cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b85pj
title: Data from: Genetic structure in the European endemic seabird, Phalacrocorax aristotelis, was shaped by a complex interaction of historical and contemporary, physical and non-physical drivers

description: Geographically separated populations tend to be less connected by gene
 flow, as a result of physical or non-physical barriers preventing
 dispersal, and this can lead to genetic structure. In this context, highly
 mobile organisms such as seabirds are interesting because the small effect
 of physical barriers means non-physical ones may be relatively more
 important. Here we use microsatellite and mitochondrial data to explore
 the genetic structure and phylogeography of Atlantic and Mediterranean
 populations of a European endemic seabird, the European Shag,
 Phalacrocorax aristotelis, and identify the primary drivers of their
 diversification. Analyses of mitochondrial markers revealed three
 phylogenetic lineages grouping the North Atlantic, Spanish/Corsican and
 Eastern Mediterranean populations, apparently arising from fragmentation
 during the Pleistocene followed by range expansion. These traces of
 historical fragmentation were also evident in the genetic structure
 estimated by microsatellite markers, despite significant contemporary gene
 flow among adjacent populations. Stronger genetic structure, probably
 promoted by landscape, philopatry and local adaptation, was found among
 distant populations and those separated by physical and ecological
 barriers. This study highlights the enduring effect of Pleistocene
 climatic changes on shag populations, especially within the Mediterranean
 Basin, and suggests a role for cryptic northern refugia, as well as known
 southern refugia, on the genetic structure of European seabirds. Finally,
 it outlines how contemporary ecological barriers and behavioral traits may
 maintain population divergence, despite long-distance dispersal triggered
 by extreme environmental conditions (e.g. population crashes).
description: MtDNA concatenated
 dataset with outgroupFasta file generated
 with CLUSTALX v.2 of 79 concatenated mtDNA (CR1 and ND2) shag sequences
 and 2 outgroup sequences, used in phylogenetic
 analyses.concatoutgroup.fasMolecular clock analysis of the shagInput file generated with BEAST v.1.8 used for the molecular clock analysis, under a relaxed clock of uncorrelated lognormal distribution model and a “Coalescent: Constant Size” prior on rates of cladogenesis.coalrelaxmolclock.xmlPopulation structure analysis using microsatellite dataInput files (including microsatellite raw data, estimation parameters and population labels) used in the STRUCTURE v.2.3.4 program to estimate the genetic structure of 28 shag populations.microsat structure.rar
DOI: 10.5061/dryad.61c8t
title: Data from: Gene-wise association of variants in four lysosomal storage disorder genes in neuropathologically confirmed Lewy Body disease

description: Objective: Variants in GBA are associated with Lewy Body (LB) pathology.
 We investigated whether variants in other lysosomal storage disorder (LSD)
 genes also contribute to disease pathogenesis. Methods: We performed a
 genetic analysis of four LSD genes including GBA, HEXA, SMPD1, and MCOLN1
 in 231 brain autopsies. Brain autopsies included neuropathologically
 defined LBD without Alzheimer Disease (AD) changes (n = 59), AD without
 significant LB pathology (n = 71), Alzheimer disease and lewy body variant
 (ADLBV) (n = 68), and control brains without LB or AD neuropathology (n =
 33). Sequencing of HEXA, SMPD1, MCOLN1 and GBA followed by ‘gene wise’
 genetic association analysis was performed. To determine the functional
 effect, a biochemical analysis of GBA in a subset of brains was also
 performed. GCase activity was measured in a subset of brain samples (n =
 64) that included LBD brains, with or without GBA mutations, and control
 brains. A lipidomic analysis was also performed in brain autopsies (n =
 67) which included LBD (n = 34), ADLBV (n = 3), AD (n = 4), PD (n = 9) and
 control brains (n = 17), comparing GBA mutation carriers to non-carriers.
 Results: In a ‘gene-wise’ analysis, variants in GBA, SMPD1 and MCOLN1 were
 significantly associated with LB pathology (p range: 0.03–4.14 x10-5).
 Overall, the mean levels of GCase activity were significantly lower in GBA
 mutation carriers compared to non-carriers (p&lt;0.001). A significant
 increase and accumulation of several species for the lipid classes,
 ceramides and sphingolipids, was observed in LBD brains carrying GBA
 mutations compared to controls (p range: p&lt;0.05-p&lt;0.01).
 Interpretation: Our study indicates that variants in GBA, SMPD1 and MCOLN1
 are associated with LB pathology. Biochemical data comparing GBA mutation
 carrier to non-carriers support these findings, which have important
 implications for biomarker development and therapeutic strategies.
description: brain_231sample_genotype_data_with_keyGenotype databrain_231sample.pedPLINK format ped filebrain_231sample.mapPLINK format map filebrain_231_sample_ageatdeath_covariateCovariates
DOI: 10.5061/dryad.dr714
title: Data from: Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function

description: CLV3/ESR (CLE) proteins are important signaling peptides in plants. The
 short CLE peptide (12–13 amino acids) is cleaved from a larger
 pre-propeptide and functions as an extracellular ligand. The CLE family is
 large and has resisted attempts at classification because the CLE domain
 is too short for reliable phylogenetic analysis and the pre-propeptide is
 too variable. We used a model-based search for CLE domains from 57 plant
 genomes and used the entire pre-propeptide for comprehensive clustering
 analysis. In total, 1628 CLE genes were identified in land plants, with
 none recognizable from green algae. These CLEs form 12 groups within which
 CLE domains are largely conserved and pre-propeptides can be aligned. Most
 clusters contain sequences from monocots, eudicots and Amborella
 trichopoda, with sequences from Picea abies, Selaginella moellendorffii
 and Physcomitrella patens scattered in some clusters. We easily identified
 previously known clusters involved in vascular differentiation and
 nodulation. In addition, we found a number of discrete groups whose
 function remains poorly characterized. Available data indicate that CLE
 proteins within a cluster are likely to share function, whereas those from
 different clusters play at least partially different roles. Our analysis
 provides a foundation for future evolutionary and functional studies.
description: Cleaned alignment of CLE
 groupsAlignments of CLEs
 within each group. Positions with excessive gaps have been removed for the
 sake of visualization.CLE_alignments_clean.zipRaw alignments of CLE groupsAlignments of CLEs within each group.CLE_alignments_raw.zip
DOI: 10.15468/dl.3jw2hd
title: Occurrence Download

description: A dataset containing 462 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Bird Community of the Regional Protected Landscape of the Vila do Conde Shoreline and the Mindelo Ornithological Reserve (PPRLVCROM) (2013-2014)"
 ]
}

 The dataset includes 462 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000676-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3ck30
title: Data from: Does long distance pollen dispersal preclude inbreeding in tropical trees? Fragmentation genetics of Dysoxylum malabaricum in an agro-forest landscape

description: Tropical trees often display long distance pollen dispersal, even in
 highly fragmented landscapes. Understanding how patterns of spatial
 isolation influence gene flow and interact with background patterns of
 fine scale spatial genetic structure are critical for evaluating the
 genetic consequences of habitat fragmentation. In the endangered tropical
 timber tree Dysoxylum malabaricum (Meliaceae) we apply eleven
 microsatellite markers with paternity and parentage analysis to directly
 estimate contemporary gene flow across a large area (216 km2) in a highly
 fragmented agro-forest landscape. A comparison of genetic diversity and
 genetic structure in adult and juvenile life stages indicates an increase
 of differentiation and fine-scale spatial genetic structure (FSGS) over
 time. Paternity analysis and parentage analysis demonstrate high genetic
 connectivity across the landscape by pollen dispersal. A comparison
 between mother trees in forest patches with low and high densities of
 adult trees shows that the frequency of short distance mating increases,
 as does average kinship among mates in low density stands. We interpret
 this as an early warning sign of potentially negative genetic consequences
 of forest fragmentation. Single isolated trees, in contrast, frequently
 receive heterogeneous pollen from distances exceeding five kilometres. We
 discuss the processes leading to the observed patterns of gene flow and
 the implications of this for conservation management of D. malabaricum and
 tropical trees more generally.
description: DryadRawData_S_IsmailExcel file with sampling locations and microsatellite genotypes for all adults and offspring.
DOI: 10.5061/dryad.1mf7q9q
title: Data from: Genetic structure and shell shape variation within a rocky shore whelk suggests both diverging and constraining selection with gene flow

description: Variation in snail shell shape has provided evolutionary biologists with
 excellent material for the study of local adaptation to local
 environments. However, assuming shell shape variation is evidence of
 distinct lineages (species) may have led to taxonomic inflation within
 some gastropod lineages. Here we compare shell shape variation and genetic
 structure of two independent lineages of New Zealand rocky shore whelks in
 order to understand the process that lead to an unusual disjunct
 distribution. We examined the Buccinulum vittatum complex (three
 subspecies plus B. colensoi) using mitochondrial DNA sequences, 849 single
 nucleotide polymorphisms, and geometric morphometric data on shell shape.
 Specimens within the range of Buccinulum colensoi shared nuclear markers
 and mtDNA haplotypes with the southern subspecies B. vittatum
 littorinoides, while the northern samples (B. v. vittatum) had distinct
 genotypes. We infer that gene flow between B. colensoi and B. v.
 littorinoides is greater than between either of these taxa and B. v.
 vittatum. The distinctive shell sculpturing of B. colensoi is maintained
 despite gene flow, suggesting a role for selection. Although the shell
 form of B. colensoi appears to be an adaptation to local conditions we did
 not observe convergent evolution in the sympatric whelk species Cominella
 maculosa.
description: Principal components of
 shell shape variation2D Geometric
 morphometrics was used to document shell shape variation of the marine
 whelk Buccinulum vittatum-complex. This shape variation is reduced to
 principal components of variation.PCbucc86lgrm.txtDNA sequences of 93 Whelks for mtDNA gene COX-1Partial DNA sequence of the mitochondrial COX-1 gene obtained from 93 Buccinulum vittatum-complex snails collected from New ZealandWhelk_co1_93.fastaNuclear genetic variation for marine snails Buccinulum vittatumNuclear data - Single nucleotide polymorphisms from ddRAD-seq. Snails Buccinulum vittatum-complex genetic variation formatted for population genetic studybatch_5310341trim.structure.txt
DOI: 10.5061/dryad.g4590
title: Data from: Historical dynamics of ecosystem services bundles

description: Managing multiple ecosystem services (ES), including addressing trade-offs
 between services and preventing ecological surprises, is among the most
 pressing areas for sustainability research. These challenges require ES
 research to go beyond the currently common approach of snapshot studies
 limited to one or two services at a single point in time. We used a
 spatiotemporal approach to examine changes in nine ES and their
 relationships from 1971 to 2006 across 131 municipalities in a mixed-use
 landscape in Quebec, Canada. We show how an approach that incorporates
 time and space can improve our understanding of ES dynamics. We found an
 increase in the provision of most services through time; however,
 provision of ES was not uniformly enhanced at all locations. Instead, each
 municipality specialized in providing a bundle (set of positively
 correlated ES) dominated by just a few services. The trajectory of bundle
 formation was related to changes in agricultural policy and global trends;
 local biophysical and socioeconomic characteristics explained the bundles’
 increasing spatial clustering. Relationships between services varied
 through time, with some provisioning and cultural services shifting from a
 trade-off or no relationship in 1971 to an apparent synergistic
 relationship by 2006. By implementing a spatiotemporal perspective on
 multiple services, we provide clear evidence of the dynamic nature of ES
 interactions and contribute to identifying processes and drivers behind
 these changing relationships. Our study raises questions about using
 snapshots of ES provision at a single point in time to build our
 understanding of ES relationships in complex and dynamic social-ecological
 systems.
description: Spatiotemporal data on
 multiple ecosystem servicesThe file provides the
 data for 7 ecosystem services, quantified from 1971 to 2006 (with a time
 step of 5 years) and across 131 municipalities of the Monteregie, a region
 located in Southern Quebec, Canada. Data on population density, distance
 from Montreal and soil capability for agriculture are provided at the same
 spatio-temporal scales. Missing data are coded as "NA" in the
 data file. For pork production, certain number are protected by a Licence
 agreement with Ministries (see the material and methods section of the
 article for more information). Those data are coded as "*" in
 this column.Renard et al spatio temporal
 data on multiple ecosystem services.txt
DOI: 10.5061/dryad.2p607j0
title: Data from: Identification of children with anaphylaxis at low risk of receiving acute inpatient therapies

description: Objective: Opportunity exists to reduce unnecessary hospitalizations for
 children with anaphylaxis given wide variation in admission rates across
 U.S. emergency departments (EDs). We sought to identify children
 hospitalized with anaphylaxis at low risk of receiving epinephrine and
 other acute inpatient therapies, as these patients may be candidates for
 ED discharge rather than inpatient hospitalization. Methods: We conducted
 a single-center retrospective cohort study of children 1–21 years of age
 hospitalized with anaphylaxis from 2009 to 2016. Acute inpatient therapies
 included intramuscular (IM) or racemic epinephrine, bronchodilators, fluid
 boluses, vasopressors, non-invasive ventilation, or intubation. We derived
 age-specific (pre-verbal [&lt;36 months] vs. verbal [≥ 36 months])
 prediction rules using recursive partitioning to identify children at low
 risk of receiving acute inpatient therapies. Results: During the study
 period 665 children were hospitalized for anaphylaxis, of whom 108 (16.2%)
 received acute inpatient therapies. The prediction rule for patients
 &lt; 36 months (no wheezing, no cardiac involvement [hypotension or
 wide pulse pressure]) had a sensitivity of 90.5% (CI 69.6–98.8%) and a
 negative predictive value of 98.3% (CI 94.1–99.8%) for identifying
 children at low risk of receipt of acute inpatient therapies during
 hospitalization. For children ≥ 36 months, the prediction rule (no
 wheezing, no cardiac involvement, presence of gastrointestinal symptoms)
 had a sensitivity of 90.8% (CI 82.7–96.0%) and a negative predictive value
 of 92.4% (CI 85.6–96.7%). Conclusions: We derived age specific prediction
 rules for children hospitalized with anaphylaxis at low risk of receiving
 epinephrine and other acute inpatient therapies. These children may be
 candidates for ED discharge rather than inpatient hospitalization.
description: Low risk anaphylaxis
 data fileDe-identified data from
 children in our cohort.2019 PLoS one deidentified
 data.csv
DOI: 10.5061/dryad.j7v42
title: Data from: EB Ford revisited: assessing the long-term stability of wing-spot patterns and population genetic structure of the meadow brown butterfly on the Isles of Scilly

description: Understanding selection in the wild remains a major aim of evolutionary
 ecology and work by Ford and colleagues on the meadow brown butterfly
 Maniola jurtina did much to ignite this agenda. A great deal of their work
 was conducted during the 1950s on the Isles of Scilly. They documented
 island-specific wing-spot patterns that remained consistent over about a
 decade, but patterns on some islands changed after environmental
 perturbation. It was suggested that these wing-spot patterns reflected
 island-specific selection and that there was little migration between
 islands. However, genetic studies to test the underlying assumption of
 restricted migration are lacking and it is also unknown whether the
 originally described wing-spot patterns have persisted over time. We
 therefore collected female butterflies from five of Ford’s original study
 locations, including three large islands (St Mary’s, St Martin’s and
 Tresco) and two small islands (Tean and St Helen’s). Wing-spot patterns
 had not changed appreciably over time on three of the islands (two large
 and one small), but were significantly different on the other two.
 Furthermore, analysis of 176 amplified fragment length polymorphisms
 revealed significant genome-wide differentiation among the five islands.
 Our findings are consistent with Ford’s conclusions that despite the close
 proximity of these islands, there is restricted gene flow among them.
description: Manila jurtina wing
 spotsThis file contains wing
 spot data for individual meadow brown butterfly
 specimens.Maniola_jurtina_wing_spots.xlsxManiola jurtina AFLP dataAFLP genotypes for the meadow brown butterfly.Maniola_jurtina_AFLP_data.xlsx
DOI: 10.25919/devj-dt50
title: Leaf and stripe rust field data for OzWheat diversity panel (V1 and V2)

description: This collection contains rust resistance phenotype data for two rust diseases, leaf (LR) and stripe rust or yellow rust (YR) collected from four different field sites within Australia of the OzWheat panel 1 and 2 in 2023 and 2024. This data was collected as part of GRDC project: ACRCP Phase 5: Optimising genetic control of wheat rusts through development of RustHapSelect (ref:CSP2304-013RTX). In this project we aim to validate a new approach to bring effective and durable rust resistance loci into elite high-yielding backgrounds much faster. This will ensure breeder take-up of this material free of deleterious background effects and increase adult plant resistance in Australian wheat varieties. Applying novel genomic selection techniques to identify resistance sources in two wheat diversity panels, Vavilov diversity panel (295 lines) and the OzWheat diversity panel (589 lines) and optimise crossing strategies to introgress into new cultivars.
DOI: 10.5061/dryad.m5648
title: Data from: Environmental and evolutionary effects on horn growth of male bighorn sheep

description: The development of male secondary sexual characters such as antlers or
 horns has substantial biological and socio-economic importance because in
 many species these traits affect male fitness positively through sexual
 selection and negatively through trophy hunting. Both environmental
 conditions and selective hunting can affect horn growth but their relative
 importance remains unexplored. We first examined how a large-scale climate
 index, the Pacific Decadal Oscillation (PDO), local weather and population
 density influenced both absolute and relative annual horn growth from
 birth to 3 years of male bighorn sheep (Ovis canadensis) over 42 years. We
 then examined the relative influence of environmental conditions and
 evolution mainly driven by trophy hunting on male horn length at 3 years
 of age. Horn growth was positively influenced by low population density
 and warm spring temperature, suggesting that ongoing climate change should
 lead to larger horns. Seasonal values of PDO were highly correlated. Horn
 growth increased with PDO in spring or summer at low density, but was weak
 at high density regardless of PDO. The interaction between population
 density and PDO in spring or summer accounted for a similar proportion of
 the observed annual variation in horn growth (32% or 37%) as did the
 additive effects of spring temperature and density (34%). When
 environmental conditions deteriorated, males allocated relatively more
 resources to summer mass gain than to horn growth, suggesting a
 conservative strategy favoring maintenance of condition over allocation to
 secondary sexual characters. Population density explained 27% of the
 variation in horn length, while evolutionary effects explained 9% of the
 variance. Thus, our study underlines the importance of both evolution and
 phenotypic plasticity on the development of a secondary sexual trait.
description: Data used in the
 paper"Databighorn"
 is a dataframe with 14 variables: 1) id = male’s identity, 2) year, 3)
 loggrowth = log-transformed annual horn growth, 4) density = number of
 adult females aged 2 years and older in June, 5) age = male’s age, 6)
 temp.spring = average temperature in spring, 7) prec.spring =
 precipitation in spring, 8) temp.summer = average temperature in summer,
 9) prec.summer = precipitation in summer, 10) temp.winter = average
 temperature in winter, 11) prec.winter = precipitation in winter, 12)
 PDOwinter = Pacific decadal oscillation in winter, 13) PDOspring = Pacific
 decadal oscillation in spring, 14) PDOsummer = Pacific decadal oscillation
 in summer. All explanatory variables have been centered and divided by the
 standard deviation.databighorn.xls
DOI: 10.5061/dryad.dn367
title: Data from: Spite versus cheats: competition among social strategies shapes virulence in Pseudomonas aeruginosa

description: Social interactions have been shown to play an important role in bacterial
 evolution and virulence. The majority of empirical studies conducted have
 only considered social traits in isolation, yet numerous social traits,
 such as the production of spiteful bacteriocins (anti-competitor toxins)
 and iron-scavenging siderophores (a public good) by the opportunistic
 pathogen Pseudomonas aeruginosa, are frequently expressed simultaneously.
 Crucially, both bacteriocin production and siderophore cheating can be
 favoured under the same competitive conditions, and we develop theory and
 carry out experiments to determine how the success of a
 bacteriocin-producing genotype is influenced by social cheating of
 susceptible competitors and the resultant impact on disease severity
 (virulence). Consistent with our theoretical predictions, we find that the
 spiteful genotype is favoured at higher local frequencies when competing
 against public good cheats. Furthermore, the relationship between spite
 frequency and virulence is significantly altered when the spiteful
 genotype is competed against cheats compared with cooperators. These
 results confirm the ecological and evolutionary importance of considering
 multiple social traits simultaneously. Moreover, our results are
 consistent with recent theory regarding the invasion conditions for strong
 reciprocity (helping cooperators and harming non-cooperators).
description: Relative growth of
 spiteful cooperators against sensitive cheatsRelative growth of
 spiteful cooperators competed against sensitive
 cooperatorsBacterial density in
 caterpillar hostsTime to death of
 infected caterpillars