cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mpg4f4qwt
title: Genotype and phenotype data for Columbia River steelhead.

description: As life history diversity plays a critical role in supporting the
 resilience of exploited populations, understanding the genetic basis of
 those life history variations is important for conservation management.
 However, effective application requires a robust understanding of the
 strength and universality of genetic associations. Here, we examine
 genetic variation of single nucleotide polymorphisms in genomic regions
 previously associated with migration phenology and age-at-maturity in
 steelhead (Oncorhynchus mykiss) from the Columbia River. We found
 chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance
 in migration timing in both coastal and inland steelhead. However,
 strength of association was much greater in coastal than inland steelhead
 (R2 0.51 vs 0.08), suggesting that genomic background and
 challenging inland migration pathways may act to moderate effects of this
 region. Further, we found that chromosome 25 candidate markers (SIX6 gene)
 were significantly associated with age and size at first return migration
 for inland steelhead, and this pattern was mediated by sex in a
 predictable pattern (males R2 = 0.139-0.170; females
 R2 = 0.096-0.111). While this encourages using these candidate
 regions in predicting life history characteristics, we suggest that stock
 specific associations and haplotype frequencies will be useful in guiding
 implementation of genetic assays to inform management.  
description: genotype-by-thousands (GTseq) genotypes; observation/measurement
 at Bonneville AFF, PIT recordings from PTAGIS
DOI: 10.5061/dryad.zkh18937r
title: Data for morphometric analysis and DNA barcode sequence for the new fish species Polymixia hollisterae

description: Two datasets are provided to support the journal article
 (https://doi.org/10.1643/i2020112) by T. C. Grande and M. V. H.
 Wilson naming the new Bermuda fish species Polymixia hollisterae. The
 first dataset is for 2-D multivariate
 morphometric comparisons of selected specimens and species of the
 fish genus Polymixia. The file is in TPS format, as a
 plain text file, for use in the application MorphoJ. The
 data are for 27 specimens with pixel coordinates for 34 landmarks
 digitized in ImageJ and used to generate Fig. 13 in the
 referenced publication. The second dataset, published here
 courtesy of Dr. R. Eytan, is a mitochondrial DNA barcode sequence
 in fasta format for the second paratype specimen, a
 small juvenile of the new species. The specimen is only the third
 one known of the new species and the only one not from Bermuda. It was
 collected in the north-central Gulf of Mexico and is now
 deposited in the Harvard University MCZ fish collection as catalog number
 MCZ 174218. The fasta file can be used as input to the barcode
 identification function at boldsystems.org, although its original
 identification in BOLD was incorrect.
description: The multivariate morphometric data were obtained using the
 PointPicker plugin for ImageJ, using images of each of 27 specimens. Data
 for each specimen occupy 36 lines, the first one giving the number of
 landmarks and the last one representing the specimen identifier.  Each of
 the other 34 lines represents the coordinates of a landmark - an
 X-coordinate and a Y-coordinate in image pixels, with the X-values
 counting from the left and the Y-values counting from the top of the
 image.
description: There are no missing values in the morphometric data. The
 specimen identifier is the last line of each specimen's entry in the
 tps text file for the morphometric analysis. The barcode sequence is in
 fasta format as a plain text file. The contents of the file can be pasted
 as an unknown into the identification function at
 boldsystems.org.
DOI: 10.5061/dryad.d2547d81b
title: Trade-off between fecundity and survival generates stabilizing selection on gall size

description: Complex interactions within multi-trophic communities are fundamental to
 the evolution of individual species that reside within them. One common
 outcome of species interactions are fitness trade-offs, where traits
 adaptive in some circumstances are maladaptive in others. Here, we
 identify a fitness trade-off between fecundity and survival in the cynipid
 wasp Callirhytis quercusbatatoides that induces multi-chambered galls on
 the stem of its host plant Quercus virginiana. We first quantified this
 trade-off in natural populations by documenting two relationships: a
 positive association between the trait gall size and fecundity, as larger
 galls contain more offspring, and a negative association between gall size
 and survival, as larger galls are attacked by birds at a higher rate.
 Next, we performed a field-based experimental evolution study where birds
 were excluded from the entire canopy of 11 large host trees for five
 years. As a result of the five-year release from avian predators, we
 observed a significant shift to larger galls per tree. Overall, our study
 demonstrates how two opposing forces of selection can generate stabilizing
 selection on a critical phenotypic trait in wild populations, and how
 traits can evolve rapidly in the predicted direction when conditions
 change.
description: This data comes from observational and experimental studies of
 the cynipid gall wasp <i>Callirhytis quercusbatatoides</i>
 that induces multi-chambered galls on the stem of its host plant
 <i>Quercus virginiana</i>. We first
 quantified this trade-off in natural populations by documenting two
 relationships: a positive association between the trait gall size and
 fecundity, as larger galls contain more offspring, and a negative
 association between gall size and survival, as larger galls are attacked
 by birds at a higher rate. Next, we performed a
 field-based experimental evolution study where birds were excluded from
 the entire canopy of 11 large host trees for five years.
DOI: 10.5061/dryad.tht76hdx3
title: Data from: Plasticity versus evolutionary divergence: what causes habitat partitioning in urban-adapted birds?

description: Habitat partitioning can facilitate the coexistence of closely related
 species, and often results from competitive interference inducing plastic
 shifts of subordinate species in response to aggressive, dominant species
 (plasticity), or the evolution of ecological differences in subordinate
 species that reduce their ability to occupy habitats where the dominant
 species occurs (evolutionary divergence). Evidence consistent with both
 plasticity and evolutionary divergence exist, but the relative
 contributions of each to habitat partitioning have been difficult to
 discern. Here we use a global dataset on the breeding occurrence of birds
 in cities to test predictions of these alternative hypotheses to explain
 previously described habitat partitioning associated with competitive
 interference. Consistent with plasticity, the presence of behaviorally
 dominant congeners in a city was associated with a 65% reduction in
 occurrence of subordinate species, but only when the dominant was a
 widespread breeder in urban habitats. Consistent with evolutionary
 divergence, increased range-wide overlap with dominant congeners was
 associated with a 56% reduction in occurrence of subordinates in cities,
 even when the dominant was absent from the city. Overall, our results
 suggest that both plasticity and evolutionary divergence play important,
 concurrent roles in habitat partitioning among closely related species in
 urban environments.
description: Please see manuscript for details.
description: Please see ReadMe file for description of data.
DOI: 10.5061/dryad.8931zcrnm
title: Data From: Breeders are less active foragers than non-breeders in wild Damaraland mole-rats

description: Eusocial insect societies are characterised by a clear division of labour
 between non-breeding workers and breeding queens and queens often do not
 contribute to foraging, defence and other maintenance tasks. It has been
 suggested that the structure and organisation of social mole-rat groups
 resembles that of eusocial insect societies. However, the division of
 labour has rarely been investigated in wild mole-rats and it is unknown
 whether breeders show decreased foraging activity compared to non-breeding
 helpers in natural groups. Here we show that, in wild Damaraland mole-rats
 (Fukomys damarensis), breeding males and females show lower activity in
 foraging areas than non-breeding group members. Both breeders and
 non-breeders displayed variation in activity across the different seasons.
 Our results suggest that group living allows social mole-rat breeders to
 reduce their investment in energetically costly and potentially risky
 foraging tasks which could contribute to the extended life-span of
 breeding individuals in this species and other social mole-rats.
DOI: 10.5061/dryad.6t1g1jwww
title: Proteolytic cleavage of Arabidopsis thaliana phosphoenolpyruvate carboxykinase-1 modifies its allosteric regulation

description: Phosphoenolpyruvate carboxykinase (PEPCK) plays a crucial role in
 gluconeogenesis. In this work, we analyze the proteolysis of Arabidopsis
 thaliana PEPCK1 (AthPEPCK1) in germinating seedlings. We found that the
 amount of AthPEPCK1 protein peaks at 24-48 hours post-imbibition.
 Concomitantly, we observed shorter versions of AthPEPCK1, putatively
 generated by metacaspase-9 (AthMC9). To study the impact of AthMC9
 cleavage on the kinetic and regulatory properties of AthPEPCK1, we
 produced truncated mutants based on the reported AthMC9 cleavage sites.
 The Δ19 and Δ101 truncated mutants of AthPEPCK1 showed similar kinetic
 parameters and the same quaternary structure than the WT. However,
 activation by malate and inhibition by glucose 6-phosphate were abolished
 in the Δ101 mutant. We propose that proteolysis of AthPEPCK1 in
 germinating seedlings operates as a mechanism to adapt the sensitivity to
 allosteric regulation during the sink-to-source transition.
DOI: 10.25338/b8633h
title: Canopy reflectance informs in-season malting barley nitrogen management: an ex-ante classification approach data

description: Malting barley (Hordeum vulgare) requires precise nitrogen (N) fertilizer
 management to achieve a narrow range of grain protein content (≈9–10.5%)
 while maintaining yields, but practical tools to accomplish this are
 lacking. This study hypothesized that canopy reflectance (Normalized
 Difference Vegetation Index (NDVI)) measured at tillering (Feekes 2–3) and
 expressed as a sufficiency index (SI), can estimate the likelihood of a
 site-specific response to in-season N fertilizer in malting barley. Canopy
 reflectance was measured from plots at tillering with a GreenSeeker and
 unmanned aerial vehicle (UAV) borne multispectral cameras in trials across
 heterogeneous California agroecosystems. Field experiments included a
 range of N fertilizer application rates (0–168 kg N ha-1) and timings
 (pre-plant, tillering, or evenly split), and resulted in a range of crop N
 sufficiency/deficiency. NDVI-based SI measurements were categorized into
 one of three quantitative categories (low, medium, and high) without
 additional experimental context using Gaussian mixture modeling. Despite
 that 85% of variation in protein yield was due to site-year, the
 reflectance-based categories indicated whether N fertilizer applied
 in-season would increase protein yield (p &lt; 0.01).
  Nitrogen application at tillering increased yield and protein
 for plots in the “low” and “medium” SI categories (45 and 4% for yield and
 16 and 12% for protein, respectively) (p &lt; 0.05), while “high” SI
 plots had neither yield (p = 0.23) nor protein (p = 0.26) increases.
 Importantly, the broader agronomic conditions of a site primarily
 determined whether response to in-season N manifested as increased yield
 or protein.
description: The .Rmd file details how the data was analyzed and used in the
 manuscript.
DOI: 10.15468/dl.yyysd3
title: Occurrence Download

description: A dataset containing 34785 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ictalurus furcatus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 34785 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002486-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7280/d1m67m
title: Supporting Data for Enhanced Gas Uptake During a-Pinene Ozonolysis Points to a Burying Mechanism

description: Understanding how gases interact with and are incorporated into
 atmospheric secondary organic aerosol particles is crucial for predicting
 particle effects on climate and human health.  This work examined
 how three gaseous organic nitrates (ON) are taken up into viscous
 particles formed from the ozonolysis of α-pinene (AP). 
 Experiments were performed in a flow reactor at room temperature under dry
 conditions, either with or without an OH scavenger present, with constant
 ozone and variable AP concentrations.  Each ON was introduced
 independently into the flow reactor and was present during particle
 formation/growth.  ON gas phase concentrations were determined by
 gas chromatography-mass spectrometry and particle phase concentrations
 were measured by high-resolution time-of-flight mass
 spectrometry.  Partition coefficients (KSOA) for each ON were
 independent of the initial AP concentration, except for 2-ethylhexyl
 nitrate which was undetectable in the particles at the lowest AP
 concentration.  Measured KSOA values were larger than those
 previously determined for equilibrium partitioning, which points to a
 potential burying mechanism for incorporation of ON during particle
 growth.  Estimated effective net uptake coefficients (gON) were
 found to increase with initial AP concentration.  Concentrations
 of gas phase oxidation products (including dimers and autoxidation
 products) predicted using an updated master chemical mechanism increased
 with AP concentration, with little change in the overall species
 distribution, consistent with increased trapping/burying of organic
 nitrates during particle growth and thus increased values of
 gON.  These results provide further evidence that
 kinetically-controlled burying can contribute significantly to particle
 growth provided that the incoming gas phase molecules have sufficient
 residence time on the particle surface to become buried via subsequent
 gas-surface collisions. 
description: The interested reader is referred to the following article for
 details about the experiments performed here: A. Vander
 Wall, L. M. Wingen, V. Perraud, Y. Zhao and B. J. Finlayson-Pitts,
 Enhanced gas uptake during a-pinene ozonolysis points to a burying
 mechanism, ACS Earth and Space Chem.,
 https://dx.doi.org/10.1021/acsearthspacechem.0c00163
description: This document contains the full updated MCM mechanism that is
 used in the manuscript referred to above.  The format is a text file that
 is suited for AtChem online box model
 (http://mcm.leeds.ac.uk/MCMv3.3.1/atchem/tutorial_intro.htt).
DOI: 10.5061/dryad.b5mkkwhb4
title: CESM1.2 simulation output for: The role of westerly wind bursts during different seasons versus ocean heat recharge in the development of extreme El Niño in a climate model

description: This is the subset of CESM1.2 model simulation output that was used for
 analysis and visualization of Yu and Fedorov [2020]
 (DOI:10.1029/2020GL088381). Please refer to README for details.
DOI: 10.5061/dryad.3j9kd51g0
title: Connectivity-based localization of human hypothalamic nuclei in functional images of standard voxel size

description: Despite their critical roles in autonomic functions, individual
 hypothalamic nuclei have not been extensively investigated in humans using
 functional magnetic resonance imaging, partly due to the difficulty in
 resolving individual nuclei contained in the small structure of the
 hypothalamus. Areal parcellation analyses enable discrimination of
 individual hypothalamic nuclei but require a higher spatial resolution,
 which necessitates long scanning time or large amounts of data to
 compensate for the low signal-to-noise ratio in 3T or 1.5T scanners. In
 this study, we present analytic procedures to estimate likely locations of
 individual nuclei in the standard 2-mm resolution based on our higher
 resolution dataset. The spatial profiles of functional connectivity with
 the cerebral cortex for each nucleus in the medial hypothalamus were
 calculated using our higher resolution dataset. Voxels in the hypothalamus
 in standard resolution images from the Human Connectome Project (HCP)
 database that predominantly shared connectivity profiles with the same
 nucleus were subsequently identified. Voxels representing individual
 nuclei, as identified with the analytic procedures, were reproducible
 across 20 HCP datasets of 20 subjects each. Furthermore, the identified
 voxels were spatially separate. These results suggest that these analytic
 procedures are capable of refining voxels that represent individual
 hypothalamic nuclei in standard resolution. Our results highlight the
 potential utility of these procedures in various settings such as patient
 studies, where lengthy scans are infeasible.
DOI: 10.5061/dryad.d51c5b010
title: Lagrangian Atmospheric Model output for the Control, Onset and Development experiments

description: This dataset consists of model outputs from the Control, Onset and
 Development experiments. Each experiment has six ensembles which were
 integrated for three years. 6-hourly instantaneous surface (1000hPa) zonal
 and meridional wind speed (m/s) between 31°S-31°N is recorded in
 uv1000hPa_{Control, Onset, Development}_ens{1, 2, 3, 4, 5, 6}.dat.
 6-hourly accumulated precipitation (mm) between 32°S-32°N is stored in
 precip_{ Control, Onset, Development}_ens{1, 2, 3, 4, 5, 6}.dat. Note the
 precip.*dat records accumulated rainfall for the past 6 hours. The missing
 data is recorded as nan.
description: Wind speed information carried by Lagrangian parcels is averaged
 in 2°-longitude by 2°-latitude grids in the tropics. Precipitation
 information is averaged in 4°-longitude by 4°-latitude grids in the
 tropics.
DOI: 10.5061/dryad.v9s4mw6sv
title: Relatedness and the composition of communities over time: evaluating phylogenetic community structure in the late Cenozoic record of bivalves

description: Understanding the mechanisms that prevent or promote the coexistence of
 taxa at local scales is critical to understanding how biodiversity is
 maintained. Competitive exclusion and environmental filtering are two
 processes thought to limit which taxa become established in a community.
 However, determining the relative importance of the two processes is a
 complex task, especially when the critical initial stages of colonization
 cannot be directly observed. Here, we explore the use of phylogenetic
 community structure for identifying filtering mechanisms in a fossil
 community. We integrated a time-calibrated molecular phylogeny of bivalve
 genera with a spatial dataset of late Cenozoic bivalves from the Pacific
 coast of North America to characterize how the community that was present
 in the semi-restricted San Joaquin Basin (SJB) embayment of present-day
 California was phylogenetically structured. We employed phylogenetic
 distance-based metrics across six time bins spanning 27-2.5 Ma and found
 no evidence of significant clustering or evenness in the SJB community
 when compared to communities randomly assembled from the regional source
 pool. Additionally, we found that new colonizers into the SJB were not
 significantly more or less closely related to native taxa than expected by
 chance. These findings suggest that neither competitive exclusion nor
 environmental filtering were overwhelmingly influential factors shaping
 the composition of the SJB community over time. We further discuss
 interpretations of these patterns in light of current understandings in
 community phylogenetics and reiterate the critical role historical
 perspectives play in how community assembly rules are assessed.
DOI: 10.5061/dryad.zkh18937s
title: Large-scale interventions may delay decline of the Great Barrier Reef

description: On the iconic Great Barrier Reef (GBR) the cumulative impacts of tropical
 cyclones, marine heatwaves and regular outbreaks of coral-eating
 crown-of-thorns starfish (CoTS) have severely depleted coral cover.
 Climate change will further exacerbate this situation over the coming
 decades unless effective interventions are implemented. Evaluating the
 efficacy of alternative interventions in a complex system experiencing
 major cumulative impacts can only be achieved through a systems-modeling
 approach. We have evaluated combinations of interventions using a coral
 reef meta-community model. The model consisted of a dynamic network of
 3753 reefs supporting communities of corals and CoTS connected through
 ocean larval dispersal, and exposed to changing regimes of tropical
 cyclones, flood plumes, marine heat waves and ocean acidification.
 Interventions included reducing flood plume impacts, expanding control of
 CoTS populations, stabilising coral rubble, managing solar radiation, and
 introducing heat tolerant coral strains. Without intervention, all climate
 scenarios resulted in precipitous declines in GBR coral cover over the
 next 50 years. The most effective strategies in delaying decline were
 combinations that protected coral from both predation (CoTS control) and
 thermal stress (solar radiation management) deployed at large scale.
 Successful implementation could expand opportunities for climate action,
 natural adaptation and socioeconomic adjustment by at least 1-2 decades.
description: The datset consists of the model plus model generated outputs
 associated with the publication: <em>Large-scale interventions may
 delay decline of the Great Barrier
 Reef</em> (RSOS-201296).  NetLogo
 code for the Coral Community Network (CoCoNet) model:
 <em>CoCoNet2_RSOS.nlogo</em> (NetLogo version 6.04 or
 later: http://ccl.northwestern.edu/netlogo/). GIS
 files used by the CoCoNet code: <em>GBR_reef_*
 </em>and<em> Coastline.*</em> 
 Excel file containing model outputs (averaged over all reefs)
 covering the historical period used for model
 calibration: <em>Condie et al 1985-2020 model data.xlsx</em>
 Excel file containing model outputs (averaged over
 all reefs) covering the future projection period used to test
 interventions: <em>Condie et al 2000-2070 model data with
 interventions.xlsx</em>
description: All data within Excel files are averaged across all reefs on the
 Great Barrier Reef.