cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m6557
title: Data from: Molecular phylogeny of Tragopogon L. (Asteraceae) based on seven nuclear loci (Adh, GapC, LFY, AP3, PI, ITS, and ETS)

description: Tragopogon is a large Eurasian genus of approximately 150 species. Despite
 the use of 6910 aligned bp of sequence data representing seven loci,
 relationships within the genus remain largely unresolved. The young age of
 the genus in combination with rapid diversification may be the best
 explanation for this poor resolution. Our studies have revealed that
 Geropogon is well supported as the immediate sister to Tragopogon.
 Sections Tragopogon, Brevirostris, Chromopappus, and Hebecarpus of
 traditional taxonomic treatments are largely monophyletic; sections
 Angustissimi, Majores, Collini, and Profundisulcati are non-monophyletic.
 The monotypic sections Macropogon, Dasypogon, and Dybjanskya appear within
 other sections and no longer merit recognition. Our molecular
 investigations of geographically widespread species in Europe, including
 T. crocifolius, T. pratensis, T. porrifolius, and T. orientalis, indicate
 that each may be non-monophyletic, comprising several cryptic species.
 These widespread diploids are the proposed parents of some of the Eurasian
 allopolyploids, as well as the parents of the recently formed T. mirus and
 T. miscellus from North America
description: Mavrodiev_et_al_2012Zip Archive contains: 1. Figures 1-7: 8 Mesquite files: seven Maximum Likelihood trees and also single file linked all ML tree files altogether. 2. Supplemental Figures 1-7: 8 Mesquite files: seven Maximum Parsimony trees and also single file linked all MP tree files altogether. 3. Appendix 1: 2 pages Excel file with Voucher data and Genbank accession numbers for individuals sequenced in study (first page) and two ITS sequences less than 200 bp long (second page) with voucher data.
DOI: 10.5061/dryad.b42r5
title: Data from: Female mate preferences for male body size and shape promote sexual isolation in threespine sticklebacks

description: Female mate preferences for ecologically relevant traits may enhance
 natural selection, leading to rapid divergence. They may also forge a link
 between mate choice within species and sexual isolation between species.
 Here, we examine female mate preference for two ecologically important
 traits: body size and body shape. We measured female preferences within
 and between species of benthic, limnetic, and anadromous threespine
 sticklebacks (Gasterosteus aculeatus species complex). We found that mate
 preferences differed between species and between contexts (i.e., within
 vs. between species). Within species, anadromous females preferred males
 that were deep bodied for their size, benthic females preferred larger
 males (as measured by centroid size), and limnetic females preferred males
 that were more limnetic shaped. In heterospecific mating trials between
 benthics and limnetics, limnetic females continued to prefer males that
 were more limnetic like in shape when presented with benthic males.
 Benthic females showed no preferences for size when presented with
 limnetic males. These results show that females use ecologically relevant
 traits to select mates in all three species and that female preference has
 diverged between species. These results suggest that sexual selection may
 act in concert with natural selection on stickleback size and shape.
 Further, our results suggest that female preferences may track adaptation
 to local environments and contribute to sexual isolation between benthic
 and limnetic sticklebacks.
description: Morphology and
 preferences of anadromous, benthic and limnetic threespine
 sticklebacksHead et al.
 Data.xlsx
DOI: 10.5061/dryad.5dr5k
title: Data from: Determining plant – leaf miner – parasitoid interactions: a DNA barcoding approach

description: A major challenge in network ecology is to describe the full-range of
 species interactions in a community to create highly-resolved food-webs.
 We developed a molecular approach based on DNA full barcoding and
 mini-barcoding to describe difficult to observe plant – leaf miner –
 parasitoid interactions, consisting of animals commonly regarded as
 agricultural pests and their natural enemies. We tested the ability of
 universal primers to amplify the remaining DNA inside leaf miner mines
 after the emergence of the insect. We compared the results of a)
 morphological identification of adult specimens; b) identification based
 on the shape of the mines; c) the COI Mini-barcode (130 bp) and d) the COI
 full barcode (658 bp) fragments to accurately identify the leaf-miner
 species. We used the molecular approach to build and analyse a tri-partite
 ecological network of plant – leaf miner – parasitoid interactions. We
 were able to detect the DNA of leaf-mining insects within their feeding
 mines on a range of host plants using mini-barcoding primers: 6% for the
 leaves collected empty and 33% success after we observed the emergence of
 the leaf miner. We suggest that the low amplification success of leaf
 mines collected empty was mainly due to the time since the adult emerged
 and discuss methodological improvements. Nevertheless our approach
 provided new species-interaction data for the ecological network. We found
 that the 130 bp fragment is variable enough to identify all the species
 included in this study. Both COI fragments reveal that some leaf miner
 species could be composed of cryptic species. The network built using the
 molecular approach was more accurate in describing tri-partite
 interactions compared with traditional approaches based on morphological
 criteria.
description: Tri-partite
 interactionsSpreadsheet where all
 interactions described using molecular method and morphological approach
 are displayed. This file has been used to calculate the network
 metrics.COI
 BarcodeSequence alignement for
 COI barcode (658bp). This alignement has been used to build ML
 treeCOI
 MinibarcodeSequence alignement for
 COI Minibarcode (130 bp). This alignement has been used to build ML
 tree.
DOI: 10.15468/dl.saqbhe
title: Occurrence Download

description: A dataset containing 342932 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rubus"
 ]
}

 The dataset includes 342932 records from 410 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000733-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.375dk
title: Ancient and modern colonization of North America by hemlock woolly adelgid, Adelges tsugae (Hemiptera: Adelgidae), an invasive insect from East Asia

description: Hemlock woolly adelgid, Adelges tsugae, is an invasive pest of hemlock
 trees (Tsuga) in eastern North America. We used 14 microsatellites and
 mitochondrial COI sequences to assess its worldwide genetic structure and
 reconstruct its colonization history. The resulting information about its
 life cycle, biogeography and host specialization could help predict
 invasion by insect herbivores. We identified eight endemic lineages of
 hemlock adelgids in central China, western China, Ulleung Island (South
 Korea), western North America, and two each in Taiwan and Japan, with the
 Japanese lineages specializing on different Tsuga species. Adelgid life
 cycles varied at local and continental scales with different sexual,
 obligately asexual and facultatively asexual lineages. Adelgids in western
 North America exhibited very high microsatellite heterozygosity, which
 suggests ancient asexuality. The earliest lineages diverged in Asia during
 Pleistocene glacial periods, as estimated using approximate Bayesian
 computation. Colonization of western North America was estimated to have
 occurred prior to the last glacial period by adelgids directly ancestral
 to those in southern Japan, perhaps carried by birds. The modern invasion
 from southern Japan to eastern North America caused an extreme genetic
 bottleneck with just two closely related clones detected throughout the
 introduced range. Both colonization events to North America involved host
 shifts to unrelated hemlock species. These results suggest that genetic
 diversity, host specialization and host phylogeny are not predictive of
 adelgid invasion. Monitoring non-native sentinel host trees and focusing
 on invasion pathways might be more effective methods of preventing
 invasion than making predictions using species traits or evolutionary
 history.
description: Havill_et_al.
 _2016_usat_data_dryadAn excel file with
 sample information and 14-locus microsatellite genotypes for hemlock
 adelgids used in this study.
DOI: 10.5061/dryad.65j02
title: Data from: Tropical forest fragmentation limits movements, but not occurrence of a generalist pollinator species

description: Habitat loss and fragmentation influence species distributions and
 therefore ecological processes that depend upon them. Pollination may be
 particularly susceptible to fragmentation, as it depends on frequent
 pollinator movement. Unfortunately, most pollinators are too small to
 track efficiently which has precluded testing the hypothesis that habitat
 fragmentation reduces or eliminates pollen flow by disrupting pollinator
 movement. We used radio-telemetry to examine space use of the green hermit
 hummingbird (Phaethornis guy), an important 'hub' pollinator of
 understory flowering plants across substantial portions of the neotropics
 and the primary pollinator of a keystone plant which shows reduced
 pollination success in fragmented landscapes. We found that green hermits
 strongly avoided crossing large stretches of non-forested matrix and
 preferred to move along stream corridors. Forest gaps as small as 50 m
 diminished the odds of movement by 50%. Green hermits occurred almost
 exclusively inside the forest, with the odds of occurrence being 8 times
 higher at points with &gt;95% canopy cover compared with points having
 &lt;5% canopy cover. Nevertheless, surprisingly. the species occurred
 in fragmented landscapes with low amounts of forest (~30% within a 2 km
 radius). Our results indicate that although green hermits are present even
 in landscapes with low amounts of tropical forest, movement within these
 landscapes ends up strongly constrained by forest gaps. Restricted
 movement of pollinators may be an underappreciated mechanism for
 widespread declines in pollination and plant fitness in fragmented
 landscapes, even when in the presence of appropriate pollinators.
description: Volpe et
 al-Fragmentation and_pollinator_movement_datasetHummingbird occurrence
 and movement data from Volpe et al. PLoS One
DOI: 10.5061/dryad.0bq15
title: Data from: Effectiveness and safety of 1 vs 4 h blood pressure profile with clinical and laboratory assessment for the exclusion of gestational hypertension and pre-eclampsia: a retrospective study in a university affiliated maternity hospital

description: Objective: We asked whether 60 compared with 240 min observation is
 sufficiently informative and safe for pregnancy day assessment (PDAC) of
 suspected pre-eclampsia (PE). Design: A retrospective study of 209
 pregnant women (475 PDAC assessments, 6 months) with routinely collected
 blood pressure (BP), symptom and laboratory information. We proposed a
 60 min screening algorithm comprising: absence of symptoms, normal
 laboratory parameters and ≤1high-BP reading (systolic blood pressure, SBP
 140 mm Hg or higher or diastolic blood pressure, DBP 90 mm Hg or higher).
 We also evaluated two less inclusive screening algorithms. We determined
 short-term outcomes (within 4 h): severe hypertension, proteinuric
 hypertension and pregnancy-induced hypertension, as well as long-term
 outcome: PE-related diagnoses up to the early puerperium. We assessed
 performance of alternate screening algorithms performance using 2×2
 tables. Results: 1 in 3 women met all screen negative criteria at 1 h.
 Their risk of hypertension requiring treatment in the next 3 h was 1.8%
 and of failing to diagnose proteinuric hypertensive PE at 4 h was 5.1%. If
 BP triggers were 5 mm Hg lower, 1 in 6 women would be screen-negative of
 whom 1.1% subsequently develops treatment-requiring hypertension and 4.5%
 demonstrate short-term proteinuric hypertension. We present sensitivity,
 specificity, negative and positive likelihood ratios for alternate
 screening algorithms. Conclusions: We endorse further research into the
 safest screening test where women are considered for discharge after
 60 min. Safety, patient and staff satisfaction should be assessed
 prospectively. Any screening test should be used in conjunction with good
 clinical care to minimise maternal and perinatal hazards of PE.
description: Dryad475 Pregnancy Day
 Assessment Attendances (PDAC) for assessment of hypertension in pregnancy
 and related conditions.Maternal date of birth, date of PDAC attendance and
 estimated date of confinement (EDC) have been modified by adding a random
 number of days between -7 and +7 in order to preserve
 anonymity.
DOI: 10.5061/dryad.157tp
title: Data from: The interplay between multiple predators and prey color divergence

description: Evolutionary divergence in the coloration of toxic prey is expected when
 geographic variation in predator composition and behavior favours shifts
 in prey conspicuousness. A fundamental prediction of predator-driven
 colour divergence is that the local coloration should experience lower
 predation risk than novel prey phenotypes. The dorsal coloration of the
 granular poison frog varies gradually from populations of conspicuous
 bright red frogs to populations of dull green and relatively cryptic
 frogs. We conducted experiments with clay models in four populations to
 examine the geographic patterns of taxon-specific predation. Birds avoided
 the local phenotype while lizards consistently selected for decreased
 conspicuousness and crab predation did not depend on frog coloration.
 Importantly, birds and lizards favoured low conspicuousness in populations
 where relatively cryptic green morphs have evolved. This study provides
 evidence for the interplay among distinct selective pressures, from
 multiple-predator taxa, acting on the divergence in protective coloration
 of prey species.
description: Dryad_granulifera_predationAttacks by birds, lizards, crabs, mammals, and unknown predators of clay models of O. granulifera of three phenotypes. 300 models of each phenotype were placed in four populations along the South Western lowlands of Costa Rica and inspected for predation marks after 72 h. Identification of predators was conducted by comparing the marks on the clay with models attacked by predators identified with trap-cameras.
DOI: 10.5061/dryad.4t140
title: Data from: Physiological conditions and genetic controls of phaeomelanin pigmentation in nestling barn swallows

description: Phaeomelanin is a common pigment that confers a reddish color to animals.
 Since phaeomelanogenesis requires the sulfhydryl group from cysteine or
 glutathione (GSH), which is an important antioxidant, this pigmentation
 and the associated coloration may be an honest signal, whereby only
 high-quality individuals (e.g., with lower oxidative stress) are able to
 develop showy plumage. The present study tested the mechanisms underlying
 the honest signal hypothesis using nestling barn swallows, Hirundo rustica
 gutturalis, which exhibit phaeomelanic throat plumage patches. We examined
 the relationship between phaeomelanin pigmentation levels and
 physiological condition during trait development, and the expression of
 the phaeomelanin-related gene agouti-signaling protein (ASIP) and the
 GSH-related gene glutathione S-transferase (GST) in throat feather
 follicles. We found that during phaeomelanogenesis, heavier nestlings
 produced more pigmented feathers, indicating that nestlings with high
 phaeomelanin concentrations are in better condition. We also found that
 phaeomelanin concentration was negatively correlated with total GSH level,
 but not significantly related with measures of oxidative stress. Among the
 GST genes, GSTM3 exhibited the highest expression in the developing
 feathers during phaeomelanogenesis. The expression levels of ASIP were
 positively associated with the amount of phaeomelanin deposition and
 negatively associated with the expression of GSTM3, reducing the amount of
 GSH that was available as an antioxidant. These findings suggest that
 high-quality individuals produce high concentrations of phaeomelanin in
 their plumage without experiencing increased oxidative stress, despite
 phaeomelanin production, which is triggered by ASIP, potentially actively
 consuming the sulfhydryl group from GSH.
description: Data of physiological
 condition,gene expression, oxidative stress for each
 nestlingSee ReadMe file for
 description of the dataArai_et_al_BEHECO_2017.xlsx
DOI: 10.3535/bnf-045-67c
title: Alcedo quadribrachys guentheri

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/lfn-gf4-7wh
title: Alcedo meninting

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/pxj-sar-pxe
title: Alcedo semitorquata

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.5061/dryad.gg6qk
title: Data from: Body-size scaling of metabolic rate in the trilobite Eldredgeops rana

description: We infer the body-size scaling slope of metabolic rate in a trilobite by
 applying a cell-size model that has been proposed to explain metabolic
 scaling in living organisms. This application is especially tractable in
 fossil arthropods with well-preserved compound eyes because the number and
 size of eye facets appear to be useful proxies for the relative number and
 size of cells in the body. As a case study, we examined the ontogenetic
 scaling of facet size and number in a ∼390-Myr-old local assemblage of the
 trilobite Eldredgeops rana, which has well-preserved compound eyes and a
 wide body-size range. Growth in total eye lens area resulted from
 increases in both facet area and number in relatively small (presumably
 young) specimens, but only from increases in facet area in large
 (presumably more mature) specimens. These results suggest that early
 growth in E. rana involved both cell multiplication and enlargement,
 whereas later growth involved only cell enlargement. If the cell-size
 model is correct, then metabolic rate scaled allometrically in E. rana,
 and the scaling slope of log metabolic rate versus log body mass decreased
 from ∼0.85 to 0.63 as these animals grew. This inferred age-specific
 change in metabolic scaling is consistent with similar changes frequently
 observed in living animals. Additional preliminary analyses of literature
 data on other trilobites also suggest that the metabolic scaling slope was
 &lt;1 in benthic species, but ∼1 in pelagic species, as has also been
 observed in living invertebrates. The eye-facet size (EFS) method featured
 here opens up new possibilities for examining the bioenergetic allometry
 of extinct arthropods.
description: Glazier et al
 Supplementary tables 1 & 2Two supplementary tables
 give the raw data used for scaling analyses of eye-facet size and number
 in relation to total eye size in Eldredgeops rana (original data) and
 other benthic and pelagic trilobites (literature data).
DOI: 10.5061/dryad.d7839
title: Data from: An evaluation of different partitioning strategies for Bayesian estimation of species divergence times

description: The explosive growth of molecular sequence data has made it possible to
 estimate species divergence times under relaxed-clock models using
 genome-scale datasets with many gene loci. In order both to improve model
 realism and to best extract information about relative divergence times in
 the sequence data, it is important to account for the heterogeneity in the
 evolutionary process across genes or genomic regions. Partitioning is a
 commonly used approach to achieve those goals. We group sites that have
 similar evolutionary characteristics into the same partition and those
 with different characteristics into different partitions, and then use
 different models or different values of model parameters for different
 partitions to account for the among-partition heterogeneity. However, how
 to partition data in practical phylogenetic analysis, and in particular in
 relaxed-clock dating analysis, is more art than science. Here, we use
 computer simulation and real data analysis to study the impact of the
 partition scheme on divergence time estimation. The partition schemes had
 relatively minor effects on the accuracy of posterior time estimates when
 the prior assumptions were correct and the clock was not seriously
 violated, but showed large differences when the clock was seriously
 violated, when the fossil calibrations were in conflict or incorrect, or
 when the rate prior was mis-specified. Concatenation produced the widest
 posterior intervals with the least precision. Use of many partitions
 increased the precision, as predicted by the infinite-sites theory, but
 the posterior intervals might fail to include the true ages because of the
 conflicting fossil calibrations or mis-specified rate priors. We analyzed
 a dataset of 78 plastid genes from 15 plant species with serious clock
 violation and showed that time estimates differed significantly among
 partition schemes, irrespective of the rate drift model used. Multiple and
 precise fossil calibrations reduced the differences among partition
 schemes and were important to improving the precision of divergence time
 estimates. While the use of many partitions is an important approach to
 reducing the uncertainty in posterior time estimates, we do not recommend
 its general use for the present, given the limitations of current models
 of rate drift for partitioned data and the challenges of interpreting the
 fossil evidence to construct accurate and informative calibrations.
description: PartitionAnalysisTimeMC.FigS1Figure S1PartitionAnalysisTimeMC.TableS1S2Tables S1 & S2MakeTree.RRelClock.R