cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.92b1f
title: Data from: Enhancing the diversity of breeding invertebrates within field margins of intensively managed grassland: effects of alternative management practices

description: Severe declines in biodiversity have been well documented for many
 taxonomic groups due to intensification of agricultural practices.
 Establishment and appropriate management of arable field margins can
 improve the diversity and abundance of invertebrate groups; however, there
 is much less research on field margins within grassland systems. Three
 grassland field margin treatments (fencing off the existing vegetation
 “fenced”; fencing with rotavation and natural regeneration “rotavated”
 and; fencing with rotavation and seeding “seeded”) were compared to a
 grazed control in the adjacent intensively managed pasture. Invertebrates
 were sampled using emergence traps to investigate species breeding and
 overwintering within the margins. Using a manipulation experiment, we
 tested whether the removal of grazing pressure and nutrient inputs would
 increase the abundance and richness of breeding invertebrates within
 grassland field margins. We also tested whether field margin establishment
 treatments, with their different vegetation communities, would change the
 abundance and richness of breeding invertebrates in the field margins.
 Exclusion of grazing and nutrient inputs led to increased abundance and
 richness in nearly all invertebrate groups that we sampled. However, there
 were more complex effects of field margin establishment treatment on the
 abundance and richness of invertebrate taxa. Each of the three
 establishment treatments supported a distinct invertebrate community. The
 removal of grazing from grassland field margins provided a greater range
 of overwintering/breeding habitat for invertebrates. We demonstrate the
 capacity of field margin establishment to increase the abundance and
 richness in nearly all invertebrate groups in study plots that were
 located on previously more depauperate areas of intensively managed
 grassland. These results from grassland field margins provide evidence to
 support practical actions that can inform Greening (Pillar 1) and
 agri-environment measures (Pillar 2) of the Common Agricultural Policy
 (CAP). Before implementing specific management regimes, the conservation
 aims of agri-environment measures should be clarified by defining the
 target species or taxonomic groups.
description: Field_margin_data_fritch_et_al_2017_univariate_analysisAbundance of invertebrates across different experimental treatments of field margins in temperate grassland. See README file for further details.Field_margin_data_fritch_multivariate_analysisAbundance of invertebrates across different experimental treatments of field margins in temperate grassland. See README file for further details.
DOI: 10.5061/dryad.q7605
title: Data from: Rapid evolution accelerates plant population spread in fragmented experimental landscapes

description: Predicting the speed of biological invasions and native species migrations
 requires an understanding of the ecological and evolutionary dynamics of
 spreading populations. Theory predicts that evolution can accelerate
 species’ spread velocity, but how landscape patchiness—an important
 control over traits under selection—influences this process is unknown. We
 manipulated the response to selection in populations of a model plant
 species spreading through replicated experimental landscapes of varying
 patchiness. After six generations of change, evolving populations spread
 11% farther than nonevolving populations in continuously favorable
 landscapes and 200% farther in the most fragmented landscapes. The greater
 effect of evolution on spread in patchier landscapes was consistent with
 the evolution of dispersal and competitive ability. Accounting for
 evolutionary change may be critical when predicting the velocity of range
 expansions.
description: Furthest seed dispersed
 in each generation for each replicateDistance of the furthest
 seed for each replicate in each generation, as well as the number of
 seedlings in the furthest pot. See metadata in ReadMe file (and
 description of Methods in the paper).2016_06_01_ArabiEvoMaxDistance.csvTraits of each genotypeMean of each of four traits for each genotype (recombinant inbred line) in the experiment: height (when growing alone), dispersal (average distance of furthest dispersed seed from a solitary individual), competitive ability (dominance in non-spreading context), and seed mass. Data to estimate height, dispersal and seed mass were from separate experiment than main experiment (see Methods). Note that ranks rather than raw data were used for analyses of all traits. See ReadMe associated with 'Furthest seed' datafile for metadata.fourtraits.csvGenotypes in Generation 6Genotype results after 6 generations of spread. 10 individuals were sampled from the leading edge (front) and 10 from the first pot in the array (back). See ReadMe associated with 'Furthest seed' datafile for metadata.Gen6_Genotypes.csvLocation and seedling density for one replicate (Fig. 1B)Number of seedlings in each pot in each generation for one replicate array in the experiment (continuous landscape, evolving treatment), as in Figure 1B. Seedlings were counted in 1 cm wide bins at the leading edge, and counted for the entire pot behind the leading edge. See ReadMe associated with 'Furthest seed' datafile for metadata.seedlings_ID49.csv
DOI: 10.5061/dryad.jm00k
title: Data from: Using digital soil maps to infer edaphic affinities of plant species in Amazonia: problems and prospects

description: Amazonia combines semi-continental size with difficult access, so both
 current ranges of species and their ability to cope with environmental
 change have to be inferred from sparse field data. Although efficient
 techniques for modeling species distributions on the basis of a small
 number of species occurrences exist, their success depends on the
 availability of relevant environmental data layers. Soil data are
 important in this context, because soil properties have been found to
 determine plant occurrence patterns in Amazonian lowlands at all spatial
 scales. Here we evaluate the potential for this purpose of three digital
 soil maps that are freely available online: SOTERLAC, HWSD, and SoilGrids.
 We first tested how well they reflect local soil cation concentration as
 documented with 1,500 widely distributed soil samples. We found that
 measured soil cation concentration differed by up to two orders of
 magnitude between sites mapped into the same soil class. The best
 map-based predictor of local soil cation concentration was obtained with a
 regression model combining soil classes from HWSD with cation exchange
 capacity (CEC) from SoilGrids. Next, we evaluated to what degree the known
 edaphic affinities of thirteen plant species (as documented with field
 data from 1,200 of the soil sample sites) can be inferred from the soil
 maps. The species segregated clearly along the soil cation concentration
 gradient in the field, but only partially along the model-estimated cation
 concentration gradient, and hardly at all along the mapped CEC gradient.
 The main problems reducing the predictive ability of the soil maps were
 insufficient spatial resolution and/or georeferencing errors combined with
 thematic inaccuracy and absence of the most relevant edaphic variables.
 Addressing these problems would provide better models of the edaphic
 environment for ecological studies in Amazonia.
description: Species and soil data
 from Amazoniaspecies_soil.csv
DOI: 10.5061/dryad.t46100m
title: Data from: From ornament to armament or loss of function? Breeding plumage acquisition in a genetically monogamous bird

description: 1. The evolution of conspicuous male traits is thought to be driven by
 female mate choice or male-male competition. These two mechanisms are
 often viewed as distinct processes, with most studies focusing on female
 choice. 2. However, both mechanisms of sexual selection can act
 simultaneously on the same trait (i.e. dual function) and/or interact in a
 synergistic or conflicting way. Dual function-traits are commonly assumed
 to originate through male-male competition before being used in female
 choice; yet, most studies focusing on such traits could not determine the
 direction of change, lacking phylogenetic information. 3. We investigated
 the role of conspicuous male seasonal plumage in male-male competitive
 interactions in the purple-crowned fairy-wren Malurus coronatus, a
 cooperatively breeding bird. Male breeding plumage in most Malurus species
 is selected by female choice through extra-pair mate choice, but unlike
 its congeners, M. coronatus is genetically monogamous, and females do not
 seem to choose males based on breeding plumage acquisition. 4. Our study
 shows that, within groups, subordinate males that were older, and
 therefore higher-ranked in the queue for breeder position inheritance,
 produced a more complete breeding plumage. In line with this, subordinate
 males that were older and/or displayed a more complete breeding plumage
 were more successful in competitively acquiring a breeder position. 5. A
 role as a signal of competitive ability was experimentally confirmed by
 presenting models of males: in breeding colours, these received more
 aggression from resident breeder males than in non-breeding colours, but
 elicited limited response from females, consistent with competitors in
 breeding plumage being perceived as a bigger threat to the breeder male.
 6. The role of the conspicuous breeding plumage in mediating male-male
 interactions might account for its presence in this genetically monogamous
 species. Since phylogenetic reconstructions suggest a past female choice
 function in M. coronatus, this could represent a sexual trait that shifted
 functions, or a dual function-trait that lost one function. These
 evolutionary scenarios imply that intra- and inter-sexual functions of
 ornaments may be gained or lost independently, and offer new perspectives
 in understanding the complex dynamics of sexual selection.
description: Extent of breeding
 plumage in male purple-crowned fairy-wrensMale breeding
 plumage.xlsxTiming of acquisition of
 a breeder position in male purple-crowned fairy-wrensTime breeder position
 gain.xlsxCase-by-case analysis of
 competitions for a breeder position in male purple-crowned
 fairy-wrensCase-by-case
 analysis.xlsxModel presentation
 experiments: effect of plumage state on strength of territorial defence in
 male purple-crowned fairy-wrensModel
 presentation.xlsx
DOI: 10.5061/dryad.9ff3r4v
title: Data from: Epidermal expression of a sterol biosynthesis gene regulates root growth by a non-cell autonomous mechanism in Arabidopsis

description: The epidermis is hypothesized to play a signalling role during plant
 development. One class of mutants showing defects in signal transduction
 and radial patterning are those in sterol biosynthesis. The expectation is
 that living cells require sterols, but it is not clear that all cell types
 express sterol biosynthesis genes. The HYDRA1 (HYD1) gene of Arabidopsis
 encodes sterol ∆8-∆7 isomerase, and although hyd1 seedlings are defective
 in radial patterning across several tissues, we show that the HYD1 gene is
 expressed most strongly in the root epidermis. Transgenic activation of
 HYD1 transcription in the epidermis of hyd1 null mutants reveals a major
 role in root patterning and growth. HYD1 expression in the vascular
 tissues and root meristem, though not endodermis or pericycle, also leads
 to some phenotypic rescue. Phenotypic rescue is associated with rescued
 patterning of the PIN1 and PIN2 auxin efflux carriers. The importance of
 the epidermis in controlling root growth and development is proposed to be
 in part due to its role as a site for sterol biosynthesis, and auxin is a
 candidate for the non-cell autonomous signal.
description: Columella
 tiersCounts of columella
 tiers on mutant and rescued linesHYD1sense3 Fig.
 3A,BRoot growth data, Fig.
 3A,BHYD1sense Fig.
 3A,B.xlsHYD1sense auxin genes
 Fig 4Gene expression data
 Fig. 4G
DOI: 10.5061/dryad.s4v35kn
title: Data from: Inconsistent use of multiple comparison corrections in studies of population genetic structure: are some type I errors more tolerable than others?

description: Studies of genetic population structure often involve numerous tests of
 Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and genetic
 differentiation. Tests of HWE or LD are important precursors to population
 structure assessments. When conducting multiple related statistical tests,
 type 1 error increases, e.g., familywise error rate (FWER) inflation. FWER
 inflation can alter the results of statistical tests and thus the
 conclusions. Authors are aware of the need to control for FWER inflation,
 but there has been low consistency of use. Furthermore, there is a
 potential for the choice of correction methods to be exploited to
 selectively use FWER corrections to avoid data exclusion or to result in
 increased the rejection of null hypotheses. We surveyed literature from
 2011-2013 to determine if studies of population structure assess LD and
 HWE and if FWER corrections were applied consistently across different
 types of genetic differentiation, linkage disequilibrium, and
 Hardy-Weinberg equilibrium tests. We found a lack of documentation of FWER
 corrections in studies, and we advocate for authors to be more cognizant
 in reporting their corrections. We also found significantly inconsistent
 FWER corrections, with a bias towards less restrictive correction on
 genetic differentiation and more restrictive corrections with LD and HWE.
 While varied adjustments of FWER for different types of analyses might be
 justified, papers with inconsistent usage across tests of HWE, LD and
 genetic differentiation did not present rationale for their FWER
 corrections. We also found a lack of documentation of HWE, LD and FWER
 corrections in studies. We encourage authors to report statistical tests
 and related FWER corrections, use FWER corrections consistently or justify
 their different methods in the same study.
description: Hauser_Appendix1_v3Appendix containing all manuscripts surveyed and used in analysis.
DOI: 10.15468/dl.98wcts
title: Occurrence Download

description: A dataset containing 2814 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Fossil, Living Specimen, Occurrence evidence)",
 "Country is one of (Peru, Colombia, Venezuela (Bolivarian Republic of), Ecuador, Bolivia (Plurinational State of), Chile, Argentina, Bhutan, Nepal, India, Pakistan)",
 "DatasetKey is one of (Colección de Entomología Médica del Instituto Colombiano de Medicina Tropical, INSDC Sequences, Registros de los dípteros causantes de la transmisión del agente etiológico del dengue en el departamento del Cauca, Colombia, Global compendium of Aedes aegypti occurrence, iNaturalist Research-grade Observations, International Barcode of Life project (iBOL), Global compendium of Aedes albopictus occurrence, Mosquito Alert Dataset, COLECCIÓN NACIONAL DE VECTORES ARTRÓPODOS CIREV - CZ9-INSPI, Colecta e identificación taxonómica de insectos en unidad rural de Universidad Pública en los llanos orientales)",
 "Issue is one of (Geodetic datum invalid, Coordinate reprojected, Coordinate uncertainty meters invalid, Country coordinate mismatch, Continent coordinate mismatch, Continent country mismatch, Continent invalid, Taxon match fuzzy, Taxon match higher rank, Taxon match aggregate, The backbone match found using the taxon IDs differs from what would be found if using the scientific names, Depth not metric, Depth unlikely, Depth min max swapped, Depth non numeric, Elevation unlikely, Elevation min max swapped, Elevation not metric, Elevation non numeric, Modified date invalid, Modified date unlikely, Identified date unlikely, Multimedia URI invalid, References URI invalid, Error during interpretation, Individual count invalid, Individual count conflicts with occurrence status, Occurrence status inferred from basis of record, Georeferenced date unlikely, Georeferenced date invalid, Ambiguous institution, Ambiguous collection, Institution collection mismatch, Possibly on loan, Different owner institution, Occurrence status unparsable, Coordinate rounded, Geodetic datum assumed WGS84, Continent derived from country, Continent derived from coordinates, Country derived from coordinates, Occurrence status inferred from individual count, Institution match none, Collection match none, Institution match fuzzy, Collection match fuzzy)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Aedes aegypti, Aedes albopictus)",
 "Year 2000-2026"
 ]
}

 The dataset includes 2814 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000734-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5cd20
title: Data from: Association between COL11A1 (rs1337185) and ADAMTS5 (rs162509) gene polymorphisms and lumbar spine pathologies in Chinese Han population: an observational study

description: Objectives: A previous study identified a significant association between
 several single nucleotide polymorphisms (SNPs) and lumbar disc
 degeneration (LDD) in Indians. To validate the association between these
 SNPs and specific lumbar spine pathologies, we performed a case-control
 study in Chinese Han population. Design: An observational study. Setting:
 University Hospital in Nanning, China. Participants: This study included
 428 LDD patients and 400 normal controls. Outcome measures: LDD Patients
 were classified into 4 subgroups, including disc herniation only (Subgroup
 1), discopathies or/and osteochondrosis associated with disc herniation
 (Subgroup 2), spinal stenosis or/and spondylolisthesis (Subgroup 3), and
 degenerative scoliosis (Subgroup 4). This study was conducted by examining
 2 aspects: environmental factors and SNP genotyping. The environmental
 factors were evaluated with a questionnaire survey including questions
 about BMI, smoking habits, the physical demands of their job and exposure
 to vibrations. Rs1337185, rs5275, rs5277, rs7575934, rs3213718 and
 rs162509 were genotyped using a PCR-based Invader assay. Results: The
 physical workload was significantly higher in patients with lumbar spine
 pathologies than in the normal controls (P=0.035). The genotype and allele
 frequencies of rs1337185 and rs162509 were significantly different between
 the LDD patients and the normal controls. In rs1337185, a significant
 association was found between the C allele (risk allele) and the presence
 of disc herniation (OR=1.80; 95%CI= 1.21-2.68; P=0.003, adjusted P=0.012),
 and the presence of spinal stenosis and spondylolisthesis (OR=1.92;
 95%CI=1.29-2.89; P= 0.001, adjusted P=0.004). In rs162509, the G allele
 represented 1.58-fold increased risk to suffer from disc herniation
 (OR=1.58; 95%CI=1.20-2.09; P=0.001, adjusted P=0.004). Conclusions: The
 SNPs rs1337185 in COL11A1 and rs162509 in ADAMTS5 are associated with
 susceptibility to LDD. The C allele of rs1337185 is risky for patients who
 are affected by lumbar pathologies such as disc herniation, stenosis and
 spondylolisthesis. The G allele of rs16250 represents a risk factor for
 the development of disc herniation.
description: DATA for open
 accessGenotype frequencies of
 rs1337185, rs5275, rs5277, rs7575934, rs3213718 and rs162509 in controls
 and cases
DOI: 10.5061/dryad.nn60m
title: Data from: Do pet dogs (Canis familiaris) follow ostensive and non-ostensive human gaze to distant space and to objects?

description: Dogs are renowned for being skilful at using human-given communicative
 cues such as pointing. Results are contradictory, however, when it comes
 to dogs' following human gaze, probably due to methodological
 discrepancies. Here we investigated whether dogs follow human gaze to one
 of two food locations better than into distant space even after comparable
 pre-training. In Experiments 1 and 2, the gazing direction of dogs was
 recorded in a gaze-following into distant space and in an object-choice
 task where no choice was allowed, in order to allow a direct comparison
 between tasks, varying the ostensive nature of the gazes. We found that
 dogs only followed repeated ostensive human gaze into distant space,
 whereas they followed all gaze cues in the object-choice task. Dogs
 followed human gaze better in the object-choice task than when there was
 no obvious target to look at. In Experiment 3, dogs were tested in another
 object-choice task and were allowed to approach a container. Ostensive
 cues facilitated the dogs’ following gaze with gaze as well as their
 choices: we found that dogs in the ostensive group chose the indicated
 container at chance level, whereas they avoided this container in the
 non-ostensive group. We propose that dogs may perceive the object-choice
 task as a competition over food and may interpret non-ostensive gaze as an
 intentional cue that indicates the experimenter's interest in the
 food location she has looked at. Whether ostensive cues simply mitigate
 the competitive perception of this situation or they alter how dogs
 interpret communicative gaze needs further investigation. Our findings
 also show that following gaze with one's gaze and actually choosing
 one of the two containers in an object-choice task need to be considered
 as different variables. The present study clarifies a number of questions
 related to gaze-following in dogs and adds to a growing body of evidence
 showing that human ostensive cues can strongly modify dog behaviour.
description: Duranton_Data_Exp1Data of Experiment 1Duranton_Data_Exp2Data of Experiment 2