cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7417k
title: Data from: Global mtDNA genetic structure and hypothesized invasion history of a major pest of citrus, Diaphorina citri (Hemiptera: Liviidae)

description: The Asian citrus psyllid Diaphorina citri Kuwayama, is a key pest of
 citrus as the vector of the bacterium causing the ‘huanglongbing’ disease
 (HLB). To assess the global mtDNA population genetic structure, and
 possible dispersal history of the pest, we investigated genetic variation
 at the COI gene collating newly collected samples with all previously
 published data. Our dataset consists of 356 colonies from 106 geographic
 sites worldwide. High haplotype diversity (H-mean = 0.702 ± 0.017), low
 nucleotide diversity (π-mean = 0.003), and significant positive selection
 (Ka/Ks = 32.92) were observed. Forty-four haplotypes (Hap) were
 identified, clustered into two matrilines: Both occur in southeastern and
 southern Asia, North and South America, and Africa; Lineages A and B also
 occur in eastern and western Asia, respectively. The most abundant
 haplotypes were Hap4 in lineage A (35.67%), and Hap9 in lineage B
 (41.29%). The haplotype network identified them as the ancestral
 haplotypes within their respective lineages. Analysis of molecular
 variance showed significant genetic structure (FST = 0.62, p &lt;
 0.0001) between the lineages, and population genetic analysis suggests
 geographic structuring. We hypothesize a southern and/or southeastern Asia
 origin, three dispersal routes, and parallel expansions of two lineages.
 The hypothesized first route involved the expansion of lineage B from
 southern Asia into North America via West Asia. The second, the expansion
 of some lineage A individuals from Southeast Asia into East Asia, and the
 third involved both lineages from Southeast Asia spreading westward into
 Africa and subsequently into South America. To test these hypotheses and
 gain a deeper understanding of the global history of D. citri more
 data-rich approaches will be necessary from the ample toolkit of next
 generation sequencing (NGS). However, the current paper may serve to guide
 such sampling and in the development of biological control programs
 against the global pest D. citri.
description: COI sequences of
 Diaphorina citri used in this studyCOI sequences of 356
 individuals of Diaphorina citri used in this studyCOI sequences of 48
 samples representing all our sampling sites from ChinaCOI sequences of 48
 samples representing all our sampling sites from ChinaLocations and accession
 numbers of Diaphorina citriLocations and accession
 numbers of Diaphorina citri in this study
DOI: 10.5061/dryad.jh3sb
title: Data from: Evolution of gliding in Southeast Asian geckos and other vertebrates is temporally congruent with dipterocarp forest development

description: Gliding morphologies occur in diverse vertebrate lineages in Southeast
 Asian rainforests, including three gecko genera, plus frogs, snakes,
 agamid lizards, and squirrels. It has been hypothesized that repeated
 evolution of gliding is related to the dominance of Asian rainforest tree
 floras by dipterocarps. For dipterocarps to have influenced the evolution
 of gliding in Southeast Asian vertebrates, gliding lineages must have
 Eocene or later origins. However, divergence times are not known for most
 lineages. To investigate the temporal pattern of Asian gliding vertebrate
 evolution, we performed phylogenetic and molecular clock analyses. New
 sequence data for geckos incorporate exemplars of each gliding genus
 (Cosymbotus, Luperosaurus, and Ptychozoon), whereas analyses of other
 vertebrate lineages use existing sequence data. Stem ages of most gliding
 vertebrates, including all geckos, cluster in the time period when
 dipterocarps came to dominate Asian tropical forests. These results
 demonstrate that a gliding/dipterocarp correlation is temporally viable,
 and caution against the assumption of early origins for apomorphic taxa.
description: Gecko
 Alignmentgecko_dryad.txtDraco Alignmentdraco_dryad.txtRhacophorus Alignmentfrog_dryad.txtChrysopelea Alignmentsnake_dryad.txtSquirrel Alignmentsquirrel_dryad.txt
DOI: 10.5061/dryad.7957
title: Data from: Modularity and scaling in fast movements: power amplification in mantis shrimp

description: Extremely fast animal actions are accomplished with mechanisms that reduce
 the duration of movement. This process is known as power amplification.
 While many studies have examined the morphology and performance of
 power-amplified systems, little is known about their development and
 evolution. Here we examine scaling and modularity in the powerful
 predatory appendages of a mantis shrimp, Gonodactylaceus falcatus
 (Crustacea, Stomatopoda). We propose that power-amplified systems can be
 divided into three units: an engine (e.g., muscle), an amplifier (e.g.,
 spring) and a tool (e.g., hammer). We tested whether these units are
 developmentally independent using geometric morphometric techniques which
 quantitatively compare shapes. Additionally, we tested whether shape and
 several mechanical features are correlated with size and sex. We found
 that the morphological regions that represent the engine, amplifier, and
 tool belong to independent developmental modules. In both sexes, body size
 was positively correlated with the size of each region. Shape, however,
 changed allometrically with appendage size only in the amplifier (both
 sexes) and tool (males). These morphological changes were correlated with
 strike force and spring force (amplifier), but not spring stiffness
 (amplifier). Overall, the results indicate that each functional unit
 belongs to different developmental modules in a power-amplified system,
 potentially allowing independent evolution of the engine, amplifier and
 tool.
description: data.filesDescription of the 4 data files: All files are tables into a text files and are comma delimited. The files “merus.txt” and “propodus.dactylus.txt” represent the superimposed coordinates for the raptorial appendages (the merus and the propodus/dactylus respectively). They include animal ID, appendage side, measurement replicates, centroid size, and X and Y coordinate for each landmarks and semi-landmarks. The file “individuals.informations.txt” includes the animal ID, the sex, the animal total body length and the strike force. Some animals do not have a strike force and have “NA” instead. The file “spring.contraction.data.txt” includes all the data relative to the spring section of the article. This is the sex of the animals, the spring force when maximally contracted, the spring stiffness, the animal total body length, the centroid size and the superimposed coordinate (X and Y) for each landmarks and semi-landmarks.
DOI: 10.5061/dryad.2h5j7
title: Data from: Molecular phylogenetics of Kosteletzkya (Malvaceae, Hibisceae) reveals multiple independent and successive polyploid speciation events

description: Kosteletzkya s.s. is a genus of 17 species (excluding the endemic species
 of Madagascar), found in the New World, continental Africa, Madagascar,
 and Southeast Asia. Recent chromosome counts revealed diploid, tetraploid,
 and hexaploid species. To estimate the history of the genus, we sequenced
 nuclear and plastid loci for nearly all Kosteletzkya spp., in the majority
 of cases, with multiple accessions per species. The African species form a
 paraphyletic grade relative to a New World clade. Polyploidy has occurred
 only in some African species, resulting in the relatively ancient
 formation of one putative autotetraploid species (K. semota), one recent
 allotetraploid species (K. borkouana), two relatively ancient
 allotetraploid species (K. begoniifolia and K. rotundalata) and one recent
 allohexaploid species (K. racemosa). Our inferences regarding the
 hypothesized parentage of the polyploids mostly corroborate previous work
 based on chromosome-pairing patterns in artificial hybrids, highlighting
 the utility of these complementary data sources.
description: Kost 3gene nuclear
 combined newCombined nexus file for
 all three nuclear data setsKost combined 5gene
 plastid newCombined nexus file for
 all 5 plastid data setsKost taxa for
 polyploidExcel spreadsheet for
 all voucher information for each accession. Note that each accession
 isidnetified by "greenhouse accession number" in matrices, which
 directly correspond to the voucher information
 presented.
DOI: 10.5061/dryad.g0v62
title: Data from: Intensifying drought eliminates the expected benefits of elevated carbon dioxide for soybean

description: Stimulation of C3 crop yield by rising concentrations of atmospheric
 carbon dioxide ([CO2]) is widely expected to counteract crop losses that
 are due to greater drought this century. But these expectations come from
 sparse field trials that have been biased towards mesic growth conditions.
 This eight-year study used precipitation manipulation and year-to-year
 variation in weather conditions at a unique open-air field facility to
 show that the stimulation of soybean yield by elevated [CO2] diminished to
 zero as drought intensified. Contrary to the prevalent expectation in the
 literature, rising [CO2] did not counteract the effect of strong drought
 on photosynthesis and yield because elevated [CO2] interacted with drought
 to modify stomatal function and canopy energy balance. This new insight
 from field experimentation under hot and dry conditions, which will become
 increasingly prevalent in the coming decades, highlights the likelihood of
 negative impacts from interacting global change factors on a key global
 commodity crop in its primary region of production.
description: Final_Data_DepositThis directory contains the raw data and the code necessary to replicate the analyses in Gray et al (2016).
DOI: 10.5061/dryad.609bp7m
title: Data from: Ordinal vs dichotomous analyses of modified Rankin Scale and 5-year outcome and cost of stroke

description: Objective – To compare how three common representations (ordinal versus
 dichotomized as 0-1/2-6 or 0-2/3-6) of the modified Rankin Scale (mRS) – a
 commonly-used trial outcome measure – relate to long-term outcomes, and
 quantify trial ineligibility rates based on pre-morbid mRS. Methods – In
 consecutive ischaemic stroke patients in a population-based, prospective
 cohort study (Oxford Vascular Study; 2002-2014), we related 3-month mRS to
 1-year and 5-year disability and death (logistic regressions), and
 health/social-care costs (generalized linear model), adjusted for age/sex,
 and compared goodness-of-fit values (c-statistic, Mean Absolute Error
 [MAE]). We also calculated the proportion of patients in whom pre-morbid
 mRS &gt;1 or &gt;2 would result in exclusion from trials using
 dichotomous analysis. Results – Among 1,607 patients, the ordinal mRS was
 more strongly related to 5-year mortality than both the 0-1/2-6 and
 0-2/3-6 dichotomies (all p&lt;0.0001). Results were similar for 5-year
 disability, and 5-year care costs were also best captured by the ordinal
 model (ΔMAE versus age/sex: -3,059 for ordinal, -2,805 for 0-2/3-6, -1,647
 for 0-1/2-6). 244 (17.1%) 3-month survivors had pre-morbid mRS&gt;2
 and 434 (30.5%) had mRS&gt;1; both proportions increased with female
 sex, socio-economic deprivation, and age (all p&lt;0.0001).
 Conclusions – The ordinal form of the 3-month mRS relates better to
 long-term outcomes and costs in survivors of ischaemic stroke than either
 dichotomy. This finding favours using ordinal approaches in trials
 analysing the mRS. Exclusion of patients with higher pre-morbid disability
 by use of dichotomous primary outcomes will also result in
 unrepresentative samples.
description: Online Supplement
 Neurology 14Jul2018 - Clean CopyContains eTables 1-19,
 eFigures 1-7
DOI: 10.5061/dryad.j3s5f
title: Data from: Unusually limited pollen dispersal and connectivity of Pedunculate oak (Quercus robur) refugial populations at the species' southern range margin

description: Low-latitudinal range margins of temperate and boreal plant species
 typically consist of scattered populations that persist locally in
 microrefugia. It remains poorly understood how their refugial habitats
 affect patterns of gene flow and connectivity, key components for their
 long-term viability and evolution. We examine landscape-scale patterns of
 historical and contemporary gene flow in refugial populations of the
 widespread European forest tree Pedunculate oak (Quercus robur) at the
 species' southwestern range margin. We sampled all adult trees (n =
 135) growing in a 20 km long valley and genotyped 724 acorns from 72
 mother trees at 17 microsatellite loci. The ten oak stands that we
 identified were highly differentiated and formed four distinct genetic
 clusters, despite sporadic historical dispersal being detectable. By far
 most contemporary pollination occurred within stands, either between local
 mates (85.6%) or through selfing (6.8%). Pollen exchange between stands
 (2.6%) was remarkably rare given their relative proximity and was
 complemented by long-distance pollen immigration (4.4%) and hybridization
 with the locally abundant Quercus pyrenaica (0.6%). The frequency of
 between-stand mating events decreased with increasing size and spatial
 isolation of stands. Overall, our results reveal outstandingly little
 long-distance gene flow for a wind-pollinated tree species. We argue that
 the distinct landscape characteristics of oaks' refugial habitats,
 with a combination of a rugged topography, dense vegetation and humid
 microclimate, are likely to increase plant survival but to hamper
 effective long-distance pollen dispersal. Moreover, local mating might be
 favoured by high tree compatibility resulting from genetic purging in
 these long-term relict populations.
description: Quercus robur tree
 genotypes.Genotypes and geographic
 coordinates for adult Quercus robur trees (n = 135) growing in a 20 km
 long valley and 684 acorns from 72 mother trees at 20 microsatellite loci.
 Samples come form 10 distinct oak populations.genotypes.xlsxPhenological data for Quercus oak trees.Data on flowering phenology for oak individual trees in 10 populations for two study years.phenology_data.xlsx
DOI: 10.15468/dl.3ynw8j
title: Occurrence Download

description: A dataset containing 348 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (Museu Paraense Emílio Goeldi - Ornithology Collection - Feathers_and_Skin, Xeno-canto - Bird sounds from around the world, Field Museum of Natural History (Zoology) Bird Collection, Vertebrate Zoology Division - Ornithology, Yale Peabody Museum, INSDC Sequences, PPBio - UFMT | Composição aves do Cerrado)",
 "OccurrenceStatus is Present",
 "TaxonKey is Neothraupis fasciata"
 ]
}

 The dataset includes 348 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000565-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0c96p
title: Data from: Colour learning when foraging for nectar and pollen: bees learn two colours at once

description: Bees are model organisms for the study of learning and memory, yet nearly
 all such research to date has used a single reward, nectar. Many bees
 collect both nectar (carbohydrates) and pollen (protein) on a single
 foraging bout, sometimes from different plant species. We tested whether
 individual bumblebees could learn colour associations with nectar and
 pollen rewards simultaneously in a foraging scenario where one floral type
 offered only nectar and the other only pollen. We found that bees readily
 learned multiple reward–colour associations, and when presented with novel
 floral targets generalized to colours similar to those trained for each
 reward type. These results expand the ecological significance of work on
 bee learning and raise new questions regarding the cognitive ecology of
 pollination.
description: All learning data for
 experiment and summaryThe first tab is a
 summary of all bees used and what they did (bees that did not collect
 nectar or pollen or only collected small amounts of one were not included
 in main learning analysis). The second tab is all behavioural data with
 key in text box.all
 data_Dryad.xlsx
DOI: 10.5061/dryad.1223s
title: Data from: Molecular analysis of caffeoyl residues related to pigmentation in green cotton fibers

description: The pigment components in green cotton fibers were isolated and identified
 as 22-O-caffeoyl-22-hydroxymonodocosanoin and
 22-O-caffeoyl-22-hydroxydocosanoic acid. The concentration of
 22-O-caffeoyl-22-hydroxymonodocosanoin was correlated positively with the
 degree of green fibers of color, indicating a role of caffeoyl derivatives
 in pigmentation of green cotton fibers. Upland cotton (Gossypium hirsutum
 L.) contains four genes (Gh4CL1 to Gh4CL4) encoding 4-coumarate:CoA ligase
 (4CL), key enzymes of the phenylpropanoid biosynthesis pathway. In 15 to
 24 days-post anthesis fibers, the expression level of Gh4CL1 was very low,
 Gh4CL3 had a similar expression level between the white and green cottons,
 Gh4CL2 had a significantly higher expression level in the green fibers
 than in the white fibers, whereas Gh4CL4 seemed to have a higher
 expression level in the white fibers than in the green fibers. According
 to enzyme kinetics analysis, Gh4CL1 displayed a preference for
 4-coumarate, Gh4CL3 and Gh4CL4 exhibited a somewhat low but still
 prominent activity towards ferulate, while Gh4CL2 had a strong preference
 for caffeate and ferulate. These results suggest that Gh4CL2 might be
 involved in the metabolism of caffeoyl residues and related to pigment
 biosynthesis in green cotton fibers. Our findings provide insights for
 understanding biochemical and molecular mechanisms of pigmentation in
 green cotton fibers.
description: Gh4CL
 gene-CDSCompounds
 informationSupplementary
 data.pdf
DOI: 10.15468/dl.5bfesy
title: Occurrence Download

description: A dataset containing 206268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Occurrence evidence)",
 "Country is Mexico",
 "GadmGid is MEX.22_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 206268 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000528-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cs5b4
title: Data from: Extinction debt of a common shrub in a fragmented landscape

description: 1. Environmental stochasticity and low demographic rates may cause delayed
 extinctions of habitat-specialist species that were initially retained
 within remnant patches after habitat loss and fragmentation. Detecting
 such extinction debts opens opportunities to counteract future
 biodiversity loss, yet knowing the underlying causes of population
 declines is a basic need for targeting specific guidelines for
 conservation and restoration (e.g. habitat quantity, quality, or
 connectivity). 2. Here, we examine the extinction debt in the common
 Mediterranean shrub Myrtus communis (myrtle) occurring in woodland patches
 of a highly fragmented region that has lost nearly half of the remnant
 woodland cover during the last fifty years (1956–2002). 3. We sampled
 myrtle occurrence in 304 woodland patches and modelled its probability of
 occurrence in relation to patch size, patch disturbance and woodland cover
 in the surrounding landscape. In order to test for extinction debt
 evidence, we tested whether myrtle occurrence is better predicted by past
 (1956) than by present (2002) woodland cover. 4. We found that the
 probability of myrtle occurrence is associated with present patch features
 (size and disturbance) that are linked to causes of individual mortality
 and/or recruitment collapse. However, it was associated with past – rather
 than present – woodland cover in the surrounding landscape, proving a
 still unpaid extinction debt. Specifically, myrtle occurrence is very
 unlikely in small and highly disturbed patches located in long-term
 deforested landscapes. 5. Synthesis and applications. Individual longevity
 of the Mediterranean shrub Myrtus communis (myrtle) can delay local
 extinctions, but paying the debt is a matter of time, especially
 considering the elevated susceptibility of small and disturbed populations
 to environmental stochasticity. However, these populations still offer
 management opportunities and reducing disturbances and improving habitat
 quality, especially within small woodland patches, should be a top
 priority for conservation and restoration.
description: Dataset_ExtinctionDebt_Gonzalez-Varo_et_al_JAPPLECOLPlease see the README file
DOI: 10.5061/dryad.4gp7g3g
title: Data from: Adsorption of heavy metal with modified eggshell membrane and in situ synthesis of Cu-Ag/MESM composites

description: The objectives of this study were to remove heavy metals from wastewater
 through biosorption method with modified biomass as both effective sorbent
 and prepare metal/biomass composites with the same modified biomass as
 direct template. Eggshell membrane (ESM) was selected and modified to
 adsorb heavy metals. Adsorption of metal ions on the modified ESM (MESM)
 might be attributed to electrostatic interaction, ion exchange and
 coordination effect with chelating ligands containing N and S on the
 surface of MESM. pH of solution was a key factor to affect the adsorption.
 The Cu-Ag/MESM composites with uniform Cu-Ag NPs were prepared with MESM
 as matrices, and with Cu2+ and Ag+ adsorbed as metal sources. The
 Cu-Ag/MESM showed excellent catalytic performance in the reduction of
 4-nitrophenol to 4-aminophenol in aqueous phase. Because of the high
 stability of the Cu-Ag NPs supported on the macro-dimension supporter,
 Cu-Ag/MESM can be easily separated after the catalytic reaction and
 recycled.
description: Adsorption of heavy
 metal with modified eggshell membrane and in situ synthesis of Cu-Ag/MESM
 compositesorigin.rar