cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31158679
title: Supplementary data for: "Scale-free localization in pseudo-Hermitian quantum walk"

description: This dataset contains all the <b>numerical data</b> used to generate the results and figures presented in the manuscript titled <b>"Scale-free localization in pseudo-Hermitian quantum walk"</b>.<b>Description of Data Structure and Content:</b><br>The dataset comprises plain text (.xlsx) files, each containing the raw or processed numerical results from our analysis of the pseudo-Hermitian quantum walk model. The files are organized and named to clearly indicate their contents and the corresponding figure in the manuscript.<br><b>How to Use This Data:</b><br>The data is provided in a simple, column-based format for maximum accessibility. It can be directly imported into any data analysis or plotting software (e.g., Origin, MATLAB, Python with NumPy, Excel).
DOI: 10.6084/m9.figshare.31158679.v1
title: Supplementary data for: "Scale-free localization in pseudo-Hermitian quantum walk"

description: This dataset contains all the <b>numerical data</b> used to generate the results and figures presented in the manuscript titled <b>"Scale-free localization in pseudo-Hermitian quantum walk"</b>.<b>Description of Data Structure and Content:</b><br>The dataset comprises plain text (.xlsx) files, each containing the raw or processed numerical results from our analysis of the pseudo-Hermitian quantum walk model. The files are organized and named to clearly indicate their contents and the corresponding figure in the manuscript.<br><b>How to Use This Data:</b><br>The data is provided in a simple, column-based format for maximum accessibility. It can be directly imported into any data analysis or plotting software (e.g., Origin, MATLAB, Python with NumPy, Excel).
DOI: 10.5067/asdc/firexaq_merge_data_2
title: FIREX-AQ Merge Data Files
DOI: 10.5067/asdc/firexaq_metnav_aircraftinsitu_dc8_data_1
title: FIREX-AQ DC8 In-Situ Meteorological and Navigational Data
DOI: 10.5061/dryad.19p14
title: Data from: Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon

description: While supportive breeding programs strive to minimize negative genetic
 impacts to populations, case studies have found evidence for reduced
 fitness of artificially produced individuals when they reproduce in the
 wild. Pedigrees of two complete generations were tracked with molecular
 markers to investigate differences in reproductive success (RS) of wild
 and hatchery-reared Chinook salmon spawning in the natural environment to
 address questions regarding the demographic and genetic impacts of
 supplementation to a natural population. Results show a demographic boost
 to the population from supplementation. On average, fish taken into the
 hatchery produced 4.7 times more adult offspring, and 1.3 times more adult
 grand-offspring than naturally reproducing fish. Of the wild and hatchery
 fish that successfully reproduced, we found no significant differences in
 RS between any comparisons but hatchery-reared males typically had lower
 RS values than wild males. Mean relative reproductive success (RRS) for
 hatchery F1 females and males was 1.11 (p = 0.84) and 0.89 (p = 0.56),
 respectively. RRS of hatchery-reared fish (H) that mated in the wild with
 either hatchery or wild origin (W) fish were generally equivalent to WxW
 matings. Mean RRS of HxW and HxH matings was 1.07 (p = 0.92) and 0.94 (p =
 0.95), respectively. We conclude that fish chosen for hatchery rearing did
 not have a detectable negative impact on the fitness of wild fish by
 mating with them for a single generation. Results suggest that
 supplementation following similar management practices (e.g., 100% local,
 wild-origin brood stock) can successfully boost population size with
 minimal impacts on the fitness of salmon in the wild.
description: MEC_12_0538_Dataset for
 Dryad_14DEC12Microsatellite data for
 individuals included in parentage analysis.
DOI: 10.5067/asdc/firexaq_metnav_aircraftinsitu_er2_data_1
title: FIREX-AQ ER-2 In-Situ Meteorological and Navigational Data
DOI: 10.5067/asdc/firexaq_radiation_aircraftinsitu_dc8_data_1
title: FIREX-AQ DC-8 In-Situ Radiation Data
DOI: 10.5061/dryad.8661
title: Data from: Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms

description: Salinity imposes a significant barrier to he distribution of many
 organisms, including diatoms. Diatoms are ancestrally marine, and the
 number of times they have independently colonized fresh waters and the
 physiological adaptations that facilitated these transitions remain
 outstanding questions in diatom evolution. The colonization of fresh
 waters by diatoms has been compared to ‘‘crossing the Rubicon,’’ implying
 that successful colonization events are rare, irreversible, and lead to
 substantial species diversification. To test these hypotheses, we
 reconstructed the phylogeny of Thalassiosirales, a diatom lineage with
 high diversity in both marine and fresh waters. We collected ~5.3 kb of
 DNA sequence data from the nuclear (SSU and partial LSU rDNA) and
 chloroplast genomes (psbC and rbcL) and reconstructed the phylogeny using
 parsimony and Bayesian methods. Alternative topology tests strongly reject
 all previous colonization hypotheses, including monophyly of the
 predominantly freshwater Stephanodiscaceae. Results showed at least three
 independent colonizations of fresh waters, and whereas previous accounts
 of freshwater-to-marine transitions have been discounted, these results
 provide compelling evidence for as many as three independent
 re-colonizations of the marine habitat, two of which led to speciation
 events. This study adds valuable phylogenetic context to previous debate
 about the nature of the salinity barrier in diatoms and provides
 compelling evidence that, at least for Thalassiosirales, the salinity
 barrier might be less formidable than previously thought.
description: concatenated 4-gene
 matrixthal.nexconcatenated 4-gene matrixthal.nex
DOI: 10.5067/asdc/firexaq_satellite_data_2
title: FIREX-AQ Satellite And Related Ancillary Data
DOI: 10.5061/dryad.r17k4
title: Data from: Local adaptation at range edges: comparing elevation and latitudinal gradients

description: Local adaptation at range edges influences species’ distributions and how
 they respond to environmental change. However, the factors that affect
 adaptation, including gene flow and local selection pressures, are likely
 to vary across different types of range edge. We performed a reciprocal
 transplant experiment to investigate local adaptation in populations of
 Plantago lanceolata and P. major from central locations in their European
 range and from their latitudinal and elevation range edges (in northern
 Scandinavia and Swiss Alps, respectively). We also characterized patterns
 of genetic diversity and differentiation in populations using molecular
 markers. Range-centre plants of P. major were adapted to conditions at the
 range centre, but performed similarly to range-edge plants when grown at
 the range edges. There was no evidence for local adaptation when comparing
 central and edge populations of P. lanceolata. However, plants of both
 species from high elevation were locally adapted when compared with plants
 from high latitude, although the reverse was not true. This asymmetry was
 associated with greater genetic diversity and less genetic differentiation
 over the elevation gradient than over the latitudinal gradient. Our
 results suggest that adaptation in some range-edge populations could
 increase their performance following climate change. However, responses
 are likely to differ along elevation and latitudinal gradients, with
 adaptation more likely at high elevation. Furthermore, based upon these
 results, we suggest that gene flow is unlikely to constrain adaptation in
 range-edge populations of these species.
description: TransplantExperiment_2012Collected in the field.TransplantExperiment_2011Collected in the fieldMicrosatMarkers_PlantagoLanceolataData from microsatellite markers for P. lanceolata.MicrosatMarkers_PlantagoMajorData from microsatellite markers for P. major.
DOI: 10.5067/asdc/firexaq_surfacemobile_aerodyne_insitu_data_1
title: FIREX-AQ Aerodyne Mobile Lab Surface Mobile In-Situ Measurements
DOI: 10.5067/asdc/firexaq_surfacemobile_carb_insitu_data_1
title: FIREX-AQ California Air Resources Board (CARB) Surface Mobile In-Situ Measurements
DOI: 10.5061/dryad.m186r
title: Data from: Parallel evolution of local adaptation and reproductive isolation in the face of gene flow

description: Parallel evolution of similar phenotypes provides strong evidence for the
 operation of natural selection. Where these phenotypes contribute to
 reproductive isolation, they further support a role for divergent,
 habitat-associated selection in speciation. However, the observation of
 pairs of divergent ecotypes currently occupying contrasting habitats in
 distinct geographical regions is not sufficient to infer parallel origins.
 Here we show striking parallel phenotypic divergence between populations
 of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting
 habitats exposed to either wave action or crab predation. This divergence
 is associated with barriers to gene exchange but, nevertheless, genetic
 variation is more strongly structured by geography than by ecotype. Using
 approximate Bayesian analysis of sequence data and AFLP markers, we show
 that the ecotypes are likely to have arisen in the face of continuous gene
 flow and that the demographic separation of ecotypes has occurred in
 parallel at both regional and local scales. Parameter estimates suggest a
 long delay between colonisation of a locality and ecotype formation,
 perhaps because the postglacial spread of crab populations was slower than
 the spread of snails. Adaptive differentiation may not be fully
 genetically independent despite being demographically parallel. These
 results provide new insight into a major model of ecologically-driven
 speciation.
description: Lsaxatilis_AFLPs-1AFLP data file. See 'readme' for additional descriptionLsaxatilis_landmarks-1Landmark coordinate fileLsaxatilis_morphometrics-1Relative warps and scar dataMitochondrial sequencesMtDNA sequences in fasta formatThioPer-2_Final-NoIndel_IntronElFac_Final-NoIndel_IntronCal-1_Final-NoIndel_Intron
DOI: 10.5067/asdc/firexaq_surfacemobile_mach2_insitu_data_1
title: FIREX-AQ MACH2 Surface Mobile In-Situ Measurements
DOI: 10.5067/asdc/firexaq_tracegas_aircraftinsitu_dc8_data_1
title: FIREX-AQ DC-8 In-Situ Trace Gas Data
DOI: 10.15468/trtzm3
title: University of North Carolina at Chapel Hill Herbarium: Fungi

description: The University of North Carolina Chapel Hill Herbarium (NCU) is a Department within the North Carolina Botanical Garden of the University of North Carolina at Chapel Hill. Important collectors include William Chambers Coker, John Nathaniel Couch, & Arthur Bliss Seymour. NCU also curates vascular plants, macroalgae, lichens, bryophytes, and plant fossils. NCU, located in the center of the UNC-CH campus, welcomes visitors & researchers; contact Curator for information on hours & parking. STATEMENT ON OFFENSIVE CONTENT ON SPECIMEN LABELS: Collection records at NCU may contain language that reflects historical place or taxon names in an original form that is no longer acceptable or appropriate in an inclusive environment. Because NCU preserves data in their original form to retain authenticity and facilitate research, we have chosen to facilitate conversations and are committed to address the problem of racial, derogatory and demeaning language that may be found in our database. Insensitive or offensive language is not condoned by NCU. We recognize the land and sovereignty of Native & Indigenous nations in Chapel Hill, in North Carolina, in North America, and across the world. The North Carolina Botanical Garden and the North Carolina Botanical Garden Foundation acknowledge that the story told about the history of the land we steward has been incomplete. Before the Morgans and Masons, these lands were home to multiple tribes and the ancestors of the Occaneechi Band of the Saponi Nation, who persist locally to this day. We recognize that at least one of the adjacent lands we steward, Mason Farm Biological Reserve, was first cleared, cultivated, and worked by Native Americans and later by African enslaved people. We invite you to reflect on our individual and community roles in knowing important and untold stories about the land we each steward.
DOI: 10.5061/dryad.18j1h
title: Data from: Variation of anal fin egg-spots along an environmental gradient in a haplochromine cichlid fish

description: Male secondary sexual traits are targets of inter- and/or intrasexual
 selection, but can vary due to a correlation with life-history traits or
 as by-product of adaptation to distinct environments. Trade-offs
 contributing to this variation may comprise conspicuousness toward
 conspecifics versus inconspicuousness toward predators, or between
 allocating resources into coloration versus the immune system. Here, we
 examine variation in expression of a carotenoid-based visual signal,
 anal-fin egg-spots, along a replicate environmental gradient in the
 haplochromine cichlid fish Astatotilapia burtoni. We quantified egg-spot
 number, area, and coloration; applied visual models to estimate the
 trait's conspicuousness when perceived against the surrounding tissue
 under natural conditions; and used the lymphocyte ratio as a measure for
 immune activity. We find that (1) males possess larger and more
 conspicuous egg-spots than females, which is likely explained by their
 function in sexual selection; (2) riverine fish generally feature fewer
 but larger and/or more intensely colored egg-spots, which is probably to
 maintain signal efficiency in intraspecific interactions in long
 wavelength shifted riverine light conditions; and (3) egg-spot number and
 relative area correlate with immune defense, suggesting a trade-off in the
 allocation of carotenoids. Taken together, haplochromine egg-spots feature
 the potential to adapt to the respective underwater light environment, and
 are traded off with investment into the immune system.
description: Reflectance
 spectraReflectance spectra of
 the second egg-spot and the area above the egg-spots on the anal fin of
 malesReflectance_data_males.xlsxAmbient light spectraDownwelling irradiance for each locality (except Lf1) at the surface and at the following depths: 10, 20, 30, 40, 50, 70 and 100 cm, or to the deepest possible point within the interval.Ambient_light_data.xlsxEgg-spot measurements based on photographsegg_var_tabelle_hochladen.xlsx
DOI: 10.5067/asdc/firexaq_tracegas_aircraftremotesensing_dc8_data_1
title: FIREX-AQ Remotely Sensed Trace Gas Data
DOI: 10.5061/dryad.rs7b0
title: Data from: Novel forests maintain ecosystem processes after the decline of native tree species

description: The positive relationship between species diversity (richness and
 evenness) and critical ecosystem functions, such as productivity, carbon
 storage, and nutrient cycling, is often used to predict the consequences
 of extinction. At regional scales, however, plant species richness is
 mostly increasing rather than decreasing because successful plant species
 introductions far outnumber extinctions. If these regional increases in
 richness lead to local increases in diversity, a reasonable prediction is
 that productivity, carbon storage, and nutrient cycling will increase
 following invasion, yet this prediction has rarely been tested
 empirically. We tested this prediction in novel forest communities
 dominated by introduced species (~ 90% basal area) in lowland Hawaiian
 rainforests by comparing their functionality to that of native forests. We
 conducted our comparison along a natural gradient of increasing nitrogen
 availability, allowing for a more detailed examination of the role of
 plant functional trait differences (specifically, N2-fixation) in driving
 possible changes to ecosystem function. Hawai'i is emblematic of
 regional patterns of species change; it has much higher regional plant
 richness than it did historically, due to &gt; 1000 plant species
 introductions and only ~ 71 known plant extinctions--resulting in an
 approximately 100% increase in richness. At local scales, we found that
 novel forests had significantly higher tree species richness and higher
 diversity of dominant tree species. We further found that aboveground
 biomass, productivity, nutrient turnover (as measured by soil-available
 and litter-cycled nitrogen and phosphorus), and belowground carbon storage
 either did not differ significantly or were significantly greater in novel
 relative to native forests. We found that the addition of introduced
 N2-fixing tree species on N-limited substrates had the strongest effect on
 ecosystem function--a pattern found by previous empirical tests. Our
 results support empirical predictions of the functional effects of
 diversity, but they also suggest basic ecosystem processes will continue
 even after dramatic losses of native species diversity if simple
 functional roles are provided by introduced species. Because large
 portions of the Earth's surface are undergoing similar transitions
 from native to novel ecosystems, our results are likely to be broadly
 applicable.
description: novel_forest_primary_datanovel_forest_primary_data2.zip is a revision of novel_forest_primary_data.zip, added on 2012-05-03.
DOI: 10.5067/asdc/firexaq_tracegas_aircraftremotesensing_er2_gcas_data_1
title: FIREX-AQ ER-2 Remotely Sensed GEOstationary Coastal and Air Pollution Events (GEO-CAPE) Airborne Simulator (GCAS)
DOI: 10.5067/asdc/firexaq_tracegas_aircraftremotesensing_er2_nasti_data_1
title: FIREX-AQ ER-2 Remotely Sensed National Polar - Orbiting Operational Environmental Satellite System Airborne Sounder Testbed - Interferometer (NAST-I) Data
DOI: 10.5061/dryad.d4j55
title: Data from: An integrated model of phenotypic trait changes and site-specific sequence evolution

description: Recent years have seen a constant rise in the availability of trait data,
 including morphological features, ecological preferences, and life history
 characteristics. These phenotypic data provide means to associate genomic
 regions with phenotypic attributes, thus allowing the identification of
 phenotypic traits associated with the rate of genome and sequence
 evolution. However, inference methodologies that analyze sequence and
 phenotypic data in a unified statistical framework are still scarce. Here,
 we present TraitRateProp, a probabilistic method that allows testing
 whether the rate of sequence evolution is associated with a binary
 phenotypic character trait. The method further allows the detection of
 specific sequence sites whose evolutionary rate is most noticeably
 affected following the character transition, suggesting a shift in
 functional/structural constraints. TraitRateProp is first evaluated in
 simulations and then applied to study the evolutionary process of plastid
 plant genomes upon a transition to a heterotrophic lifestyle. To this end,
 we analyze 25 plastid genes across 85 orchid species, spanning different
 lifestyles and representing different genera in this large family of
 flowering plants. Our results indicate higher evolutionary rates following
 repeated transitions to a heterotrophic lifestyle in all but four of the
 loci analyzed.
description: SuppMaterial_TraitRateProprevised_SuppMaterial_TraitRateProp.docxSuppTable_S1SuppTable_S2TRP_on_orchid_genesTRP_on_OM_genes
DOI: 10.5067/asdc/firexaq_tracegas_aircraftremotesensing_er2_shis_data_1
title: FIREX-AQ ER-2 Scanning High-Resolution Interferometer Sounder (S-HIS)
DOI: 10.6084/m9.figshare.31160704
title: Simulation landscapes and config files associated with Buffan et al. "<i>Palaeoclimate alone fails to explain the asymmetry of the Great American Biotic Interchange"</i>

description: This data are associated with the publication "<i>Palaeoclimate alone fails to explain the asymmetry of the Great American Biotic Interchange</i>" (Buffan et al).See also scripts and associated data here: https://github.com/Buffan3369/GABI-gen3sis.git
DOI: 10.6084/m9.figshare.31160704.v1
title: Simulation landscapes and config files associated with Buffan et al. "<i>Palaeoclimate alone fails to explain the asymmetry of the Great American Biotic Interchange"</i>

description: This data are associated with the publication "<i>Palaeoclimate alone fails to explain the asymmetry of the Great American Biotic Interchange</i>" (Buffan et al).See also scripts and associated data here: https://github.com/Buffan3369/GABI-gen3sis.git
DOI: 10.5067/asdc/suborbital/firexaq_jvalue_aircraftinsitu_n48_data_1
title: FIREX-AQ NOAA-CHEM Twin Otter Photolysis Rate (j value) Data
DOI: 10.5067/asdc/suborbital/firexaq_metnav_aircraftinsitu_n48_data_1
title: FIREX-AQ NOAA-CHEM Twin Otter In Situ Meteorological and Navigational Data
DOI: 10.5067/asdc/suborbital/firexaq_aerosol_aircraftinsitu_n48_data_1
title: FIREX-AQ NOAA-CHEM Twin Otter In Situ Aerosol Data
DOI: 10.5061/dryad.q1f65
title: Data from: Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming

description: 1. Species distribution shifts in response to climate change require that
 recruitment increase beyond current range boundaries. For trees with long
 lifespans, the importance of climate-sensitive seedling establishment to
 the pace of range shifts has not been demonstrated quantitatively. 2.
 Using spatially explicit, stochastic population models combined with data
 from long-term forest surveys, we explored whether the climate-sensitivity
 of recruitment observed in climate manipulation experiments was sufficient
 to alter populations and elevation ranges of two widely distributed,
 high-elevation North American conifers. 3. Empirically observed,
 warming-driven declines in recruitment led to rapid modeled population
 declines at the low-elevation, “warm edge” of subalpine forest and slow
 emergence of populations beyond the high-elevation, “cool edge”. Because
 population declines in the forest occurred much faster than population
 emergence in the alpine, we observed range contraction for both species.
 For Engelmann spruce, this contraction was permanent over the modeled time
 horizon, even in the presence of increased moisture. For limber pine,
 lower sensitivity to warming may facilitate persistence at low elevations
 – especially in the presence of increased moisture – and rapid
 establishment above treeline, and, ultimately, expansion into the alpine.
 4. Synthesis. Assuming 21st century warming and no additional moisture,
 population dynamics in high-elevation forests led to transient range
 contractions for limber pine and potentially permanent range contractions
 for Engelmann spruce. Thus, limitations to seedling recruitment with
 warming can constrain the pace of subalpine tree range shifts.
description: Models and results for
 "Declines in low-elevation subalpine tree populations outpace growth
 in high-elevation populations with warming"The models and results
 shown in the manuscript figures 3 and 4 are archived as text files for use
 with RAMAS GIS (Version 5).Conlisk_etal_JEcol2017_model_archive06282017.zip
DOI: 10.5067/asdc/suborbital/firexaq_analysis_n48_data_1
title: FIREX-AQ NOAA-CHEM Twin Otter Analysis Data
DOI: 10.5067/asdc/suborbital/firexaq_n46_data_1
title: FIREX-AQ NOAA-MET Twin Otter Data
DOI: 10.5067/asdc/suborbital/firexaq_tracegas_aircraftinsitu_n48_data_1
title: FIREX-AQ NOAA-CHEM Twin Otter In Situ Trace Gas