or because they might
 reproduce with locally maladapted individuals. The amount by which the
 mean relative population fitness is kept below one creates an opportunity
 for modifiers of the genetic architecture to spread due to selection.
 Prior work that separately considered modifiers changing dispersal or
 recombination rates, or altering dominance or epistasis, has typically
 focused on the direction of selection rather than its absolute magnitude.
 We here develop methods to determine the strength of selection on
 modifiers of the genetic architecture, including modifiers of the
 dispersal rate, after populations evolved local adaptation. We consider
 scenarios with up to five loci contributing to local adaptation and derive
 a matrix model for the deterministic spread of modifiers. We find that
 selection for modifiers of epistasis and dominance is stronger than
 selection for decreased recombination, and that selection for partial
 reductions in recombination are extremely weak, regardless of the number
 of loci contributing to local adaptation. The spread of modifiers for a
 reduction in dispersal depends on the number of loci, pre-existing
 epistasis and extent of migration load. We identify a novel effect, that
 modifiers of dominance are more strongly selected when they are unlinked
 to the locus that they modify. Overall, these results help explain
 population differentiation and reproductive isolation and 
 provide a benchmark to compare selection on genetic architecture modifiers
 in finite population sizes and under demographic stochasticity.
description: Code and figures that were developed for the paper "The
 relative strength of selection on modifiers of genetic architecture under
 migration load". 
description: This code reguires  Wolfram Research Mathematica. The included
 code consists of Mathematica notebooks (.nb) files, Wolfram Language
 Script files (.wls) and compiled Mathematica code (.mx) files.
DOI: 10.5061/dryad.4f4qrfjfs
title: Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns

description: Long term evolution experiments have tested the importance of genetic and
 environmental factors in influencing evolutionary outcomes. Differences in
 phylogenetic history, recent adaptation to distinct environments, and
 chance events all influence the fitness of a population. However, the
 interplay of these factors on a population's evolutionary potential
 remains relatively unexplored. We tracked the outcome of 2,000 generations
 of evolution of four natural isolates of Escherichia coli
 bacteria that were engineered to also create differences in shallow
 history by adding previously identified mutations selected in a separate
 long-term experiment. Replicate populations started from each progenitor
 were evolved in four environments. We found that deep and shallow
 phylogenetic histories both contributed significantly to differences in
 evolved fitness, though by different amounts in different selection
 environments. With one exception, chance effects were not significant.
 Whereas the effect of deep history did not follow any detectable pattern,
 effects of shallow history followed a pattern of diminishing-returns
 whereby fitter ancestors had smaller fitness increases. These results are
 consistent with adaptive evolution being contingent on the interaction of
 several evolutionary forces but demonstrate that the nature of these
 interactions is not fixed and may not be predictable even when the role of
 chance is small.
description: One-day competitive fitness
 were used to quantify the relative fitness of evolved populations.
 Populations were started with three-fold replicaiton from one of 16
 founder strains and were seperately evovled for 2000 generations in
 acetate, trypsin, casamino acids, or glucoxse. Evovled populaitons were
 able to utilize arabinose (Ara+) and were competed against otherwise
 isogenic Ara- derivatives of corresponding ancestral strains. After
 pre-conditioning competitors were mixed at equal ratios and diluted
 1000-fold into competition cultures. A sample was immediately plated on TA
 agar to determine the initial frequency of each competitor. A second
 sample was plated following 24 hours of competition. The ratioj of
 Malthusian parameters of each competitor was used to estimate relative
 fitness of evolved strains. We also estimated absolute fitness of
 progenitor strains from analysis of growth curves in relevant
 environemtns. In some cases competitions were plated on multiple plates to
 increase the number of colonies of each competitor observed and reduce
 sampling error. In these cases the count of that competitor is reported as
 a mean over the plates that were counted.
description: Scripts run using R. Input files are called by scripts.
DOI: 10.5061/dryad.cfxpnvx85
title: Response of distribution patterns of two closely related species in Taxus genus to climate change since last inter-glacial

description: Climate change affects species' spatio-temporal distribution deeply.
 However, how climate affects the spatio-temporal distribution pattern of
 related species on the large scale remains largely unclear. Here, we
 selected two closely related species in the Taxus genus, Taxus
 chinensis and Taxus mairei, to explore their
 distribution pattern. Four environmental variables were employed to
 simulate the distribution patterns using the optimized Maxent model. The
 results showed that the highly suitable area of T.
 chinensis and T. mairei in the current period was
 1.616 × 105 km2 and 3.093 × 105 km2, respectively. The
 distribution area of T. chinensis was smaller than that
 of T. mairei in different periods. Comparison of different
 periods shows that the distribution area of the two species was almost in
 stasis from LIG to the future periods. Temperature and precipitation were
 the main climate factors that determined the potential distribution of the
 two species. The centroids of T.
 chinensis and T. mairei were in Sichuan and Hunan
 provinces in current period, respectively. In the future, the centroid
 migration direction of the two species would shift towards the northeast.
 Our results revealed that the average elevation distribution
 of T. chinensis was higher than that of T.
 mairei. This study sheds new insights into the habitat preference and
 limiting environmental factors of the two related species and provides a
 valuable reference for the conservation of these two threatened species.
DOI: 10.5061/dryad.5tb2rbp6j
title: Data collected for: The contrasted impacts of grasshoppers on soil microbial activities in function of ecosystem productivity and herbivore diet

description: Herbivory can have contrasted impacts on soil microbes and nutrient
 cycling, which has stimulated the development of conceptual frameworks
 exploring the links between below- and aboveground processes. The
 “productivity model” predicts that herbivores stimulate microbial
 activities and accelerate nutrient mineralization in productive
 ecosystems, while they have an opposite effect in less productive
 ecosystems. In parallel, the “diet model” predicts that herbivores feeding
 on conservative plants accelerate nutrient cycling while those feeding on
 exploitative plants decelerate nutrient cycling, due to changes in litter
 inputs. Since these two frameworks can lead to conflicting predictions in
 some cases, experimental evidence combining herbivore diet and
 productivity is required. During two consecutive years, we conducted an
 experiment controlling the presence of three grasshopper species consuming
 either grasses, forbs or both in twelve natural and managed alpine
 grasslands of contrasted productivities. In order to assess the effects of
 herbivory on soil microbes, we measured their enzymatic activities, their
 biomass and the soil potential nitrogen mineralization (PNM). Soil and
 vegetation characteristics were also determined in order to test if they
 modulated the effects of herbivory on microbes. Contrary to the
 predictions of the diet model, the effects of herbivory on microbial
 characteristics did not depend on the herbivores diet but relied on
 ecosystem productivity. The most productive sites were characterized by
 exploitative plant species which depleted N resources in the soil, and by
 microbes producing relatively few extracellular enzymes, leading to a
 lower PNM. Herbivory increased microbial biomass and decreased the
 production of extracellular enzymes in those sites, possibly through the
 stimulation of root exudates produced by exploitative species. The least
 productive sites were characterized by conservative plants, which led to
 the sequestration of soil C, and by microbes having a resource acquisition
 strategy (more extracellular enzymes, higher PNM). Herbivory decreased
 microbial biomass and increased the production of extracellular enzymes in
 those sites. This pattern can be explained by the loss of carbon
 associated with insect respiration, which increases the need for microbes
 to acquire resources and by a lower production of root exudates by
 conservative species. Therefore, the effects of two years of herbivory on
 soil microbes were at odds with the productivity model, which focuses
 instead on longer term effects corresponding to herbivory-induced changes
 in plant species composition. This highlights the multidimensional feature
 of the impacts of herbivory on ecosystem functioning, both in space and
 time.