cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zs7h44j6v
title: Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

description: C4 photosynthesis evolved multiple times independently in angiosperms, but
 most origins are relatively old so that the early events linked to
 photosynthetic diversification are blurred. The grass Alloteropsis
 semialata is an exception, as this species encompasses C4 and non-C4
 populations. Using phylogenomics and population genomics, we infer the
 history of dispersal and secondary gene flow before, during, and after
 photosynthetic divergence in A. semialata. We further analyse the genome
 composition of individuals with varied ploidy levels to establish the
 origins of polyploids in this species. Detailed organelle phylogenies
 indicate limited seed dispersal within the mountainous region of origin
 and the emergence of a C4 lineage after dispersal to warmer areas of lower
 elevation. Patterns of differentiation across nuclear genomes highlight
 repeated secondary gene flow. In particular, the nuclear genome associated
 with the C4 phenotype was swept into a distantly related maternal lineage
 probably via unidirectional pollen flow. Multiple segmental allopolyploidy
 events mediated additional secondary genetic exchanges between
 photosynthetic types. Overall, our results show that limited dispersal and
 isolation allowed lineage divergence, with photosynthetic innovation
 happening after migration to new environments, and pollen-mediated gene
 flow led to the rapid spread of the derived C4 physiology away from its
 region of origin.
description: Organelle genome alignments of 75 accessions of the grass
 <em>Alloteropsis semialata</em>. Refer to the manuscript for
 details on the methods used for organelle genome assembly.
description: The second inverted repeat of the plastid genomes was removed.
 Both alignments were trimmed to remove sites covered by less than 90% of
 individuals.
DOI: 10.5061/dryad.6m905qfz2
title: Phylogeny and biogeography of some Cretaceous spatangoid echinoids with special emphasis on taxa from the Western Interior Seaway

description: Members of the echinoid order Spatangoida, a highly diverse and abundant
 marine invertebrate clade, were important denizens of the Cretaceous
 Western Interior Seaway (WIS), an epicontinental seaway that divided North
 America in two during an interval of greenhouse conditions between roughly
 100 and 65 million years ago. A phylogenetic analysis of spatangoids was
 conducted using a character matrix of 32 characters from 21
 species.  Species that occur in the WIS were considered
 comprehensively, and species from other regions such as South America,
 Europe, and North Africa were also incorporated into the
 analysis.  Phylogenetic patterns retrieved are largely congruent
 with pre-existing family-level classifications; however, species within
 several genera, especially Hemiaster and Heteraster, need to be
 re-assigned so that classification better reflects phylogeny. The genera
 Washitaster and Heteraster are closely related, as are Mecaster,
 Palhemiaster, and Proraster; Pliotoxaster, Macraster, and Hemiaster; and
 Micraster and Diplodetus. Biogeographic patterns were also considered
 using the phylogeny, and several episodes of vicariance and range
 expansion were identified. These were possibly related to some of the
 various major episodes of sea-level rise and fall during the Cretaceous.
 In particular, Valangian – mid-Aptian regressions may have caused
 vicariance within Heteraster and Washitaster while other early spatangoid
 vicariance may be related to regressions during the late Aptian – early
 Cenomanian. Further, vicariance caused by regressions during the
 mid-Cenomanian – Maastrichtian may have driven diversification within
 Micraster and Diplodetus. Lastly, transgressions during the late Aptian –
 early Cenomanian seem to have spurred prominent range expansions in
 Mecaster and Hemiaster.
description: Dataset was collected using comparative morphological study of
 test features of fossil specimens. All morphological characters were
 coded.
description: <em>Toxaster retusus</em> was used as the outgroup. 
 Missing data indicated by "?". A branch and
 bound search was employed to find the most parsimonious tree using PAUP
 4.0. Character and character state descriptions
 provided in associated published paper. All multi-state
 characters were treated as unordered. Characters were
 weighted equally. Analyses were run with and without
 <em>Linthia variabilis</em>. Characters
 were mapped to the phylogeny using PAUP 4.0, which employs ACCTRAN
 (phylogeny only shown for analysis conducted without <em>Linthia
 variabilis</em>).
DOI: 10.7272/q6mw2fcp
title: Data for: Cytoprotection by a naturally occurring variant of ATP5G1 in Arctic ground squirrel neural progenitor cells

description: Many organisms in nature have evolved mechanisms to tolerate severe
 hypoxia or ischemia, including the hibernation-capable Arctic ground
 squirrel (AGS). Although hypoxic or ischemia tolerance in AGS involves
 physiological adaptations, little is known about the critical cellular
 mechanisms underlying intrinsic AGS cell resilience to metabolic stress.
 Through cell survival-based cDNA expression screens in neural progenitor
 cells, we identify a genetic variant of AGS Atp5g1 that confers cell
 resilience to metabolic stress. Atp5g1 encodes a subunit of the
 mitochondrial ATP synthase. Ectopic expression in mouse cells and
 CRISPR/Cas9 base editing of endogenous AGS loci revealed causal roles of
 one AGS-specific amino acid substitution in mediating cytoprotection by
 AGS ATP5G1. AGS ATP5G1 promotes metabolic stress resilience by modulating
 mitochondrial morphological change and metabolic functions. Our results
 identify a naturally occurring variant of ATP5G1 from a mammalian
 hibernator that critically contributes to intrinsic cytoprotection against
 metabolic stress.
description: Contains 2 files: 1) Source data for
 manuscript figures in Prism format (see methods and figure legends for
 details) 2) Survival screen gene set in excel format
 from sequenced plasmids (see methods for details)
DOI: 10.5061/dryad.c59zw3r5r
title: The contribution of the edaphic factor as a driver of recent plant diversification in a Mediterranean biodiversity hotspot

description: 1. The high diversification rates of plant lineages in the Mediterranean
 Basin hotspot have been linked to a complex interaction of climatic
 stressors, geographic isolation and soil type, but the question remains as
 to which of these factors has been the most significant environmental
 driver of recent speciation. 2. Here, we draw on distributional data for
 the entire endemic flora of the Iberian Peninsula, together with DNA-based
 phylogenies and spatial phylogenetic methods, to explore patterns of
 relative phylogenetic endemism at different spatial resolutions and
 phylogenetic scales (superclades) and assess how environmental factors
 contribute to explain these patterns. 3. We found that recent
 diversification of angiosperms as a whole, and particularly of eudicots,
 has been boosted by environmental stressors including high values of soil
 pH and dry-seasonal climatic conditions, while diversification of monocots
 has not been associated with soil conditions but with high elevation and
 less seasonal climate. 4. Synthesis. These results provide robust insights
 into the environmental factors driving recent plant diversification in the
 Mediterranean Basin, including a role of soil properties that had not been
 quantified before. The contrasting environmental drivers of
 diversification in Eudicots and Monocots highlight the importance of
 analyzing spatial phylogenetic patterns at multiple phylogenetic scales to
 get a better understanding of the processes that shape biodiversity.
DOI: 10.5061/dryad.xsj3tx9d5
title: Model output for: Attributing causes of future climate change in the California Current System with multi-model downscaling

description: Regional Ocean Modeling System outputs from dynamic downscaling of Coupled
 Model Intercomparison Project climate forcings in the California Current
 system, including projections with full climate forcings, as well as
 attribution experiments with only changes in wind, heat fluxes and other
 properties changing stratification, and boundary biogeochemical forcings.
 Output variables include euphotic zone integrated net primary
 productivity, and incident photosytnehtically available radiation, and
 ocean temperature, salinity, vertical velocity, and dissolved oxygen and
 nitrate concentrations at select depths.
description: Configuration and methods are described in detail in the
 associated manuscript in Global Biogeochemical Cycles, as well as in
 https://doi.org/10.1101/2020.02.10.942730 and
 https://doi.org/10.1101/2020.02.10.942565. Projections of ~2100 ocean
 conditions are generated by applying global earth system model outputs to
 regional model boundary forcings, which are dynamically downscaled through
 the regional ocean model. Presented variables are interpolated to select
 depth horizons form the bathymetry-following following model
 grid.
DOI: 10.5061/dryad.4b8gthtb7
title: Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions

description: The Rio Grande drainage of the southwestern United States and Mexico has
 undergone intense anthropogenic alteration by water diversions, extraction
 and associated habitat changes. These alterations have disproportionately
 impacted the pelagic broadcast spawning guild of minnows (pelagophils).
 Several Rio Grande endemic pelagophils, including the co-occurring Rio
 Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis
 aestivalis), have experienced dramatic recent range-wide declines yet have
 slipped under the radar of conservation efforts. The status of N.
 jemezanus and M. aestivalis in the Rio Grande and Pecos River was
 evaluated and standing genetic variation were characterized. Genetic
 evidence indicates that populations of both species found in the Rio
 Grande and Pecos River are genetically distinct. Additionally, 159 outlier
 loci were identified in M. aestivalis suggesting possible local adaptation
 in the Rio Grande and Pecos River populations. Though range-wide genetic
 data are limited, N. jemezanus populations in both rivers harbor
 considerable genetic diversity. Mitochondrial data from both taxa are
 consistent with a history of secondary contact between formerly isolated
 populations with deeply divergent haplotypes found within the Rio Grande
 and Pecos River populations of N. jemezanus and within the Rio Grande
 population of M. aestivalis. Extensive survey efforts in the lower Rio
 Grande and its tributaries in Texas document significant range contraction
 and near extirpation of N. jemezanus from this part of the basin;
 highlighting the need for immediate action to protect the
 species. 
description: Mitochodrial DNA sequence data collected using Sanger sequencing
 of DNA isolated from fin clip tissue samples. Sequences were edited and
 verified using Sequencher. Haplotype sequences are deposited on
 Genbank. Microsatellite data collected using ABI3130
 capillary sequencer and verified usign Genemapper software.
 ddRAD sequence data is provided in .vcf files for Notropis
 jemezanus and Macrhybopsis aestivalis. Data processing steps are provided
 on GITHUB. Detail are provided in the associated publication.
description: Missing values in microsatellite data are indicated by
 "0" Ambiguous base calls are indicated by
 "n"
DOI: 10.5061/dryad.wdbrv15mm
title: Research Education: Neurology Resident EEG Education: A Survey of US Neurology Residency Program Directors

description: Objective: To better understand the EEG education provided to adult
 neurology residents by surveying program directors (PDs) of adult
 neurology residency programs in the US. Methods: An online survey focused
 on characteristics of neurology residency programs and their EEG teaching
 systems was distributed to the 161 adult neurology residency PDs listed in
 the ACGME website at the time of the study. Results: Forty-seven (29%) out
 of the 161 PDs completed the survey – most of the participating programs
 (89%) were academic. The mean number of 1-month EEG rotation(s) required
 to graduate was 1.7 (range 0-4, median 1.75). EEG rotations involved the
 inpatient and outpatient setting in 91% and 70% of programs, respectively.
 The average number of EEGs read during a typical EEG rotation varied from
 more than 40, in about one-third of programs, to 0-10,
 in about 14% of programs. There was significant variability in the
 requirements for successful completion of EEG rotations, and most PDs
 (64%) reported not utilizing objective measures to assess EEG milestones.
 The most commonly used educational methods were didactics throughout the
 year (95%) and EEG teaching during EEG rotations (93%). The most commonly
 reported barriers to EEG education were insufficient EEG exposure (32%)
 and ineffective didactics (11%); possible solutions are summarized
 in table 1. Conclusion: Our study identified a lack of
 consistency in teaching and evaluating residents during residency and
 presented EEG education barriers alongside possible solutions. We
 encourage PDs across the country to re-evaluate their EEG teaching systems
 in order to optimize EEG education.
DOI: 10.6084/m9.figshare.31046280
title: Reduced nitrous oxide emissions from andosol upland field applied with nitrogen-enriched cattle manure compost pellets

description: Manure compost pellets (MCP) are cylindrically shaped manure composts. Their physical characteristics greatly facilitate handling in transportation, spreading by machine, and storage, but emissions of nitrous oxide (N<sub>2</sub>O) are much larger after soils are amended with MCP versus non-pelleted manure composts (MC) and nitrogen fertilizers. Emissions of N<sub>2</sub>O have been reported to be lower, however, when soils are amended with pellets of nitrogen-enriched manure composts, which are byproducts of compost deodorization, than with MCP. The objective of this study was to confirm the reduction of N<sub>2</sub>O emissions from soils amended with nitrogen-enriched manure compost pellets (N+MCP) and to assess the environmental conditions that affect N<sub>2</sub>O emissions by conducting field experiments where cabbage was cultivated through five cropping seasons. During two cropping seasons when soil temperatures at the time of pellet application were relatively high (24–29°C), cumulative emissions of N<sub>2</sub>O from the N+MCP treatment were significantly reduced (by 66–75%) relative to those from the MCP treatment, and the initial peak of N<sub>2</sub>O emissions from the MCP treatment was very large compared to the peak from the N+MCP treatment. During the other three cropping seasons, when soil temperatures at the time of pellet application were relatively low (7–18°C), the reduction of N<sub>2</sub>O emissions from the N+MCP treatment compared to the MCP treatment was less (42% reduction) or none. These results suggested that the environmental conditions at the time of pellet application (e.g. soil temperature) were important determinants of N<sub>2</sub>O emissions from soils amended with MCP and of the reduction of N<sub>2</sub>O emissions from soils amended with N+MCP. The effect of adding urea to manure compost pellets (U+MCP) to reduce N<sub>2</sub>O emissions was explored using urea-added pellets with the same total nitrogen content as the N+MCP (4% of dry material) during the final two cropping seasons. Total N<sub>2</sub>O emissions from the U+MCP treatment were 33–52% lower than from the MCP treatment, but the reductions of N<sub>2</sub>O emissions were less than those from the N+MCP treatment. Total N<sub>2</sub>O emissions from soils amended with N+MCP or U+MCP were not significantly different from soils amended with non-pelleted MC throughout this study.
DOI: 10.6084/m9.figshare.31046280.v2
title: Reduced nitrous oxide emissions from andosol upland field applied with nitrogen-enriched cattle manure compost pellets

description: Manure compost pellets (MCP) are cylindrically shaped manure composts. Their physical characteristics greatly facilitate handling in transportation, spreading by machine, and storage, but emissions of nitrous oxide (N<sub>2</sub>O) are much larger after soils are amended with MCP versus non-pelleted manure composts (MC) and nitrogen fertilizers. Emissions of N<sub>2</sub>O have been reported to be lower, however, when soils are amended with pellets of nitrogen-enriched manure composts, which are byproducts of compost deodorization, than with MCP. The objective of this study was to confirm the reduction of N<sub>2</sub>O emissions from soils amended with nitrogen-enriched manure compost pellets (N+MCP) and to assess the environmental conditions that affect N<sub>2</sub>O emissions by conducting field experiments where cabbage was cultivated through five cropping seasons. During two cropping seasons when soil temperatures at the time of pellet application were relatively high (24–29°C), cumulative emissions of N<sub>2</sub>O from the N+MCP treatment were significantly reduced (by 66–75%) relative to those from the MCP treatment, and the initial peak of N<sub>2</sub>O emissions from the MCP treatment was very large compared to the peak from the N+MCP treatment. During the other three cropping seasons, when soil temperatures at the time of pellet application were relatively low (7–18°C), the reduction of N<sub>2</sub>O emissions from the N+MCP treatment compared to the MCP treatment was less (42% reduction) or none. These results suggested that the environmental conditions at the time of pellet application (e.g. soil temperature) were important determinants of N<sub>2</sub>O emissions from soils amended with MCP and of the reduction of N<sub>2</sub>O emissions from soils amended with N+MCP. The effect of adding urea to manure compost pellets (U+MCP) to reduce N<sub>2</sub>O emissions was explored using urea-added pellets with the same total nitrogen content as the N+MCP (4% of dry material) during the final two cropping seasons. Total N<sub>2</sub>O emissions from the U+MCP treatment were 33–52% lower than from the MCP treatment, but the reductions of N<sub>2</sub>O emissions were less than those from the N+MCP treatment. Total N<sub>2</sub>O emissions from soils amended with N+MCP or U+MCP were not significantly different from soils amended with non-pelleted MC throughout this study.
DOI: 10.5061/dryad.7m0cfxpsc
title: Tropicalisation and kelp loss shift trophic composition and lead to more winners than losers in fish communities

description: Climate-mediated species redistributions are causing novel interactions
 and leading to profound regime shifts globally.  For species that
 expand their distribution in response to warming, survival depends not
 only on their physiological capacity, but also on the ability to coexist
 or be competitive within the established community. In temperate marine
 reefs from around the world, the range expansion of tropical species,
 known as ‘tropicalisation’, has been linked to the disappearance of
 temperate habitat-forming kelps and shifts to dominance by low-biomass
 turfing algae. The consequences of these range expansions and habitat
 changes on resident fish communities are, however, unclear. Here, we use
 data derived from baited remote underwater video (BRUV) surveys to analyse
 changes in diversity and abundance of marine fishes over a 17-year period
 in warming reefs that have experienced kelp loss (occurring c. 2009).
 Despite the loss of kelp, we found that species richness and overall
 abundance of fishes (measured as probability of occurrence and relative
 abundance), including both tropical and temperate species, increased
 through time. We also found dramatic shifts in the trophic composition of
 fish assemblages. Tropical herbivorous fish increased most markedly
 through time and temperate-associated planktivores were the only group
 that declined, a potential consequence of tropicalisation not previously
 identified. At the species level we, identified 22 tropical and temperate
 species from four trophic guilds that significantly increased in
 occurrence, while only three species (all temperate associated) declined.
 Morphological trait space models suggest increases in fish diversity and
 overall occurrence are unlikely to be driven by uniqueness of traits
 amongst tropical range expanders. Our results show more winners than
 losers and suggest that pathways of energy flow will change in
 tropicalised systems, as planktonic inputs become less important and a
 higher proportion of algal productivity gets consumed locally by
 increasingly abundant herbivores.
description: Data collected as part of a lomg term BRUV survey effort in the
 Solitary Islands Marine Park. We specifically selected for reefs where
 kelp loss is recorded.
description: See 'Readme.txt' file
DOI: 10.5061/dryad.5tb2rbp2w
title: Small invertebrate consumers produce consistent size spectra across reef habitats and climatic zones

description: Changes in invertebrate body size-distributions that follow loss of
 habitat-forming species can potentially affect a range of ecological
 processes, including predation and competition. In the marine environment,
 small crustaceans and other mobile invertebrates (‘epifauna’) represent a
 basal component in reef food webs, with a pivotal secondary production
 role that is strongly influenced by their body size-distribution. Ongoing
 degradation of reef habitats that affect invertebrate size distributions,
 particularly transformation of coral and kelp habitat to algal turf, may
 thus fundamentally affect secondary production. Here we explored variation
 in size spectra of shallow epifaunal assemblages (i.e. the slope and
 intercept of the linear relationship between log abundance and body size
 at the assemblage level) across 21 reef microhabitats distributed along an
 extensive eastern Australian climatic gradient from the tropical northern
 Great Barrier Reef to cool temperate Tasmania. When aggregated across
 microhabitats at the site scale, invertebrate body size spectra (0.125 to
 8 mm range) were consistently log-linear (R2 ranging 0.87 to 0.98). Size
 spectra differed between, but not within, major groups of microhabitats,
 and exhibited little variability between tropical and temperate biomes.
 Nevertheless, size spectra showed significant tropical/temperate
 differences in slopes for epifauna sampled on macroalgal habitats, and in
 elevation for soft coral and sponge habitats. Our results reveal epifaunal
 size spectra to be a highly predictable macro-ecological feature. Given
 that variation in epifaunal size spectra among groups of microhabitats was
 greater than variation between tropical and temperate biomes, we postulate
 that ocean warming will not greatly alter epifaunal size spectra directly.
 However, transformation of tropical coral and temperate macroalgal
 habitats to algal turfs due to warming will alter reef food web dynamics
 through redistribution of the size of prey available to fishes.