cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.59645
title: Data from: Patterns of selection on Plasmodium falciparum erythrocyte binding antigens after the colonisation of the New World

description: Pathogens, which have recently colonized a new host species or new
 populations of the same host, are interesting models for understanding how
 populations may evolve in response to novel environments. During its
 colonization of South America from Africa Plasmodium falciparum, the main
 agent of malaria, has been exposed to new conditions in distinctive new
 human populations (Amerindian and populations of mixed origins), that
 likely exerted new selective pressures on the parasite's genome.
 Among the genes that might have experienced strong selective pressures in
 response to these environmental changes, the eba genes (erythrocyte
 binding antigens genes), which are involved in the invasion of the human
 red blood cells, constitute good candidates. In this study, we analyzed,
 in South America, the polymorphism of three eba genes (eba-140, eba-175,
 eba-181) and compared it to the polymorphism observed in African
 populations. The aim was to determine whether these genes faced selective
 pressures in South America distinct from what they experienced in Africa.
 Patterns of genetic variability of these genes were compared to the
 patterns observed at two housekeeping genes (adsl and serca) and 272 SNPs
 to separate adaptive effects from demographic effects. We show that,
 conversely to Africa, eba-140 seemed to be under stronger diversifying
 selection in South America than eba-175. In contrast, eba-181 did not show
 any sign of departure from neutrality. These changes in the patterns of
 selection on the eba genes could be the consequence of changes in the host
 immune response, the host receptor polymorphisms, and / or the ability of
 the parasite to silence or express differentially its invasion proteins.
description: 272 SNP dataset_South
 America_Yalcindag272 SNPs from South
 American populationsadsl_sequencesSequences alignment of adsl geneserca_sequencesSequences alignment of serca geneeba140_sequencesSequences alignment of eba-140 geneeba175_sequencesSequences alignment of eba-175 geneeba181_sequencesSequences alignment of eba-181 geneSupp table 1 Yalcindag et alSampling details for each population
DOI: 10.15468/dl.5paran
title: Occurrence Download

description: A dataset containing 19158 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.27327 43.24908,3.31744 43.24908,3.31744 43.27665,3.27327 43.27665,3.27327 43.24908))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 19158 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001608-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5jhzew
title: Occurrence Download

description: A dataset containing 3741 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Teleogryllus emma"
 ]
}

 The dataset includes 3741 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001610-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jt2b5
title: Data from: Programmed death in a unicellular organism has species-specific fitness effects

description: Programmed cell death (PCD) is an ancient phenomenon and its origin and
 maintenance in unicellular life is unclear. We report that programmed
 death provides differential fitness effects that are species specific in
 the model organism Chlamydomonas reinhardtii. Remarkably, PCD in this
 organism not only benefits others of the same species, but also has an
 inhibitory effect on the growth of other species. These data reveal that
 the fitness effects of PCD can depend upon genetic relatedness.
description: Absorbance
 dataRaw data of absorbances
 of culture relating to Fig 2 in main textcount
 dataCell count raw data for
 Fig 2 in main text
DOI: 10.5061/dryad.m0204
title: Data from: Genetic analysis of safflower domestication

description: Background: Safflower (Carthamus tinctorius L.) is an oilseed crop in the
 Compositae (a.k.a. Asteraceae) that is valued for its oils rich in
 unsaturated fatty acids. Here, we present an analysis of the genetic
 architecture of safflower domestication and compare our findings to those
 from sunflower (Helianthus annuus L.), an independently domesticated
 oilseed crop within the same family. We mapped quantitative trait loci
 (QTL) underlying 24 domestication-related traits in progeny from a cross
 between safflower and its wild progenitor, Carthamus palaestinus Eig.
 Also, we compared QTL positions in safflower against those that have been
 previously identified in cultivated x wild sunflower crosses to identify
 instances of colocalization. Results: We mapped 61 QTL, the vast majority
 of which (59) exhibited minor or moderate phenotypic effects. The two
 large-effect QTL corresponded to one each for flower color and leaf
 spininess. A total of 14 safflower QTL colocalized with previously
 reported sunflower QTL for the same traits. Of these, QTL for three traits
 (days to flower, achene length, and number of selfed seed) had cultivar
 alleles that conferred effects in the same direction in both species.
 Conclusions: As has been observed in sunflower, and unlike many other
 crops, our results suggest that the genetics of safflower domestication is
 quite complex. Moreover, our comparative mapping results indicate that
 safflower and sunflower exhibit numerous instances of QTL colocalization,
 suggesting that parallel trait transitions during domestication may have
 been driven, at least in part, by parallel genotypic evolution at some of
 the same underlying genes.
description: C. palaestinus
 transcriptome assemblyAssembly is based on RNA
 extracted from leaves, florets, and ovules of PI 235663Cpal_miracap_assembly.fasta
DOI: 10.5061/dryad.b5d6b
title: Data from: Phylogeography of Heliconius cydno and its closest relatives: disentangling their origin and diversification

description: The origins of phenotypic variation within mimetic Heliconius butterflies
 have long fascinated biologists and naturalists. However, the evolutionary
 processes that have generated this extraordinary diversity remain
 puzzling. Here we examine intraspecific variation across Heliconius cydno
 diversification and compare this variation to that within the closely
 related H. melpomene and H. timareta radiations. Our data, which consist
 of both mtDNA and genome scan from nearly 2250 AFLP loci, reveal a complex
 history of differentiation and admixture at different geographic scales.
 Both mtDNA and AFLP phylogenies suggest that H. timareta and H. cydno are
 probably geographic extremes of the same radiation that likely diverged
 from H. melpomene during the Pliocene-Pleistocene boundary. MtDNA suggest
 that this radiation originated in Central America or the Northwestern
 region of South America, with a subsequent colonization of the eastern and
 western slopes of the Andes. Our genome-scan data indicate significant
 admixture among sympatric H. cydno/H.timareta and H. melpomene populations
 across the extensive geographic ranges of the two radiations. Within H.
 cydno, both mtDNA and AFLP data indicate significant population structure
 at local scales, with strong genetic differences even among adjacent H.
 cydno color pattern races. These genetic patterns highlight the importance
 of past geoclimatic events, intraspecific gene flow, and local population
 differentiation in the origin and establishment of new adaptive forms.
description: AFLP Data:
 Phylogeography of Heliconius cydno and its closest relatives-
 disentangling their origin and diversificationArlequin data file with
 2257 polymorphic AFLP loci for 194 individuals representing H. cydno, H.
 timareta and H. melpomene radiation.AriasCetal2014AFLPdata.arpAriasCetal2014CO1alignmentCO1 Beast Tree FilemtDNA-CO1 Trees File: a subset of 1001trees from Beast analysisAriasCetal2014CO1tree1001.nexAFLP structure input fileAFLP input file for STRUCTURE analysisAriasetal2014AFLPstructure-inputArlequin AFLP input fileAFLP data: Input file for Arlequin analysisAriasetal2014AFLPArlequin-input.arpmtDNA-CO1 Arlequin Input FilemtDNA-CO1 input file for Arlequin AnalysisAriasetal2014mtDNAArlequin-input.arp
DOI: 10.5061/dryad.tp979
title: Data from: Evolutionary constraints in high-dimensional trait sets

description: Genetic variation for individual traits is typically abundant, but for
 some multivariate combinations it is very low, suggesting that
 evolutionary limits might be generated by the geometric distribution of
 genetic variance. To test this prediction, we artificially selected along
 all eight genetic eigenvectors of a set of eight quantitative traits in
 Drosophila serrata. After six generations of 50% truncation selection, at
 least one replicate population of all treatments responded to selection,
 allowing us to reject a null genetic subspace as a cause of evolutionary
 constraint in this system. However, while all three replicate populations
 of the first five selection treatments displayed a significant response,
 the remaining three, characterized by low genetic variance in their
 selection indexes in the base population, displayed inconsistent responses
 to selection. The observation that only four of the nine replicate
 populations evolved in response to the direct selection applied to them in
 these low genetic variance treatments, led us to conclude that a nearly
 null subspace did limit evolution. Dimensions associated with low genetic
 variance are often found in multivariate analyses of standing genetic
 variance in morphological traits, suggesting that the nearly null genetic
 subspace may be a common mechanism of evolutionary constraint in nature.
description: Half-sib genetic design
 dataThis file contains CHC
 log contrast data of male Drosophila serrata and their pedigree from a
 half-sib genetic design. The flies came from a lab-adapted population
 derived from a natural population in Brisbane,
 Australia.CHCdataRED.csvSelection experiment dataThis file contains the CHC log contrast data of Drosophila serrata males from the artificial selection experiment.log contrasts all blocks - batch and control corrected.csvSelection indicesThis file contains the eight indices (T1 to T8) used in the artificial selection experiment on the CHC log contrasts.selection indices.xlsx
DOI: 10.5061/dryad.hd765
title: Data from: Discovery of a relict lineage and monotypic family of passerine birds

description: Analysis of one of the most comprehensive datasets to date of the largest
 passerine bird clade, Passerida, identified 10 primary well-supported
 lineages corresponding to Sylvioidea, Muscicapoidea, Certhioidea,
 Passeroidea, the ‘bombycillids’ (here proposed to be recognized as
 Bombycilloidea), Paridae/Remizidae (proposed to be recognized as
 Paroidea), Stenostiridae, Hyliotidae, Regulidae (proposed to be recognized
 as Reguloidea) and spotted wren-babbler Spelaeornis formosus. The latter
 was found on a single branch in a strongly supported clade with
 Muscicapoidea, Certhioidea and Bombycilloidea, although the relationships
 among these were unresolved. We conclude that the spotted wren-babbler
 represents a relict basal lineage within Passerida with no close extant
 relatives, and we support the already used name Elachura formosa and
 propose the new family name Elachuridae for this single species.
description: Photos of Elachura
 formosa, Jiangxi, ChinaPhotos of Elachura
 formosa, Wuyi Shan, Jiangxi province, China, April 2013. DNA sample number
 IOZ 18251. Photos: Per AlstromElachura formosa
 Jiangxi.zipPhotos of Elachura
 formosa, Arunachal Pradesh, IndiaPhotos of Elachura
 formosa, Arunachal Pradesh, India. Sample number DH56. Photos: Daniel
 Hooper.Elachura formosa Arunachal
 Pradesh, India.zipSong of Elachura
 formosa, Fujian, ChinaSong of Elachura
 formosa, Wuyi Shan, Fujian province, China, April 1993. Recording: Per
 AlstromElachura formosa Wuyi Shan,
 Fujian, China, April 1993 Per
 Alstrom.wavDNA
 alignmentDNA alignment, all loci,
 with script for MrBayes analysis.Elachuridae matrix All
 loci.nexSamples and GenBank
 accession numbers ElachuridaeDetails of samples and
 GenBank accession numbers.
DOI: 10.5061/dryad.2n9g6
title: Data from: Analysis and prediction of effects of the Manchester Triage System on patient waiting times in an emergency department by means of agent-based simulation

description: A simulation of complex clinical processes is a challenging task and
 suitable methods need to be found which can capture the influence of
 relevant factors and their relationships. The Manchester triage system
 (MTS) is widely used in German emergency departments (ED), however the
 impact on patient waiting times remain difficult to predict. The purpose
 of this work is the assessment of MTS particularly with regard to the
 waiting times of different degrees of severity. The methodology of agent
 based simulation was found suitable for the ED domain and the agent based
 simulation tool SeSAm was chosen due to its intuitive user interface and
 easy adaption of the simulation models. Altogether four agent classes
 could be implemented based on the information derived from a process
 model. The model permits a dynamic simulation of the ED processes and a
 reliable assessment of patient waiting times. In addition, the
 implementation of a triage nurse allowed the simulation of the triage
 process and a direct comparison to the current state without a
 standardized triage procedure. Essential influencing factors (e.g. number
 of patients, manning level) were implemented and their effects on the ED
 processes and patient waiting times assessed. The simulation runs
 delivered correct results based on the underlying process model and the
 collected statistical data. The process flow and the waiting times of an
 ED could be mapped exactly. In all simulation runs the waiting times of
 high triage levels (MTS-levels 1 and 2) could be reduced. Especially
 patients of MTS-level 2 in the waiting area of the ED benefit
 significantly from the implementation of a standardized triage procedure
 and the associated permanent monitoring.
description: The simulation tool,
 simulation runs and results.ReadMeSimulation.zip
DOI: 10.5061/dryad.8kk36
title: Data from: Gallium-mediated siderophore quenching as an evolutionarily robust antibacterial treatment

description: Background and objectives: Conventional antibiotics select strongly for
 resistance and are consequently losing efficacy worldwide. Extracellular
 quenching of shared virulence factors could represent a more promising
 strategy because (a) it reduces the available routes to resistance (since
 extracellular action precludes any mutations blocking a drug's entry
 into cells or hastening its exit) and (b) it weakens selection for
 resistance, since fitness benefits to emergent mutants are diluted across
 all cells in a cooperative collective. Here, we tested this hypothesis
 empirically. Methodology: We used gallium to quench the iron-scavenging
 siderophores secreted and shared among pathogenic Pseudomonas aeruginosa
 bacteria, and quantitatively monitored its effects on growth in vitro. We
 assayed virulence in acute infections of caterpillar hosts (Galleria
 mellonella), and tracked resistance emergence over time using experimental
 evolution. Results: Gallium strongly inhibited bacterial growth in vitro,
 primarily via its siderophore quenching activity. Moreover, bacterial
 siderophore production peaked at intermediate gallium concentrations,
 indicating additional metabolic costs in this range. In vivo, gallium
 attenuated virulence and growth – even more so than in infections with
 siderophore-deficient strains. Crucially, while resistance soon evolved
 against conventional antibiotic treatments, gallium treatments retained
 their efficacy over time. Conclusions: Extracellular quenching of
 bacterial public goods could offer an effective and evolutionarily robust
 control strategy.
description: Primary data for all
 figures and analysesThis file contains all
 primary data used to generate the figures and analyses in the article. The
 file is in Excel format, with separate sheets for each
 figure.Ross-Gillespie_et_al_2014_EMPH_RawData.xlsx
DOI: 10.7910/dvn/xs7jo5
title: SIEX 35443 - Bioprospecção de linhagens de Sorgo e Milho com potencial para resistência ao Meloidogyne incognita

description: Os nematoides constituem um dos principais desafios fitossanitários da agricultura brasileira, exigindo a adoção integrada de diferentes estratégias de manejo para possibilitar a redução efetiva das suas populações no campo. O controle genético é uma das estratégias mais importantes para o manejo dos nematoides, pois pode ser aplicada em grandes extensões de terras e não possuem toxicidade ao meio ambiente e aos seres humanos. Entretanto, para que os produtores tenham acesso aos cultivares altamente produtivos e resistentes aos nematoides, é necessário que as
empresas de melhoramento genético direcionem seus esforços no desenvolvimento desses cultivares resistentes. Sendo assim, Parceria Público-Privada (PPP) possibilitam alinhar as necessidades das empresas do setor produtivo em acompanhar os avanços tecnológicos, com as Universidades, que podem apoiar o uso de inovações relevantes para o sistema agrícola. Empresas de melhoramento genético demandam de ensaios de bioprospecção de híbridos de sorgo e milho com potencial resistência a nematoides. Tais ensaios apresentam elevada complexidade e requerem expertise técnica para sua correta execução.
DOI: 10.5061/dryad.hq564
title: Data from: The life cycle of Drosophila orphan genes

description: Orphans are genes restricted to a single phylogenetic lineage and emerge
 at high rates. While this predicts an accumulation of genes, the gene
 number has remained remarkably constant through evolution. This paradox
 has not yet been resolved. Because orphan genes have been mainly analyzed
 over long evolutionary time scales, orphan loss has remained unexplored.
 Here we study the patterns of orphan turnover among close relatives in the
 Drosophila obscura group. We show that orphans are not only emerging at a
 high rate, but that they are also rapidly lost. Interestingly, recently
 emerged orphans are more likely to be lost than older ones. Furthermore,
 highly expressed orphans with a strong male-bias are more likely to be
 retained. Since both lost and retained orphans show similar evolutionary
 signatures of functional conservation, we propose that orphan loss is not
 driven by high rates of sequence evolution, but reflects lineage specific
 functional requirements.
description: Gene features in
 Drosophila pseudoobscuraSupplementary_File_4.xlsx
DOI: 10.5061/dryad.3kn08
title: Data from: Glacial history of the European marine mussels Mytilus, inferred from distribution of mitochondrial DNA lineages

description: Mussels of the genus Mytilus have been used to assess the circumglacial
 phylogeography of the intertidal zone. These mussels are representative
 components of the intertidal zone and have rapidly evolving mitochondrial
 DNA, suitable for high resolution phylogeographic analyses. In Europe, the
 three Mytilus species currently share mitochondrial haplotypes, owing to
 the cases of extensive genetic introgression. Genetic diversity of Mytilus
 edulis, Mytilus trossulus and Mytilus galloprovincialis was studied using
 a 900-bp long part of the most variable fragment of the control region
 from one of their two mitochondrial genomes. To this end, 985 specimens
 were sampled along the European coasts, at sites ranging from the Black
 Sea to the White Sea. The relevant DNA fragments were amplified, sequenced
 and analyzed. Contrary to the earlier findings, our coalescence and nested
 cladistics results show that only a single M. edulis glacial refugium
 existed in the Atlantic. Despite that, the species survived the glaciation
 retaining much of its diversity. Unsurprisingly, M. galloprovincialis
 survived in the Mediterranean Sea. In a relatively short time period,
 around the climatic optimum at 10 ky ago, the species underwent rapid
 expansion coupled with population differentiation. Following the
 expansion, further contemporary gene flow between populations was limited.
description: Alignments of DNA
 sequences, input file for GeoDis, formatted MSN from Network software, and
 output from IM, IMa2The archive contain the
 README.txt file describing each file in detailsupplementary_data_files_HDY-13-OR0355R.zip
DOI: 10.5061/dryad.bq4p7
title: Data from: Population clustering and clonal structure evidence the relict state of Ulmus minor Mill. in the Balearic Islands

description: Field elm (Ulmus minor) is a riparian tree that grows in rare, small
 populations scattered along temporary watercourses in the Balearic
 Islands, nowadays mostly covered with Mediterranean vegetation.
 Agriculture and farming on the fertile land along the periodically flooded
 plains have reduced the elm populations to sparse tree lines along the
 creek beds. The presence of field elm in this very anthropic landscape has
 led some authors to consider it as an introduced species in the Balearics.
 However, pollen data suggest these elms may be the remains of larger
 populations experiencing continuous population shrinkage during the
 Holocene, and hence be native to the isles. In this paper, we apply
 genetic markers to assess whether field elm is or is not indigenous to the
 Balearic Islands. We compare the genetic variation in nine nuclear
 microsatellites of six Balearic populations (three in each of the largest
 islands, Majorca and Minorca) with that of three natural Iberian
 populations located in two regions, one geologically (Baetic mountains, SE
 Iberia) and another historically (Catalonia, NE Iberia) related to the
 islands. Principal coordinates analysis and Bayesian clustering methods
 reveal a strong genetic differentiation of the Balearic populations from
 the Iberian ones, and even among islands, which support their native
 origin. Genotypic variation in the islands is very low and clonal
 reproduction is very high compared with the mainland, as it is frequently
 observed in populations of clonal species where sexual reproduction is
 limited. We discuss the practical implications of these findings for the
 conservation of elm genetic resources of these findings.
description: HDY-12_ORO379_nSSR_dataGenetic data and spatial coordinates from nine field populations of Ulmus minor Mill. located in Majorca and Minorca Islands (Balearics), Baetic mountains in SE Iberia and Catalonia in NE Iberia. DNA extracted from fresh tissue was amplified by nine microsatellite loci, six of them specifically developed for Ulmus minor (Ulmi1-11, Ulmi1-21, Ulmi1-98, Ulmi1-165, Ulmi2-16 and Ulmi2-20 (Collada et al., 2004)) and three developed for U. laevis (Ulm2, Ulm3 and Ulm8 (Whiteley et al 2003)). A Li-Cor 4300 sequencer (Li-Cor Biosciences, Lincoln, USA) was used to obtain banding profiles. Allele sizes given in base pairs were determined using the SequamarkTM molecular size standard (Invitrogen, Carlsbad, USA) and the software Gene ImagIR 3.56 (Scanalytics).