cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ttdz08kw1
title: Data associated with "Floral pigmentation has responded rapidly to global change in ozone and temperature"

description: Across kingdoms, organisms ameliorate UV stress by increasing UV-absorbing
 pigmentation. Rapid ozone degradation during the 20th century resulted in
 elevated UV incidence, yet pigmentation responses to this aspect of global
 change have yet to be demonstrated. In flowering plants, UV exposure
 favors larger areas of UV-absorbing pigmentation on petals, which protects
 pollen from UV-damage. Pigmentation also affects floral thermoregulation,
 suggesting climate warming may additionally impact pigmentation. We used
 1238 herbarium specimens collected from 1941 to 2017 to test whether
 change in UV floral pigmentation was associated with altered ozone and
 temperature in 42 species spanning three continents. We tested three
 predictions: First, UV-absorbing pigmentation will increase temporally and
 be correlated with reduced ozone (higher UV) when accounting for effects
 of temperature; second, taxa that experienced larger ozone declines will
 display larger increases in pigmentation; and third, taxa with anthers
 exposed to ambient UV will respond more strongly than those with anthers
 protected by petals. Globally, the extent of petal UV pigmentation
 increased significantly across taxa by ~2% per year. However, temporal
 change was species specific—increasing in some taxa but declining in
 others. Species with exposed anthers experiencing larger declines in ozone
 displayed more dramatic pigmentation increases. For taxa with anthers
 enclosed within petals, pigmentation declined with increases in
 temperature, supporting a thermoregulatory role of UV pigmentation.
 Results document a rapid phenotypic response of floral pigmentation to
 anthropogenic climatic change, suggesting that global change may alter
 pollination through its impact on floral color, with repercussions for
 plant reproductive fitness.
description: Phenotypic data on ultraviolet floral pigmentation were collected
 from herbarium records using digital UV photographs of flowers analyzed in
 imageJ.  Code from SAS and R used to run statistics and a tree file used
 for comparative analyses are provided.
DOI: 10.5281/zenodo.18393589
title: Energy Efficiency in RFID Systems: A Systematic Review of Trends, Trade-offs, and Validation Methodologies
DOI: 10.5061/dryad.gtht76hjm
title: Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

description: The pace of the sequencing and computational assembly of novel reference
 genomes is accelerating. Though DNA sequencing technologies and assembly
 software tools continue to improve, biological features of genomes such as
 repetitive sequence as well as molecular artifacts that often accompany
 sequencing library preparation can lead to fragmented or chimeric
 assemblies. If left uncorrected, defects like these trammel progress on
 understanding genome structure and function, or worse, positively mislead
 this research. Fortunately, integration of additional, independent streams
 of information, such as a marker-dense genetic map and conserved
 orthologous gene order from related taxa, can be used to scaffold together
 unlinked, disordered fragments and to restructure a reference genome where
 it is incorrectly joined. We present a tool set for automating these
 processes, one that additionally tracks any changes to the assembly and to
 the genetic map, and which allows the user to scrutinize these changes
 with the help of web-based, graphical visualizations. Chromonomer takes a
 user-defined reference genome, a map of genetic markers, and, optionally,
 conserved synteny information to construct an improved reference genome of
 chromosome models: a “chromonome”. We demonstrate Chromonomer’s
 performance on genome assemblies and genetic maps that have disparate
 characteristics and levels of quality.
description: This dataset consists of several genome integrations, combining
 an assembled genome and a genetic map, to create chromosome-level
 assembly. The software chromonomer is used for the integration. There are
 three integrations of teleost fish, including: 
 Gulf pipefish (<i>Sygnathus scovelli</i>)
 Platyfish (<i>Xiphophorus maculatus</i>)
 Black rockcod (<i>Notothenia
 coriiceps</i>) The gulf pipefish
 integration began with data from the sequence read archive (SRA), NCBI
 BioProject Accession PRJNA355893, while the <i>Sygnathus
 acus</i> reference genome (NCBI accession GCA_901709675.1,
 BioProject PRJEB32741) was used as a base for the <em>Sygnathus
 scovelli</em> gene annotationa. The platyfish integration began with
 SRA data from NCBI accession GCA_002775205.2, BioProject PRJNA72525, with
 raw read data obtained from SRA accessions SRR7207855 - SRR7207868. The
 black rockcod genome assembly was obtained from NCBI accession
 GCA_000735185.1, BioProject PRJNA66471. The genetic map
 for each fish is included in this repository, named
 *_unprocessed_consensus_genetic_map.tsv and the RADseq markers
 corresponding with the map are also provided as all_markers.fa.gz in each
 respective directory.
description: Each integration includes a shell script (chrr.sh) outlining how
 the chromonomer software was executed.
DOI: 10.5061/dryad.4j0zpc88p
title: Data from: Higher dominance rank is associated with lower glucocorticoids in wild female baboons: A rank metric comparison

description: In vertebrates, glucocorticoid secretion occurs in response to energetic
 and psychosocial stressors that trigger the hypothalamic-pituitary-adrenal
 (HPA) axis. Measuring glucocorticoid concentrations can therefore shed
 light on the stressors associated with different social and environmental
 variables, including dominance rank. Using 14,172 fecal samples from 237
 wild female baboons, we test the hypothesis that high-ranking females
 experience fewer psychosocial and/or energetic stressors than
 lower-ranking females. We predicted that high-ranking females would have
 lower fecal glucocorticoid (fGC) concentrations than low-ranking females.
 Because dominance rank can be measured in multiple ways, we employ an
 information theoretic approach to compare 5 different measures of rank as
 predictors of fGC concentrations: ordinal rank; proportional rank; Elo
 rating; and two approaches to categorical ranking (alpha vs non-alpha and
 high-middle-low). Our hypothesis was supported, but it was also too
 simplistic. We found that alpha females exhibited substantially lower fGCs
 than other females (typical reduction = 8.2%). If we used proportional
 rank instead of alpha- versus non-alpha status in the model, we observed a
 weak effect of rank such that fGCs rose 4.2% from the highest- to
 lowest-ranking female in the hierarchy. Models using ordinal rank, Elo
 rating, or high-middle-low categories alone failed to explain variation in
 female fGCs. Our findings shed new light on the association between
 dominance rank and the stress response, the competitive landscape of
 female baboons as compared to males, and the assumptions inherent in a
 researcher's choice of rank metric.
description: The 3 attached files are: The raw
 data from which all statistical analyses were derived
 A spreadsheet of model results (calculated using the raw
 data) that facilitates reproducting Figure 2 in the manuscript
 A script to recreate all ananlyses in R. If you are not familiar
 with R, this file will still be useful as a readme file if you look at the
 comments (lines starting with a #) Missing
 values: Because we did not have hybrid scores for all individuals, missing
 hybrid score values are expected.
DOI: 10.15468/dl.2q86jj
title: Occurrence Download

description: A dataset containing 117229 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is New Zealand",
 "OccurrenceStatus is Present",
 "TaxonKey is Ochrophyta"
 ]
}

 The dataset includes 117229 records from 155 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002471-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1ns1rn8rp
title: Scripts from: Controlling evolution in genetically engineered systems through repeated introduction

description: Genetically engineered transgenes evolve in the same way as other genetic
 material. However, evolution in engineered genes is often undesirable and
 can negatively affect their stability, frequency, and efficacy over time.
 Methods that maintain the stability of engineered genomes are therefore
 critical to the successful design and use of genetically engineered
 organisms. One potential method to limit unwanted evolution is by taking
 advantage of the ability of gene-flow to counter local adaption, a process
 of supplementation. Here we investigate the feasibility of supplementation
 as a mechanism to offset the evolutionary degradation of a transgene in
 three model systems: a bioreactor, a gene drive, and a transmissible
 vaccine. In each model, continual introduction from a stock is used to
 balance mutation and selection against the transgene. Each system has its
 unique features. The bioreactor system is especially tractable and has a
 simple answer: the level of supplementation required to maintain the
 transgene at a frequency is approximately , where s is the selective
 disadvantage of the transgene. Supplementation is also feasible in the
 transmissible vaccine case but is probably not practical to prevent the
 evolution of resistance against a gene drive. We note, however, that the
 continual replacement of even a small fraction of a large population can
 be challenging, limiting the usefulness of supplementation as a means of
 controlling unwanted evolution.
description: The data represents a collection of scripts and code necessary to
 reproduce all findings and figures in the paper.
description: The input files used in the fig3 and fig4 R scripts were
 generated using the associated c++ code (.cpp)
DOI: 10.5061/dryad.dv41ns1vw
title: Laccase/TEMPO-mediated graft hydrophobization of jute fibres to enhance the mechanical properties of jute/PLA composites

description: In this work, the hydrophobization of lignocellulosic jute fibres was
 achieved via the laccase/TEMPO-mediated grafting of octadecylamine (OA) on
 their surface, with the aim to improve the interfacial compatibility with
 nonpolar polylactic (PLA) resins in fibre-reinforced composites. The
 modified jute fibres were analyzed by Fourier transform infrared
 spectroscopy (FTIR) and scanning electron microscopy-energy dispersive
 spectroscopy (SEM-EDS). The characteristic vibrations of methylene groups
 and the increase in the surface C/O ratio of the jute fibres after the
 enzymatic treatment indicated that OA molecules were successfully grafted
 onto the jute fibre surface mediated by the laccase/TEMPO system. It was
 shown that the grafted jute fibres had increased surface hydrophobicity
 and reduced polarity with water contact angle of 124.2°, diiodomethane
 contact angle of 94.1° and surface free energy of 11.44 mJ/m2, which were
 attributed to the presence of the OA nonpolar alkyl chains on their
 surface. The tensile, bending, and dynamic mechanical properties of the
 hydrophobized jute/PLA composites were enhanced, which suggested stronger
 interfacial adhesion between the jute fibres and the PLA matrix. The
 mechanical stability was investigated by water immersion measurements and
 it was found that the modified jute/PLA composites were better in this
 regards than the control jute/PLA composites. Therefore, this enzymatic
 hydrophobic modification could be used as an effective and eco-friendly
 method to produce natural lignocellulosic fibre-reinforced composites with
 excellent performance.
DOI: 10.25345/c5pz5210j
title: MassIVE MSV000100610 - Metabolomic profiling of 2000 LC-MS/MS samples for chemical diversity analysis
title: This dataset contains 2000 mzML files from an LC-MS/MS metabolomics study focused on chemical diversity and molecular networking using GNPS2.
DOI: 10.5061/dryad.1vhhmgqqz
title: Growth and flowering responses of eelgrass to simulated grazing and fecal addition by brant geese

description: These data represent the responses of eelgrass (Zostera marina) beds to a
 series of experimental treatments conducted in 2004 and 2005 in the
 vicinity of Hookton Channel, Humboldt Bay, California, USA. We measured
 eelgrass density, growth, biomass, and flowering as the primary response
 variables to clipping, brant (Branta bernicla) fecal addition, clipping
 and fecal addition, and control treatments in a 2004 destructively sampled
 randomized block design meant to simulate different effects of brant
 grazing and test the compensatory growth hypothesis as fully
 described in an associated publication, Shaughnessy et al. (2021)
 in Ecosphere. We measured density, growth, and flowering as
 primary response variables to control, moderate, and severe clipping
 treatments, all with fecal addition, in a 2005 destructively sampled
 randomized block design meant to simulate different levels of brant
 grazing also described in Shaughnessy et al. (2021).
description: These data and associated methodologies were described and used
 to draw inferences in Shaughnessy et al. (2021), and complete methods are
 available there. Data on eelgrass growth rates, above-ground and
 below-ground biomass, leaf area index (leaf area per unit area), epiphyte
 weight, shoot length, and shoot count were collected in 140 0.0625
 m<sup>2</sup> sample plots (4 treatments each - control, fecal
 addition, clipping, and fecal + clipping - in 35 blocks) in 2004 during
 experiment 1 and 69 0.0625 m<sup>2</sup> sample plots (3
 treatments each - control, moderate clipping + fecal addition, and severe
 clipping + fecal addition in 23 blocks) in 2005 during experiment 2. Some
 variables were summarized as within-plot sample means or within-group
 means prior to visualization or analysis as noted in Shaughnessy et al.
 (2021) and metadata presented here.
description: The README.txt file describes each variable included in each of
 the eight data files presented here, and additional details of methods are
 available in Shaughnessy et al. (2021) and the associated appendix.
 Missing values in these data are represented by empty cells.
DOI: 10.5061/dryad.q2bvq83h0
title: Foraging in a dynamic environment: response of four sympatric sub-Antarctic albatross species to interannual environmental variability

description: Seasonal and annual climate variations are linked to fluctuations in the
 abundance and distribution of resources, posing a significant challenge to
 animals that need to adjust their foraging behaviour accordingly.
 Particularly during adverse conditions, and while energetically
 constrained when breeding, animals ideally need to be flexible in their
 foraging behaviour. Such behavioural plasticity may separate ‘winners’
 from ‘losers’ in light of rapid environmental changes due to climate
 change. Here, the foraging behaviour of four sub-Antarctic albatross
 species was investigated from 2015/16 to 2017/18, a period characterized
 by pronounced environmental variability. Over three breeding seasons on
 Marion Island, Prince Edward Archipelago, incubating wandering (WA,
 Diomedea exulans; n=45), grey-headed (GHA, Thalassarche chrysostoma;
 n=26), sooty (SA, Phoebetria fusca; n=23) and light-mantled (LMSA, P.
 palpebrata; n=22) albatrosses were tracked with GPS loggers. The response
 of birds to environmental variability was investigated by quantifying
 inter-annual changes in their foraging behaviour along two axes: spatial
 distribution, using kernel density analysis, and foraging habitat
 preference, using generalized additive mixed models and Bayesian mixed
 models. All four species were shown to respond behaviourally to
 environmental variability, but with substantial differences in their
 foraging strategies. WA was most general in its habitat use defined by sea
 surface height, eddy kinetic energy, wind speed, ocean floor slope and sea
 level anomaly, with individuals foraging in a range of habitats. In
 contrast, the three smaller albatrosses exploited two main foraging
 habitats, with habitat use varying between years. Generalist habitat use
 by WA and inter-annually variable use of habitats by GHA, SA and LMSA
 would likely offer these species some resilience to predicted changes in
 climate such as warming seas and strengthening of westerly winds. However,
 future investigations need to consider other life history stages coupled
 with demographic studies, to better understand the link between
 behavioural plasticity and population responses.
description: Over three consecutive
 breeding seasons (2015/16, 2016/17 and 2017/18), GPS data loggers
 (CatLog-S GPS loggers, Perthold Engineering LLC USA, 50×22×8 mm, 34 g)
 were deployed on four albatross species on Marion Island during the
 incubation period (46°55’ S; 37°40’ E): wandering, grey-headed, sooty and
 light-mantled albatrosses. Loggers recorded locations at one-hour interval
 and were retrieved after one foraging trip.
description: All locations on land have been removed.
DOI: 10.5061/dryad.cc2fqz649
title: The distribution of climbing chalk on climbed boulders and its impact on rock-dwelling fern and moss species

description: Rock climbing is popular and the number of climbers rises worldwide.
 Numerous studies on the impact of climbing on rock-dwelling plants have
 reported negative effects, which were mainly attributed to mechanical
 disturbances such as trampling and removal of soil and vegetation.
 However, climbers also use climbing chalk (magnesium carbonate hydroxide)
 whose potential chemical effects on rock-dwelling species have not been
 assessed so far. Climbing chalk is expected to alter the pH and nutrient
 conditions on rocks, which may affect rock-dwelling organisms. We
 elucidated two fundamental aspects of climbing chalk: Its distribution
 along non-overhanging climbing routes was measured on regularly spaced
 raster points on gneiss boulders used for bouldering (ropeless climbing at
 low height). These measurements revealed elevated climbing chalk levels
 even on 65% of sampling points without any visual traces of climbing
 chalk. The impact of climbing chalk on rock-dwelling plants was assessed
 with four fern and four moss species in an experimental set-up in a
 climate chamber. The experiment showed significant negative, though varied
 effects of elevated climbing chalk concentrations on the germination and
 survival of both ferns and mosses. The study thus suggests that along
 climbing routes elevated climbing chalk concentration can occur even were
 no chalk traces are visible and that climbing chalk can have negative
 impacts on rock-dwelling organisms.
DOI: 10.15468/dl.6mm9zy
title: Occurrence Download

description: A dataset containing 139 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calpurnia sericea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 139 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002528-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2280gb5q1
title: Supporting fisheries management with genomic tools: a case study of kingklip (Genypterus capensis) off southern Africa

description: Kingklip, Genypterus capensis, is a valuable fish resource in southern
 African waters, with a wide geographic distribution spanning
 South Africa and Namibia. Previous studies have provided evidence for
 multiple stocks in South Africa, but the extent of stock structuring
 across the Southern African region remains unclear. In this study, we
 genotyped over 40 000 SNPs to characterise the spatial distribution of
 genomic variation for G. capensis throughout its core distribution.
 Results suggest that fish sampled at the northernmost range (off central
 Namibia) are characterised by lower genomic diversity, although the region
 exhibited the highest number of private SNPs, suggesting some degree of
 geographic isolation. Using neutral and putative outlier loci
 independently, we show that kingklip exhibits three population clusters,
 “northern Benguela”, “southern Benguela” and South African “South Coast”.
 Population differentiation was observed only using “outlier” loci,
 suggesting that local adaptation might be one of the main drivers of the
 observed differentiation. Overall, our research provides novel insights
 into the regional dynamics that can support the sustainable long-term
 exploitation of this valuable fisheries resource.
description: ReadMe File: Allele frequency file of
 biallelic SNPs, identified based on a minimum count of four, a minimum
 coverage of 20 and a maximum coverage of 500 reads &gt;
 "MAA.420500.txt" Input allele frequency files
 for corresponding "Full" (MAA.FULL.txt), "Neutral"
 (MAA.NEUTRAL.txt) and "Outlier" (MAA.OUTLIER.txt) datasets used
 for population sub-structuring analyses (Minimum count of 4,minimum
 coverage of 28 and maximum coverage of 100). Scripts
 used for bioinformatic analyses and pipeline &gt;
 "Scripts.txt" R-script,
 "PopStructure.R", used for estimates of pairwise differentiation
 levels, using the 'diffCalc' command of diveRsity (Keenan et
 al.,2013).