cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.76hdr7sxd
title: Assortative mating for between-patch dispersal status in a wild bird population: Exploring the role of direct and indirect underlying mechanisms

description: Previous studies have reported functional integration between dispersal
 and other phenotypic traits allowing individuals to alleviate dispersal
 costs, and such associations can affect dispersal evolution in return. In
 sexually reproducing species, assortative mating according to dispersal
 can shape the maintenance of such trait associations. Despite the
 potentially crucial consequences of dispersal in natural populations,
 assortative mating for dispersal and its underlying mechanisms remain
 largely unexplored. Here, we assessed assortative mating for between-patch
 dispersal status in a fragmented population of a small passerine bird, the
 collared flycatcher, and explored whether such assortative mating could
 result from (i) direct mate choice based on dispersal-related behavioural
 (aggressiveness and boldness) and morphological traits (tarsus and wing
 length), (ii) biased mating due to spatio-temporal heterogeneity in the
 distribution of dispersal phenotypes and/or (iii) post-mating adjustment
 of dispersal phenotype or dispersal-related traits. We found intrinsic
 assortative mating (i.e. positive among-pair correlation) for current
 dispersal status (in the year of mating) but not for natal dispersal
 status, even though we could not exclude it due to limited power. We also
 found assortative mating for boldness and age category (yearlings vs.
 older adults), and the probability for pair members to be assorted for
 current dispersal status was higher when both pair members were of similar
 boldness score and of the same age compared to mixed-age pairs. Mate
 choice based on boldness and age thus appears as a possible mechanism
 underlying assortative mating for dispersal status. Our analyses however
 remained correlative and only an experimental manipulation of these traits
 could allow inferring causal links. Non-random mating for
 dispersal-related traits may affect the evolution of dispersal syndromes
 in this population. More work is nevertheless needed to fully assess the
 evolutionary implications of age- and behaviour-based assortative mating
 for dispersal.
description: The dataset was collected during several field word between 1986
 and 2013 at the Island of Gotland (Sweden) where the population of
 collared flycatcher was monitored since 1980s.  We performed univariate
 and bivariate Bayesian model (MCMCglmm) to identify an assortative mating
 based on dispersal status and to investigate possible underlying
 mechanisms (e.g. assortative mating based on behavioural and morphological
 traits and age) that could be explain this type of assortative mating in
 order to produce a MS accepted for publication in Journal of Evolutionary
 Biology.
DOI: 10.5061/dryad.2bvq83bqx
title: Data from: Fine-scale spatial associations between functional traits and tree growth

description: This data set relates to a 40x60 m2 stem-mapped plot that was established
 in a temperate rainforest of southern Chile. It contains data for each
 individual stem located within the plot. Each individual is characterized
 by a species code, diameter at breast height (dbh, 1.35 m),
 diameter at coring height (dch, ca. 30 cm), x and y coordinates, basal
 area index of the last 10 years (bai, cm2), and growth efficiency (ge,
 cm2/cm2).
description: The data set was collected in May 2016. Each tree contained in
 the plot was measured in dbh and dch and 1-2 cores were extracted from
 each single stem to derive bai and ge. The species name
 codes are: 1. Amomyrtus luma (Al); 2. Azara lanceolata
 (Az); 3. Drimys winteri (Dw); 4. Embothrium coccineum (Ec); 5.
 Laureliopsis philippiana (Lp); 6. Lomatia ferruginea (Lf); 7. Maytenus
 magellanica (Mm); 8. Nothofagus antarctica (Na); 9. Nothofagus betuloides
 (Nb); 10. Podocarpus nubigenus (Pn); 11. Raukua latevirens (Rl).
description: The data set is very straightforward and simple. If otherwise
 indicated (mandatory), I think it is not necessary to include a readme
 file.
DOI: 10.5061/dryad.c866t1g7m
title: Root traits along a subarctic tundra elevational gradient

description: While root trait research has received increasing attention over the past
 two decades, the relationship between root traits and environmental
 factors remains elusive. At the same time, knowledge about these
 relationships is necessary if we are to understand plant community
 responses to environmental change. Here, we assessed the relationships
 between elevation (i.e., temperature) and fine root traits of plant
 species and communities. We focused on the sub-arctic tundra where plant
 communities are expected to experience extreme environmental change by the
 end of the century.
description: There are missing values for some chemical traits in the trait
 dataset, denoted by "n/a" and for the vegetation pinpointing
 data absent of hits in a plot was denoted as "null".
DOI: 10.25338/b8kh0x
title: Data From: Polygenic basis and the role of genome duplication in adaptation to similar selective environments

description: Genetic changes underlying adaptation vary greatly in terms of complexity
 and, within the same species, genetic responses to similar selective
 pressures may or may not be the same. We examine both complex (supergene)
 and simple (SNP) genetic variants occurring in populations of rainbow
 trout (Oncorhynchus mykiss) independently isolated from ocean access and
 compared them to each other and to an anadromous below-barrier population
 representing their ancestral source to search for signatures of both
 parallel and non-parallel adaptation. All landlocked populations displayed
 an increased frequency of a large inversion on chromosome Omy05, while
 three of the four populations exhibited elevated frequencies of another
 inversion located on chromosome Omy20. In addition, we identified numerous
 regions outside these two inversions that also show significant shifts in
 allele frequencies consistent with adaptive evolution. However, there was
 little concordance among above-barrier populations in these specific
 genomic regions under selection. In part, the lack of concordance appears
 to arise from ancestral autopolyploidy in rainbow trout that provides
 duplicate genomic regions of similar functional composition for selection
 to act upon. Thus, while selection acting on landlocked populations
 universally favors the resident ecotype, outside of the major chromosomal
 inversions, the resulting genetic changes are largely distinct among
 populations. Our results indicate that selection on standing genetic
 variation is likely the primary mode of rapid adaptation, and that both
 supergene complexes and individual loci contribute to adaptive evolution,
 further highlighting the diversity of adaptive genomic variation involved
 in complex phenotypic evolution.
description: RADseq following Ali et al. (2016), see associated manuscript of
 this data set for details.
description: See metadata spreadsheet for linking sequence files to sample
 names.
DOI: 10.15468/dl.hyt3vp
title: Occurrence Download

description: A dataset containing 5099 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Ukraine",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (CR, EN, VU)",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta",
 "Year 2016-2026"
 ]
}

 The dataset includes 5099 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002926-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wwpzgmskg
title: Data set for: Long-term Perfluorooctanesulfonic acid (PFOS) exposure alters anxiety-like behaviour but not boldness in zebrafish (Danio rerio)

description: Perfluorooctanesulfonic acid (PFOS) is an organic pollutant that is
 commonly detected in wildlife, humans, and the environment.  PFOS
 can cause a variety of toxic effects in zebrafish, however, the impact on
 complex behaviours like boldness and anxiety-like behaviour is unknown. To
 investigate the behavioural effects of PFOS in zebrafish, we exposed adult
 zebrafish to either 0, 0.1, or 1.0 mg/L PFOS for 40 days. After 20- and
 40-days anxiety-like behaviour and boldness were assessed using the novel
 approach test and novel tank dive test, respectively. After 40- day
 exposure at a concentration of 1.0 mg/L, PFOS caused a significant
 increase in time spent in the upper zone and a significant decrease in
 time spent in the bottom zone of the novel tank dive test, suggesting
 decreased anxiety-like behaviour compared to controls. Neither 0.1 or 1.0
 mg/L had an impact on zebrafish boldness at any time point. Exposure to
 1.0 mg/L PFOS significantly decreased locomotion in the novel tank dive
 test after 20 days, whereas after 40 days there was no impact of PFOS on
 locomotion at any concentration, indicating potential short-term
 influences on locomotion. These results suggest chronic PFOS exposure can
 modulate anxiety-like behaviour, while exploratory activity and locomotion
 are not altered.
description: This dataset contains videos recorded from a Basler  monochrome
 camera that was positioned 1m above the arena and utilized a 4-8 mm F1:1.4
 manual iris and focus lens (Computar). Adult wild-type zebrafish
 (<em>Danio rerio</em>) were gently netted and placed into the
 center of the arena and recording was tested immediately. The data was
 analyzed using motion tracking software EthoVision XT (version 10, Noldus,
 VA, USA) which quantified the time spent in the thigmotaxis and center
 zones, as well as the total distance travelled during the trial for the
 novel object approach test. In the novel tank dive test, the time spent in
 the top, middle, and bottom zone, as well as distance moved during
 each trial was quantified and analyzed using EthoVision XT (version 10,
 Noldus, VA, USA). The camera was positioned 1m away from the tank dive
 test to capture the vertical axis of the tank. The zones were drawn and
 mapped onto the arena within the EthoVision XT software for both the novel
 object approach test and the novel tank dive test.
DOI: 10.5061/dryad.b2rbnzsg3
title: Sexual dimorphism in size and shape of the head in the sea snake Emydocephalus annulatus

description: In snakes, divergence in head size between the sexes has been interpreted
 as an adaptation to intersexual niche divergence. By overcoming
 gape-limitation, a larger head enables snakes of one sex to ingest larger
 prey items. Under this hypothesis, we do not expect a species that
 consumes only tiny prey items to exhibit sex differences in relative head
 size, or to show empirical links between relative head size and
 fitness-relevant traits such as growth and fecundity. Our field studies on
 the sea snake Emydocephalus annulatus falsify these predictions. Although
 these snakes feed exclusively on fish eggs, the heads of female snakes are
 longer and wider than those of males at the same body length. Individuals
 with wider heads grew more rapidly, reproduced more often, and produced
 larger litters. Thus, head shape can affect fitness and can diverge
 between the sexes even without gape-limitation. Head size and shape may
 facilitate other aspects of feeding (such as the ability to scrape eggs
 off coral) and locomotion (hydrodynamics); and a smaller head may
 advantage the sex that is more mobile, and that obtains its prey in narrow
 crevices rather than in more exposed situations (i.e., males).
description: Annual mark-recapture surveys in small bays beside Noumea, New
 Caledonia. Snakes measured and released soon after capture.
 Every January from 2004 to 2021, we snorkelled through the study
 sites at least 20 times in total (30 to 60 minutes per session). All
 snakes seen were captured by hand, and processed at a nearby laboratory
 (measured, weighed, assessed for sex, palpated for pregnancy and litter
 size; implanted with a microchip, and released at the site of capture). We
 determined sex based on tail shape and scale rugosity. We used calipers to
 measure the length of the head (tip of snout to rear end of
 quadrate-articular projection of the lower jaw) and maximum width of the
 head. We did not include the rostral spine of males in our measurement of
 head length. We only took data from a snake once per year, at its first
 capture in that period, but many snakes were recaptured in subsequent
 years. In total, we have data on 1,293 individual snakes (662 males, 631
 females) captured a total of 3,012 times over the period January 2004 to
 January 2021.
description: See ReadMe file.
DOI: 10.5061/dryad.sn02v6x4n
title: Co-parasitism in the face of predation: Effects of natural enemies on a neotropical mockingbird

description: Co-parasitism is ubiquitous and has important consequences for the ecology
 and evolution of wild host populations. Studies of parasite co-infections
 remain limited in scope, with few experimental tests of the fitness
 consequences of multiple parasites, especially in natural populations. We
 measured the separate and combined effects of Philornis seguyi nest flies
 and shiny cowbirds (Molothrus bonariensis) on the fitness of a shared
 host, the chalk-browed mockingbird (Mimus saturninus) in Argentina. Using
 a two-factor experimental approach, we manipulated the presence of nest
 flies and cowbirds in mockingbird nests and assessed their effects on
 mockingbird hemoglobin levels, begging and provisioning rates, body size,
 and fledging success. We also monitored rates of nest predation in
 relation to parasitism by flies and cowbirds. Nest flies reduced the
 hemoglobin concentration, body size, and fledging success of mockingbirds,
 likely because mockingbirds did not compensate for parasitism by begging
 more or feeding their nestlings more. Cowbirds also reduced the fledging
 success of mockingbirds, even though they had no detectable effect on
 hemoglobin or body size. Nests with cowbirds, which beg more than
 mockingbirds, attracted more nest predators. There was no significant
 interaction between the effects of flies and cowbirds on any component of
 mockingbird fitness. The combined effects of nest flies and cowbirds were
 strictly additive. In summary, we show that nest flies and cowbirds both
 reduce host fitness, but do not have interactive effects in co-parasitized
 nests. Our results further suggest that predators exacerbate the effects
 of nest flies and cowbirds on their hosts. Our study shows that the
 fitness consequences of co-parasitism are complex, especially in the
 context of community-level interactions.
DOI: 10.5061/dryad.fttdz08tk
title: Oviposition preference and performance of Plutella xylostella are modulated by natural enemies, larval odours and immune status

description: Insect herbivores frequently must balance host plant quality and the risk
 of attack by their natural enemies when making oviposition decisions. Yet,
 which factor is more important remains unresolved in plant-insect
 ecology. Here, we report the oviposition preference and larval
 performance of the brassicaceous specialist Plutella xylostella,
 in the context of plant quality (cabbage Brassica oleracea, vs.
 mustard B. juncea) and associated natural
 enemies. Despite the greater larval weight and adult life-span on
 cabbage, ovipositing females strongly preferred mustard. Both the egg
 parasitoid Trichogrammatoidea bactrae and the larval
 ectoparasitoid Bracon brevicornis are more likely to
 attack P. xylostella that feed on cabbage; thus, mustard
 represents enemy-reduced space from these two
 parasitoids. However, larval diet had no impact on the
 parasitization rate of specialist Cotesia vestalis. Feeding on
 mustard improved larval immunity. The total hemocytes number, diversity
 and phenoloxidase activity was higher on mustard-fed larvae that increased
 their survival against the entomopathogen, Bacillus
 thuringiensis. Interestingly, host plants altered the larval body
 odour profile. Mustard fed larvae emitted allyl isothiocyanate (AITC) and
 butyl isothiocyanate (BITC) while cabbage fed larvae emitted dimethyl
 disulphide (DMDS) and dimethyl trisulphide (DMTS) that served as
 short-range cues for larval parasitoids. For B. brevicornis, host
 body odour guided oviposition choice was crucial as their fitness was
 affected by the host larval diet. Although, C.
 vestalis showed a clear preference towards volatiles emitted by
 mustard fed larvae, their fitness was unaltered. Taken together,
 our results illustrate that P. xylostella prefers to lay
 eggs on mustard plants providing enemy-reduced space from some, but not
 all, natural enemies.
description: All the methodological details are
 given in the main manuscript and supplementary files.
DOI: 10.5061/dryad.69p8cz92z
title: Ascorbic acid supports ex vivo generation of plasmacytoid dendritic cells from circulating hematopoietic stem cells: RNA-seq dataset

description: Plasmacytoid dendritic cells (pDCs) constitute a rare type of immune cell
 with multifaceted functions, but their potential use as a cell-based
 immunotherapy is challenged by the scarce cell numbers that can be
 extracted from blood. Here, we systematically investigate culture
 parameters for generating pDCs from hematopoietic stem and progenitor
 cells (HSPCs). Using optimized conditions combined with implementation of
 HSPC pre-expansion, we generate an average of 465 million HSPC-derived
 pDCs (HSPC-pDCs) starting from 100,000 cord blood-derived HSPCs.
 Furthermore, we demonstrate that such protocol allows HSPC-pDC generation
 from whole blood HSPCs, and these cells display a pDC phenotype and
 function. Using GMP compliant medium, we observe a remarkable loss of
 TLR7/9 responses, which is rescued by ascorbic acid supplementation.
 Ascorbic acid induces transcriptional signatures associated with
 pDC-specific innate immune pathways suggesting an undescribed role of
 ascorbic acid for pDC functionality. This constitutes the first protocol
 for generating pDCs from whole blood, and lay the foundation for
 investigating HSPC-pDCs for cell-based immunotherapy.
description: HSPC-pDCs were
 stored in RNAprotect Cell Reagent at -80 degrees until total RNA was
 extracted using the RNeasy Plus Micro Kit (Qiagen), which efficiently
 eliminates genomic DNA without the need for DNase treatment. The total RNA
 was sent to BGI Europe for RNA-seq. Here, a non-stranded &
 polyA-selected mRNA library was prepared from the total RNA and subjected
 to PE100 sequencing using the BGISEQ platform. The samples generated on
 average about 4.84 Gb bases per sample on DNBSEQ. Low quality reads were
 filtered and the remaining reads were mapped to the genome with an average
 mapping ratio with the reference genome at 92.74%, the average gene
 mapping ratio at 79.90%.
DOI: 10.5061/dryad.76hdr7sxf
title: Quantifying representativeness in RCTs using ML fairness metrics - Data and codes

description: The "Quantifying representativeness in RCTs using ML
 fairness metrics - Data and codes" is used to quantify
 representativeness in randomized clinical trials (RCTs) and provide
 insights to improve the clinical trial equity and health
 equity. We developed RCT representativeness metrics based on
 Machine Learning (ML) Fairness Research. Visualizations and statistical
 tests based on proposed metrics enable researchers and physicians to
 rapidly visualize and assess subgroup representation in RCTs. The approach
 enables users to determine underrepresentation, absence, or other
 misrepresentation of subgroups indicating potential limitations of RCTs.
 The method could help support generalizability evaluation of existing RCT
 cohorts, enrollment target decisions for new RCTs (if eligibility criteria
 are included), and monitoring of RCT enrollment, ultimately contributing
 to more equitable public health outcomes. We apply the proposed
 RCT representativeness metrics to three landmark clinical trials released
 in the last decade: Action to Control Cardiovascular Risk in Diabetes
 (ACCOD), Antihypertensive and Lipid-Lowering Treatment to Prevent Heart
 Attack Trial (ALLHAT), and Systolic Blood Pressure Intervention Trial
 (SPRINT). This dataset contains the processed data and results for the
 experiments and visualization codes in the paper titled "Quantifying
 representativeness in randomized clinical trials using machine learning
 fairness metrics."
description: The raw NHANES and RCT datasets are downloaded directly from the
 websites. <br> The target population summary data are processed by
 following "NHANES Survey Methods and Analytic Guidelines" using
 R "haven" and "survey" packages. <br> The RCT
 sample summary data are calculated through R "count()"
 function.
description: All information are provided in
 the MIAOQI_QuantifyingRepresentativenessInRCTsUsingMLFairnessMetricsDataAndCodes_Readme.txt.
DOI: 10.5061/dryad.d2547d83m
title: Trachymyrmex ant and Leucocoprinus fungus genotypes

description: Over the past few decades, large-scale phylogenetic analyses of
 fungus-gardening ants and their symbiotic fungi have depicted strong
 concordance among major clades of ants and their symbiotic fungi, yet
 within clades, fungus sharing is widespread among unrelated ant lineages.
 Sharing has been explained using a diffuse coevolution model within major
 clades. Understanding horizontal exchange within clades has been limited
 by conventional genetic markers that lack both interspecific and
 geographic variation. To examine whether reports of horizontal exchange
 were indeed due to symbiont sharing or the result of employing relatively
 uninformative molecular markers, samples of Trachymyrmex
 arizonensis and Trachymyrmex pomonae and their
 fungi were collected from native populations in Arizona and genotyped
 using conventional marker genes and genome-wide single nucleotide
 polymorphisms (SNPs). Conventional markers of the fungal symbionts
 generally exhibited cophylogenetic patterns that were consistent with some
 symbiont sharing, but most fungal clades had low support. SNP analysis, in
 contrast, indicated that each ant species exhibited fidelity to its own
 fungal subclade with only one instance of a colony growing a fungus that
 was otherwise associated with a different ant species. This evidence
 supports a pattern of codivergence
 between Trachymyrmex species and their fungi, and thus a
 diffuse coevolutionary model may not accurately predict symbiont exchange.
 These results suggest that fungal sharing across host species in these
 symbioses may be less extensive than previously thought.
description: DNA was extracted from 14 <i>Trachymyrmex
 arizonensis</i> and <i>T. pomonae</i> workers and their
 <i>Leucocoprinus</i> sp. Symbionts that were collected from
 colonies in Arizona, USA. Three genes for ants and one gene for fungi were
 sequenced by Sanger (“conventional”) sequencing, and
 genotyping-by-sequencing was used to analyze SNPs. Alignments of each data
 type were used to estimate ant and fungus maximum likelihood trees in
 RAxML version 8.2.11. ParaFit and PACo were used to examine the congruence
 between ant and fungus trees, and the results from these analyses were
 compared to evaluate the differences in congruence between phylogenetic
 trees that were based on Sanger sequencing and those that were based on
 genotyping-by-sequencing methods.
description: The “SNP_RAxML_Pipeline.txt” file contains additional details on
 how to use the vcf_ref_extraction.py script
 (https://github.com/kbeigel/vcf_ref_extraction) and the raxml_ascbias
 script (https://github.com/btmartin721/raxml_ascbias), starting with VCF
 and Phylip files and ending with phylogenetic tree visualization. The
 vcf_ref_extraction script was written and run in PyCharm IDE Community
 Edition 2019.3.3 with the Python 3.8 interpreter. A tab-delimited text
 file (SampleID_VCFcode.txt) shows the ant and fungus samples used in the
 SNP analysis and their corresponding coded names in the VCF.