cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31167373
title: A dataset on microbial traits and mineral protection controlling the temperature sensitivity of soil carbon decomposition in eroded and depositional agricultural soils

description: This dataset documents erosion-induced changes in the temperature sensitivity of soil organic carbon decomposition (<i>Q</i><sub>10</sub>) across four erosion-prone regions in China: the Northeast Rolling Hills, the Loess Plateau, the Sichuan Basin, and the Yunnan–Guizhou Plateau. Together, the provinces encompassing these regions account for 26.20% of China’s land area but contribute 56.95% of the national soil erosion area.Soil samples were collected from intensively managed sloping farmlands during the 2021 harvest season (September–November). In each region, four geographically independent hillslopes (&gt;200 m apart) were selected as replicates. Along each hillslope, four geomorphic positions representing an erosion–deposition sequence were identified: non-eroded (NE) summit positions, moderately eroded (ME) shoulder slopes, severely eroded (SE) backslopes, and depositional (DP) footslopes. In total, 64 plots were established (4 regions × 4 hillslopes × 4 erosion classes).Within each plot, three soil profiles were excavated to 60 cm depth, and samples were collected at 20 cm intervals for physicochemical and microbial analyses. Soil subsamples were incubated under variable temperature regimes, and CO₂ release was measured to quantify <i>Q</i><sub>10</sub>.The dataset includes <i>Q</i><sub>10</sub> values and associated soil properties, including microbial community indicators, carbon fractions, enzyme activities, soil texture, aggregate stability, nutrient stoichiometry, and physical properties.
DOI: 10.6084/m9.figshare.31167373.v1
title: A dataset on microbial traits and mineral protection controlling the temperature sensitivity of soil carbon decomposition in eroded and depositional agricultural soils

description: This dataset documents erosion-induced changes in the temperature sensitivity of soil organic carbon decomposition (<i>Q</i><sub>10</sub>) across four erosion-prone regions in China: the Northeast Rolling Hills, the Loess Plateau, the Sichuan Basin, and the Yunnan–Guizhou Plateau. Together, the provinces encompassing these regions account for 26.20% of China’s land area but contribute 56.95% of the national soil erosion area.Soil samples were collected from intensively managed sloping farmlands during the 2021 harvest season (September–November). In each region, four geographically independent hillslopes (&gt;200 m apart) were selected as replicates. Along each hillslope, four geomorphic positions representing an erosion–deposition sequence were identified: non-eroded (NE) summit positions, moderately eroded (ME) shoulder slopes, severely eroded (SE) backslopes, and depositional (DP) footslopes. In total, 64 plots were established (4 regions × 4 hillslopes × 4 erosion classes).Within each plot, three soil profiles were excavated to 60 cm depth, and samples were collected at 20 cm intervals for physicochemical and microbial analyses. Soil subsamples were incubated under variable temperature regimes, and CO₂ release was measured to quantify <i>Q</i><sub>10</sub>.The dataset includes <i>Q</i><sub>10</sub> values and associated soil properties, including microbial community indicators, carbon fractions, enzyme activities, soil texture, aggregate stability, nutrient stoichiometry, and physical properties.
DOI: 10.5061/dryad.0gb5mkm25
title: Unexpected cryptic species among streptophyte algae most distant to land plants

description: Streptophytes are one of the major groups of the green lineage
 (Chloroplastida or Viridiplantae). During one-billion-years of evolution,
 streptophytes have radiated into an astounding diversity of uni- and
 multicellular green algae as well as land plants. Most divergent from land
 plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp., and
 Chlorokybophyceae. All three lineages are species-poor and the
 Chlorokybophyceae consist of a single described species, Chlorokybus
 atmophyticus. In this study, we used phylogenomic analyses to shed light
 into the diversity within Chlorokybus using a sampling of isolates across
 its known distribution. We uncovered a consistent deep genetic structure
 within the Chlorokybus isolates, which prompted us to formally extend the
 Chlorokybophyceae by describing four new species. Gene expression
 differences among Chlorokybus species suggest certain constitutive
 variability that might influence their response to environmental factors.
 Failure to account for this diversity can hamper comparative genomic
 studies aiming to understand the evolution of stress response across
 streptophytes. Our data highlight that future studies on the evolution of
 plant form and function can tap into an unknown diversity at key deep
 branches of the streptophytes.
DOI: 10.5061/dryad.n5tb2rbws
title: Data from 90-day quantitative inhalation toxicology study evaluating the dose-response and fate in the lung and pleura of chrysotile-containing brake dust

description: The final results from this multi-dose, 90-day inhalation toxicology study
 in the rat with life-time post-exposure observation have shown a
 significant fundamental difference in pathological response and
 tumorgenicity between brake dust generated from brake pads manufactured
 with chrysotile or from chrysotile alone in comparison to the amphiboles,
 crocidolite and amosite asbestos. The groups exposed to brake dust showed
 no significant pathological or tumorigenic response in the respiratory
 track compared to the air control group at exposure concentrations and
 deposited doses well above those at which humans have been exposed. Slight
 alveolar/interstitial macrophage accumulation of particles was noted.
 Wagner grades were 1–2 (1 = control group), similar to the TiO2 particle
 control group. Chrysotile was not biopersistent, exhibiting in the lung a
 deterioration of its matrix which results in breakage into particles and
 short fibers which can be cleared by alveolar macrophages and which can
 continue to dissolve. Particle-laden macrophage accumulation was observed,
 leading to a very-slight interstitial inflammatory response (Wagner grade
 1–3). There was no peribronchiolar inflammation, occasional very-slight
 interstitial fibrosis (Wagner grade 4), and no exposure-related
 tumorigenic response. The pathological response of crocidolite and amosite
 compared to the brake dust and chrysotile was clearly differentiated by
 the histopathology and the confocal analysis. Crocidolite and amosite
 induced persistent inflammation, microgranulomas, persistent fibrosis
 (Wagner grades 4), and a dose-related lung tumor response. Confocal
 microscopy quantified extensive inflammatory response and collagen
 development in the lung, visceral and parietal pleura as well as pleural
 adhesions. These results provide a clear foundation for differentiating
 the innocuous effects of brake dust exposure from the adverse effects
 following amphibole asbestos exposure.
DOI: 10.15468/dl.k48vxc
title: Occurrence Download

description: A dataset containing 989 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Discolampa ethion"
 ]
}

 The dataset includes 989 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002949-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8sf7m0cph
title: Combining species delimitation, species trees, and tests for gene flow illuminates complex speciation in scrub-jays

description: Complex speciation, involving rapid divergence and multiple bouts of
 post-divergence gene flow, can obfuscate phylogenetic relationships and
 species limits. In North America, cases of complex speciation are common,
 due at least in part to the cyclical Pleistocene glacial history of the
 continent. Scrub-jays in the genus Aphelocoma provide a useful case study
 in complex speciation because their range throughout North America is
 structured by phylogeographic barriers with multiple cases of secondary
 contact between divergent lineages. Here, we show that a comprehensive
 approach to genomic reconstruction of evolutionary history, i.e.,
 synthesizing results from species delimitation, species tree
 reconstruction, demographic model testing, and tests for gene flow, is
 capable of clarifying evolutionary history despite complex speciation. We
 find concordant evidence across all statistical approaches for the
 distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti),
 culminating in support for the species status of this lineage under any
 commonly applied species concept. We also find novel genomic evidence for
 the species status of a Texas endemic lineage A. w. texana, for which
 equivocal species delimitation results were clarified by demographic
 modeling and spatially explicit models of gene flow. Finally, we find that
 complex signatures of both ancient and modern gene flow between the
 non-sister California Scrub-Jay (A. californica) and Woodhouse’s Scrub-Jay
 (A. woodhouseii), result in discordant gene trees throughout the species’
 genomes despite clear support for their overall isolation and species
 status. In sum, we find that a multi-faceted approach to genomic analysis
 can increase our understanding of complex speciation histories, even in
 well-studied groups. Given the emerging recognition that complex
 speciation is relatively commonplace, the comprehensive framework that we
 demonstrate for interrogation of species limits and evolutionary history
 using genomic data can provide a necessary roadmap for disentangling the
 impacts of gene flow and incomplete lineage sorting to better understand
 the systematics of other groups with similarly complex evolutionary
 histories.
description: Unfiltered SNPs called across all 115 samples are available as a
 gzipped vcf file called 'populations.snps_(1).vcf.gz'.
 Supplementary methods associated with the paper are contained in the file
 'supplemental.material.may1.2022.docx'.
DOI: 10.5061/dryad.bk3j9kdd1
title: APL synapses distribution on PN and KC meshes, primary data, calcium imaging macros and python scripts from Prisco et al.

description: To identify and memorize discrete but similar environmental inputs, the
 brain needs to distinguish between subtle differences of activity patterns
 in defined neuronal populations. The Kenyon cells of the Drosophila adult
 mushroom body (MB) respond sparsely to complex olfactory input, a property
 that is thought to support stimuli discrimination in the MB. To understand
 how this property emerges, we investigated the role of the inhibitory
 anterior paired lateral neuron (APL) in the input circuit of the MB, the
 calyx. Within the calyx, presynaptic boutons of projection neurons (PNs)
 form large synaptic microglomeruli (MGs) with dendrites of postsynaptic
 Kenyon cells (KCs). Combining EM data analysis and in vivo calcium
 imaging, we show that APL, via inhibitory and reciprocal synapses
 targeting both PN boutons and KC dendrites, normalizes odour-evoked
 representations in MGs of the calyx. APL response scales with the PN input
 strength and is regionalized around PN input distribution. Our data
 indicate that the formation of a sparse code by the Kenyon cells requires
 APL-driven normalization of their MG postsynaptic responses. This work
 provides experimental insights on how inhibition shapes sensory
 information representation in a higher brain centre, thereby supporting
 stimuli discrimination and allowing for efficient associative memory
 formation.
description: This dataset contains all the source data contained in Prisco et
 al., sorted by Figure.
DOI: 10.5061/dryad.dv41ns207
title: Data from: Range-edge populations of seaweeds show niche unfilling and poor adaptation to increased temperatures

description: Data used for the study entitled "Range-edge populations of seaweeds
 show niche unfilling and poor adaptation to increased temperatures".
 These are the distribution data collected from literature and personal
 communications to complete the GBIF and OBIS distributional records of the
 Atlantic European coast, the weekly growth data taken from the study
 individuals as well as the binomial survival data used for the graphs of
 the last week of the experiment.
DOI: 10.5061/dryad.j9kd51cdd
title: Urbanization alters interactions between Darwin’s finches and Tribulus cistoides on the Galápagos Islands

description: Emerging evidence suggests that humans shape the ecology and evolution of
 species interactions. Islands are particularly susceptible to
 anthropogenic disturbance due to the fragility of their ecosystems;
 however, we know little about the susceptibility of species interactions
 to urbanization on islands. To address this gap, we studied how the
 earliest stages of urban development affect interactions between Darwin’s
 finches and its key food resource, Tribulus cistoides, in three towns on
 the Galápagos Islands. We measured variation in mericarp predation rates,
 mericarp morphology, and finch community composition using population
 surveys, experimental manipulations, and finch observations conducted in
 habitats within and outside of each town. We found that both seed and
 mericarp removal rates were higher in towns compared to natural habitats.
 We also found that selection on mericarp size and defense differed between
 habitats in the survey and experimental populations, and that towns
 supported smaller and less diverse finch communities than natural
 habitats. Together, our results suggest that even moderate levels of
 urbanization can alter ecological interactions between Darwin’s finches
 and T. cistoides, leading to modified natural selection on T. cistoides
 populations. Our study demonstrates that trophic interactions on islands
 may be susceptible to the anthropogenic disturbance associated with
 urbanization. Synthesis: Despite containing the highest diversity in the
 world, studies of urbanization are lacking from the tropics. Our study
 identified signatures of urbanization on species interactions in a
 tropical island ecosystem and suggests that changes to the ecology of
 species interactions has the potential to alter evolution in urban
 environments.
DOI: 10.5061/dryad.wdbrv15q4
title: Saguaro cactus within-species phylogenomics

description: Reconstructing accurate historical relationships between populations
 within a species poses numerous challenges, not least in many plant groups
 in which gene flow can extend well beyond species boundaries. Nonetheless,
 the extent of tree-like history within a species is an empirical question
 on which it is now possible to bring large amounts of genome sequence to
 bear. We assess phylogenetic structure across the geographic range of the
 saguaro cactus, an emblematic member of Cactaceae, a clade known for
 extensive hybridization and porous species boundaries. Using 200 Gb of
 whole genome resequencing data from 20 individuals sampled from 10
 localities, we assembled two data sets comprising 150,000 biallelic single
 nucleotide polymorphisms (SNPs) from protein coding sequences. From these
 we infer a population tree and evaluate its significance and robustness
 using five qualitatively different inference methods. Despite the low
 sequence diversity, large census population sizes, and presence of
 wide-ranging pollen and seed dispersal agents, population trees were well
 resolved and highly consistent across both data sets and all methods. We
 inferred that the most likely root, based on marginal likelihood
 comparisons, is to the east and south of the region of highest genetic
 diversity, which lies along the coast of the Gulf of California. Together
 with striking decreases in marginal likelihood found to the north, this
 supports hypotheses that saguaro's current range reflects
 post-glacial expansion from the far south following retreat to refugia
 there. We conclude with observations about practical and theoretical
 issues raised by phylogenomic data sets within species, in which SNP-based
 methods must be used rather than gene tree methods that are widely used
 when sequence divergence is higher. These include computational
 scalability, inference of gene flow, and proper assessment of statistical
 support in the presence of linkage effects.
description: This data set is a tarred and gzipped archive of all phylogenetic
 data sets, VCF files, scripts and analysis results used in our study of
 saguaro within-species phylogenomics. Also included is the Supplementary
 Information document from the published paper.
description: After uncompressing and unpacking the archive, the user will find
 a README file in each directory in the hierarchy.
DOI: 10.5061/dryad.18931zczb
title: Data from: A coherent biogeographic framework for Old World Neogene and Pleistocene mammals

description: In order to understand mammalian evolution and compute a wide range of
 biodiversity indices, we commonly use spatial division adapted to
 ecological and evolutionary constraints called bioregion. While commonly
 conducted by neontologists, the establishment of bioregions in
 palaeontology is generally a secondary analysis, shaped on subjective time
 scales and areas specific to the investigated questions and groups. This
 heterogeneity, coupled with the scale-dependency of biodiversity indices,
 prevents the clear identification of macroecological and macroevolutionary
 trends for large taxonomic groups like extinct mammals. Here we tackle
 this issue by providing a coherent framework for Neogene and Pleistocene
 mammals of the Old World following two steps: (A) a temporal scale adapted
 to mammalian evolutionary history (i.e. evolutionary fauna) is defined by
 poly-cohort analysis, and (B) bioregions are then computed for each
 evolutionary fauna by clustering, ordination and intermediate approaches
 at multiples spatial scales (i.e. continental to regional) for Eurasia and
 Africa. Additionally, providing a coherent framework for a wide range of
 mammalian datasets, our results show: (1) the synchronous emergence and
 fall of five mammalian evolutionary faunas identified at chronological
 scales varying from the epoch to the geological stage; (2) a transition
 from a longitudinal to a latitudinal biogeographical structuring between
 the Miocene and Pliocene, especially in Europe; (3) the long-term affinity
 of southern Asian with African faunas, in sharp contrast with the modern
 Palearctic bioregion extension; and (4) the establishment of a vast
 Mediterranean bioregion from fragmented areas in late Miocene to its full
 extent in the Pleistocene.
description: RData files to explore locality and taxa names, as well as an R
 script to reproduce the analysis. This repository
 includes .RData files, R scripts and personnal R functions.
 Public data extracted from NOWdatabase are included.
DOI: 10.5061/dryad.sf7m0cg79
title: Data from: Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments

description: Understanding how eco-evolutionary processes and environmental factors
 drive population differentiation and adaptation are key challenges in
 evolutionary biology of relevance for biodiversity
 protection. Differentiation requires at least partial
 reproductive separation, which may result from different modes of
 isolation such as geographic isolation (allopatry) or isolation by
 distance (IBD), resistance (IBR), and environment
 (IBE). Despite that multiple modes might
 jointly influence differentiation, studies that compare the
 relative contributions are scarce. Using RADseq, we analyse
 neutral and adaptive genetic diversity and structure in 11 pike (Esox
 lucius) populations along a latitudinal gradient (54.9 - 63.6°N), to
 investigate the relative effects of IBD, IBE and IBR, and to assess
 whether the effects differ between neutral and adaptive variation, or
 across structural levels. Patterns of neutral and adaptive
 variation differed, likely reflecting that they have been differently
 affected by stochastic and deterministic processes. The
 importance of the different modes of isolation differed between neutral
 and adaptive diversity, yet were consistent across structural levels.
 Neutral variation was influenced by interactions among all three modes of
 isolation, with IBR (seascape features) playing a central role, wheares
 adaptive variation was mainly influenced by IBE (environmental
 conditions). Taken together, this and previous studies suggest
 that it is common that multiple modes of isolation interactively shape
 patterns of genetic variation, and that their relative contributions
 differ among systems. To enable identification of general
 patterns and understand how various factors influence the relative
 contributions, it is important that several modes are simultaneously
 investigated in additional populations, species and environmental
 settings.
DOI: 10.25349/d9402j
title: Teaching undergraduates with quantitative data in the social sciences at University of California Santa Barbara

description: The interview data was gathered for a project investigating the practices
 of instructors who use quantitative data to teach undergraduate courses
 within the Social Sciences. The study was undertaken by employees of the
 University of California, Santa Barbara (UCSB) Library, who participated
 in this research project with 19 other colleges and universities across
 the U.S. under the direction of Ithaka S+R. Ithaka S+R is a New York-based
 research organization that, among other goals, seeks to develop
 strategies, services, and products to meet evolving academic trends and
 support faculty and students. The field of Social Sciences has been
 notoriously known for valuing the contextual component of data and
 increasingly entertaining more quantitative and computational approaches
 to research in response to the prevalence of data literacy skills needed
 to navigate both personal and professional contexts. Thus, this study
 becomes particularly timely to identify current instructors’ practices and
 strategies to teach with data challenges and opportunities to help them
 advance their instructional efforts. The fundamental goal of this study is
 fourfold: 1) Explore the ways in which instructors teach undergraduates
 with data, 2) Understand instructors’ support needs going forward, 3)
 Develop actionable recommendations for stakeholders, and 4) Build
 relationships within UCSB and across higher education institutions. This
 research project was IRB-approved and exempted by the UCSB’s Office of
 Research in July 2020 (Protocol 1-20-0491).
description: # Teaching undergraduates with quantitative data in the social sciences at
 University of California Santa Barbara
 [https://doi.org/10.25349/D9402J](https://doi.org/10.25349/D9402J) ##
 Description of the data and file structure This deposit includes a
 `deid-transcripts.zip` folder containing 10 pdf files with de-identified
 transcripts of semi-structured interviews. It also includes a copy of the
 recruitment email sent to participants, the interview guide, and the
 codebook with key themes.