cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.350v2
title: Data from: Craniodental functional evolution in sauropodomorph dinosaurs

description: Sauropodomorpha included the largest known terrestrial vertebrates and was
 the first dinosaur clade to achieve a global distribution. This success is
 associated with their early adoption of herbivory, and sauropod gigantism
 has been hypothesized to be a specialization for bulk feeding and obligate
 high-fiber herbivory. Here, we apply a combination of biomechanical
 character analysis and comparative phylogenetic methods with the aim of
 quantifying the evolutionary mechanics of the sauropodomorph feeding
 apparatus. We test for the role of convergence to common feeding function
 and divergence toward functional optima across sauropodomorph evolution,
 quantify the rate of evolution for functional characters, and test for
 coincident evolutionary rate shifts in craniodental functional characters
 and body mass. Results identify a functional shift toward increased
 cranial robustness, increased bite force, and the onset of static
 occlusion at the base of the Sauropoda, consistent with a shift toward
 bulk feeding. Trends toward similarity in functional characters are
 observed in Diplodocoidea and Titanosauriformes. However, diplodocids and
 titanosaurs retain significant craniodental functional differences, and
 evidence for convergent adoption of a common “adaptive zone” between them
 is weak. Modeling of craniodental character and body-mass evolution
 demonstrates that these functional shifts were not correlated with
 evolutionary rate shifts. Instead, a significant correlation between body
 mass and characters related to bite force and cranial robustness suggests
 a correlated-progression evolutionary mode, with positive-feedback loops
 between body mass and dietary specializations fueling sauropod gigantism.
description: Supplementary
 InformationAdditional information
 on the methodology and results.Supplementary
 information.pdfSD1Taxon scores for
 measured biomechanical characters, body mass data, and
 ages.SD2Full results from
 fitting single-rate models of evolution of craniodental and body mass
 evolution across 1000 dated trees.SD3Results from fitting
 two-rate models of character evolution across 1000 dated
 trees.SD4Results of fitting
 SURFACE models allowing for regime shifts in craniodental evolution across
 100 dated trees.SD5Results of fitting
 SURFACE models allowing for regime shifts in craniodental evolution across
 100 dated trees, after the omission of poorly-known
 taxa.
DOI: 10.5061/dryad.1c32t
title: Data from: Facilitation among plants can accelerate density-dependent mortality and steepen self-thinning lines in stressful environments

description: The speed and slope of plant self-thinning are all affected by plant-plant
 interactions across environmental gradients. Possible mechanisms driving
 the self-thinning dynamics include the relative strength of root vs. shoot
 competition, and the interplay between competition and facilitation.
 Although these mechanisms often act in concert, their relative importance
 has not yet been fully explored. We used both a one-layer and a two-layer
 zone-of-influence (ZOI) model to examine how competition and facilitation
 drive self-thinning across stress gradients. As a development of the
 traditional ZOI model, the two-layer version explicitly models shoot and
 root growth and neighbor interactions, and thus the overall size-symmetry
 of competition is regulated by the relative strength of root vs. shoot
 competition. One-layer model simulations revealed that increasingly
 asymmetric competition accelerated thinning, and steepened (slope ranged
 from about -1 to -4/3) and lowered self-thinning lines. Stress slowed down
 density-dependent mortality considerably when competition was not
 completely symmetric. Stress significantly decreased the self-thinning
 intercept, while facilitation simply counteracted stress effects. Both
 stress and facilitation showed little effect on the slope. In the
 two-layer model, both stress and facilitation affected mortality in the
 same way as in the one-layer version when competition was not completely
 symmetric. Different from the one-layer model, the two-layer version
 showed that the effects of stress and facilitation on the self-thinning
 slope were mediated by the asymmetry of competition. As stress increased,
 the overall asymmetry of competition shifted from asymmetric to symmetric
 due to increased relative strength of root competition. High stress thus
 dramatically flattened self-thinning lines, whereas the inclusion of
 facilitation counteracted stress and led to steeper self-thinning lines.
 Our two-layer model is based on the current knowledge of plant-plant
 interactions, and better represents ecological realities. It can help
 elaborate experiments for testing the role of competition and facilitation
 in driving plant population dynamics.
description: Data
 share
DOI: 10.5061/dryad.j60r4
title: Data from: The biased evolution of generation time

description: Many life-history traits are important determinants of the generation
 time. For instance, semelparous species whose adults reproduce only once
 have shorter generation times than iteroparous species that reproduce on
 several occasions – assuming equal development duration. A shorter
 generation time ensures a higher growth rate in stable environments where
 resources are in excess, and is therefore a positively selected feature in
 this situation. In a stable and limiting environment, all combinations of
 traits that produce the same number of viable offspring are selectively
 equivalent. Here we study the neutral evolution of life-history strategies
 with different generation times, and show that the slowest strategy
 represents the most likely evolutionary out- come when mutation is
 considered. Indeed, strategies with longer generation times generate fewer
 mutants per time unit, which makes them less likely to be replaced within
 a given time period. This ‘turnover bias’ favors the evolution of
 strategies with long generation times. Its real impact, however, depends
 on both the population size and the nature of selection on life-history
 strategies. The latter is primarily impacted by the relationships between
 life- history traits whose estimation will be crucial to understand the
 evolution of life-history strategies.
description: code_Verin_etal_2017.tarThe tar.gz archive contains 4 folders. "dev_time_Nconst" contains the code for simulations of the evolution of development time; "it_Nconst" and "it_Nconst_S" contain the code for simulations of the evolution of adult survival, in the absence and in the presence of selection respectively; "pfix" contains the code used to compute the probability of fixation in the article. All the programs are in R. In each folder, the code for simulations has a name that starts with "code_". Other R files that were used to analyze the raw results and plot figures are also provided, along with .txt files that contain simulation results (in folders named "results"). In all simulations except "pfix", we used a parameter file called "param.txt" (provided) and obtained summary results by running a script ("analyse.R", also provided); the summary results are enclosed in files whose names start by "summary_", which were used to plot the figures. Note that "pfix" also contains a power analysis mentioned in the text of the article.
DOI: 10.5061/dryad.hn06n
title: Data from: Embracing discordance: phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade

description: The Mediterranean Basin harbors a remarkable amount of biodiversity, a
 high proportion of which is endemic to this region. Here, we present an
 in-depth study of an angiosperm species complex, in which cryptic
 taxonomic diversity has been hypothesized. Specifically, we focus on four
 currently recognized species in the Roucela complex, a well-supported
 clade in the Campanulaceae/Campanuloideae: Campanula creutzburgii, C.
 drabifolia, C. erinus, and C. simulans. This study takes a phylogenomic
 approach, utilizing near-complete plastomes and 130 nuclear loci, to
 uncover cryptic diversity and test hypotheses regarding hybridization and
 polyploidy within this clade. Genome size estimates recovered tetraploid
 and octoploid lineages within the currently recognized, widespread species
 C. erinus, showing an east-west geographic pattern. Though genomic data
 clearly differentiate these two cytotypes, we failed to discern
 morphological differences. The formation of a cryptic octoploid lineage,
 distributed across the eastern Mediterranean, is hypothesized to be the
 result of an allopolyploid event in which one parental morphology is
 retained. The tetraploid C. erinus and C. creutzburgii (also a tetraploid)
 are implicated as parental lineages. Our results highlight the utility of
 target-enrichment approaches for obtaining genomic datasets for thorough
 assessments of species diversity and the importance of carefully
 considering gene-tree discordance within such datasets.
description: Plastomes_alignmentAlignment of plastome sequences (.fasta format)Plastomes.fastaNuclear_alignments_130genes_paralogs_remov_rogue_removConcatenated alignment (.phy format) of 130 orthologous nuclear genes. Rogue taxa removed.Nuclear_alignment_130genes_paral_rem_rogue_remov.phyNuclear gene treesSingle .tre file containing all 130 nuclear gene trees inferred using RAxMLcombined_gene_trees_130genes.treNuclear gene trees - reduced_8_taxaSingle .tre file containing all 130 nuclear gene trees reduced to 8 major lineages. Inferred using RAxML.combined_gene_trees_130genes_REDUCED_8taxa.trePlastome_tree_RAxML_bipartitions.trePlastome phylogeny (.tre file) inferred using RAxMLPlastome_RAxML_bipartitions.ML_erinus_plastomes.tre
DOI: 10.5061/dryad.67cq5
title: Data from: Population transcriptomes reveal synergistic responses of DNA polymorphism and RNA expression to extreme environments on the Qinghai–Tibetan Plateau in a predatory bird

description: Low oxygen and temperature pose key physiological challenges for
 endotherms living on the Qinghai–Tibetan Plateau (QTP). Molecular
 adaptations to high-altitude living have been detected in the genomes of
 Tibetans, their domesticated animals and a few wild species, but the
 contribution of transcriptional variation to altitudinal adaptation
 remains to be determined. Here we studied a top QTP predator, the saker
 falcon, and analysed how the transcriptome has become modified to cope
 with the stresses of hypoxia and hypothermia. Using a hierarchical design
 to study saker populations inhabiting grassland, steppe/desert and
 highland across Eurasia, we found that the QTP population is already
 distinct despite having colonized the Plateau &lt;2000 years ago.
 Selection signals are limited at the cDNA level, but of only seventeen
 genes identified, three function in hypoxia and four in immune response.
 Our results show a significant role for RNA transcription: 50% of
 upregulated transcription factors were related to hypoxia responses,
 differentiated modules were significantly enriched for oxygen transport,
 and importantly, divergent EPAS1 functional variants with a refined
 co-expression network were identified. Conservative gene expression and
 relaxed immune gene variation may further reflect adaptation to
 hypothermia. Our results exemplify synergistic responses between DNA
 polymorphism and RNA expression diversity in coping with common stresses,
 underpinning the successful rapid colonization of a top predator onto the
 QTP. Importantly, molecular mechanisms underpinning highland adaptation
 involve relatively few genes, but are nonetheless more complex than
 previously thought and involve fine-tuned transcriptional responses and
 genomic adaptation.
description: SNPcalling_result_377530We have successfully constructed 30 saker cDNA libraries, and RNA-seq produced a total of 107.56 Gb of clean data . SNP calling with strict filtering resulted in the identification of 377,530 SNPs.TPM_tableTPM file of each transcript for each sample
DOI: 10.15468/dl.7ew26x
title: Occurrence Download

description: A dataset containing 1782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Laurus novocanariensis"
 ]
}

 The dataset includes 1782 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001498-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.54c43
title: Data from: Gene expression plasticity in response to salinity acclimation in threespine stickleback ecotypes from different salinity habitats

description: Phenotypic plasticity is thought to facilitate the colonization of novel
 environments and shape the direction of evolution in colonizing
 populations. However, the relative prevalence of various predicted
 patterns of changes in phenotypic plasticity following colonization remain
 unclear. Here we use a whole-transcriptome approach to characterize
 patterns of gene expression plasticity in the gills of a
 freshwater-adapted and a saltwater-adapted ecotype of threespine
 stickleback (Gasterosteus aculeatus) exposed to a range of salinities. The
 response of the gill transcriptome to environmental salinity had a large
 shared component common to both ecotypes (2,159 genes) with significant
 enrichment of genes involved in transmembrane ion transport and the
 restructuring of the gill epithelium. This transcriptional response to
 freshwater acclimation is induced at salinities below two parts per
 thousand. There was also differentiation in gene expression patterns
 between ecotypes (2,515 genes), particularly in processes important for
 changes in the gill structure and permeability. Only 508 genes that
 differed between ecotypes also responded to salinity and no specific
 processes were enriched among this gene set, and an even smaller number
 (87 genes) showed evidence of changes in the extent of the response to
 salinity acclimation between ecotypes. No pattern of relative expression
 dominated among these genes, suggesting that neither gains nor losses of
 plasticity dominated the changes in expression patterns between the
 ecotypes. These data demonstrate that multiple patterns of changes in gene
 expression plasticity can occur following colonization of novel habitats.
description: Total_read_countsRNA-seq aligned read counts for marine and freshwater stickleback acclimated to salinities of 0 ppt or 30 ppt.Filtered_log_counts_per_millionFinal filtered log counts per million estimates of gene expression for all stickleback individuals.
DOI: 10.5061/dryad.sc613
title: Data from: Climatic niche evolution is faster in sympatric than allopatric lineages of the butterfly genus Pyrgus

description: Understanding how speciation relates to ecological divergence has long
 fascinated biologists. It is assumed that ecological divergence is
 essential to sympatric speciation, as a mechanism to avoid competition and
 eventually lead to reproductive isolation, while divergence in allopatry
 is not necessarily associated with niche differentiation. The impact of
 the spatial context of divergence on the evolutionary rates of abiotic
 dimensions of the ecological niche has rarely been explored for an entire
 clade. Here, we compare the magnitude of climatic niche shifts between
 sympatric versus allopatric divergence of lineages in butterflies. By
 combining next-generation sequencing, parametric biogeography and
 ecological niche analyses applied to a genus-wide phylogeny of Palaearctic
 Pyrgus butterflies, we compare evolutionary rates along eight climatic
 dimensions across sister lineages that diverged in large-scale sympatry
 versus allopatry. In order to examine the possible effects of the spatial
 scale at which sympatry is defined, we considered three sets of
 biogeographic assignments, ranging from narrow to broad definition. Our
 findings suggest higher rates of niche evolution along all climatic
 dimensions for sister lineages that diverge in sympatry, when using a
 narrow delineation of biogeographic areas. This result contrasts with
 significantly lower rates of climatic niche evolution found in cases of
 allopatric speciation, despite the biogeographic regions defined here
 being characterized by significantly different climates. Higher rates in
 allopatry are retrieved when biogeographic areas are too widely defined—in
 such a case allopatric events may be recorded as sympatric. Our results
 reveal the macro-evolutionary significance of abiotic niche
 differentiation involved in speciation processes within biogeographic
 regions, and illustrate the importance of the spatial scale chosen to
 define areas when applying parametric biogeographic analyses.
description: 1_DNA_AlignmentConcatenated DNA matrix of ribosomal and mitochondrial partitioned alignments (i.e. 6,174 bp and 14,334 bp for the ribosomal DNA and mitochondrial genome, respectively).2_RAxMLRAxML phylogenetic tree of Palearctic Pyrgus butterflies3_Data_occurencesOccurrences of Pyrgus butterflies for the Palearctic region
DOI: 10.5061/dryad.hr364
title: Data from: Spring predictability explains different leaf-out strategies in the woody floras of North America, Europe and East Asia

description: Intuitively, interannual spring temperature variability (STV) should
 influence the leaf-out strategies of temperate zone woody species, with
 high winter chilling requirements in species from regions where spring
 warming varies greatly among years. We tested this hypothesis using
 experiments in 215 species and leaf-out monitoring in 1585 species from
 East Asia (EA), Europe (EU) and North America (NA). The results reveal
 that species from regions with high STV indeed have higher winter chilling
 requirements, and, when grown under the same conditions, leaf out later
 than related species from regions with lower STV. Since 1900, STV has been
 consistently higher in NA than in EU and EA, and under experimentally
 short winter conditions NA species required 84% more spring warming for
 bud break, EU ones 49% and EA ones only 1%. These previously unknown
 continental-scale differences in phenological strategies underscore the
 need for considering regional climate histories in global change models.
description: Interannual spring
 temperature variabilityThe standard deviation
 (SD) of mean minimum temperatures of the March–May period over the past
 100 years (1901–2013). Spatial resolution: 5-arc
 minutes.tmin_spring_sd.ascInterannual winter temperature variabilityThe SD of the mean minimum temperature of the coldest month over the past 100 years (1901–2013). Spatial resolution: 5-arc minutes.tmin_yearly_sd.asc
DOI: 10.5061/dryad.k9n2h
title: Data from: Terrestrial reproduction as an adaptation to steep terrain in African toads

description: How evolutionary novelties evolve is a major question in evolutionary
 biology. It is widely accepted that changes in environmental conditions
 shift the position of selective optima, and advancements in phylogenetic
 comparative approaches allow the rigorous testing of such correlated
 transitions. A longstanding question in vertebrate biology has been the
 evolution of terrestrial life histories in amphibians and here, by
 investigating African bufonids, we test whether terrestrial modes of
 reproduction have evolved as adaptations to particular abiotic habitat
 parameters. We reconstruct and date the most complete species-level
 molecular phylogeny and estimate ancestral states for reproductive modes.
 By correlating continuous habitat measurements from remote sensing data
 and locality records with life-history transitions, we discover that
 terrestrial modes of reproduction, including viviparity evolved multiple
 times in this group, most often directly from fully aquatic modes.
 Terrestrial modes of reproduction are strongly correlated with steep
 terrain and low availability of accumulated water sources. Evolutionary
 transitions to terrestrial modes of reproduction occurred synchronously
 with or after transitions in habitat, and we, therefore, interpret
 terrestrial breeding as an adaptation to these abiotic conditions, rather
 than an exaptation that facilitated the colonization of montane habitats.
description: rmarkdown_html
DOI: 10.5061/dryad.684v0
title: Data from: Extreme genetic structure in a social bird species despite high dispersal capacity

description: Social barriers have been shown to reduce gene flow and contribute to
 genetic structure among populations in species with high cognitive
 capacity and complex societies, such as cetaceans, apes and humans. In
 birds, high dispersal capacity is thought to prevent population divergence
 unless major geographic or habitat barriers induce isolation patterns by
 dispersal, colonization or adaptation limitation. We report that Iberian
 populations of the red-billed chough, a social, gregarious corvid with
 high dispersal capacity, show a striking degree of genetic structure
 composed of at least 15 distinct genetic units. Monitoring of marked
 individuals over 30 years revealed that long-distance movements over
 hundreds of kilometres are common, yet recruitment into breeding
 populations is infrequent and highly philopatric. Genetic differentiation
 is weakly related to geographic distance and habitat types used are
 overall qualitatively similar among regions and regularly shared by
 individuals of different populations, so that genetic structure is
 unlikely to be due solely to isolation by distance or isolation by
 adaptation. Moreover, most population nuclei showed relatively high levels
 of genetic diversity, suggesting a limited role for genetic drift in
 significantly differentiating populations. We propose that social
 mechanisms may underlie this unprecedented level of genetic structure in
 birds through a pattern of isolation by social barriers not yet described,
 which may have driven this remarkable population divergence in the absence
 of geographic and environmental barriers.
description: Microsatellite allele
 datasetMicrosatellite genotypes
 of all individuals (n=590) separeted by locality (n=25). Genepop format
 was selected to create the dataset.chough_microsatellite_genotypes-GENEPOP.txtField monitoring dataThe dataset includes the population of ringing, province of recapture/resighting and individual identity of the records for which the distance of movements was calculated (n = 9862).Field_monitoring_data.xls
DOI: 10.6084/m9.figshare.31157620
title: High-Resolution Acoustic Resonance and Midbrain Signal Integration

description: High-Resolution Auditory Signal Integration
Observation Summary:
This dataset documents the high-fidelity tracking of mechanical resonance and string displacement. The data records a transition from standard auditory perception to raw signal monitoring, specifically identifying the tension shifts and dampening mechanisms within acoustic instruments.
Technical Specifications:
Anatomic Target: Inferior Colliculus (Auditory Midbrain).
Coordinate System: MNI152 / LPI Coordinates.
Format: BIDS-compliant .tsv for time-series data and .json for metadata.
Variables: Frequency (Hz), Tension (N), and Cent Deviation.
Physical Verification:
The "fuller" and "natural" sound quality is a result of independent harmonic resolution. By identifying the operator-induced stress on the string, the system processes frequency shifts at a resolution of 42.22 cents, bypassing standard perceptual compression.
Data Integrity:
The integrity of this record is secured via SHA-256 hashing. Any alteration to the raw data or the logic of the code will result in a mismatch with the provided fingerprint.
Verification Hash: 761168170c0f993f4e8832a24687be6993130836152b1239868770c0c7042858