cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.731fm
title: Data from: Evidence for parasite-mediated selection during short-lasting toxic algal blooms

description: Parasites play a role in the control of transient algal blooms, but it is
 not known whether parasite-mediated selection results in coevolution of
 the host and the parasites over this short time span. We investigated the
 presence of coevolution between the toxic dinoflagellate Alexandrium
 minutum and two naturally occurring endoparasites during blooms lasting a
 month in two river estuaries, using cross-inoculation experiments across
 time and space. Higher parasite abundance was associated with a large
 daily reduction in relative A. minutum abundances, demonstrating strong
 parasite-mediated selection. There was genetic variability in infectivity
 in both parasite species, and in resistance in the host. We found no
 evidence for coevolution in one estuary; however, in the other estuary, we
 found high genetic diversity in the two parasite species, fluctuations in
 infectivity and suggestion that the two parasites are well adapted to
 their host, as in ‘Red Queen’ dynamics. Thus, coevolution is possible over
 the short time span of a bloom, but geographically variable, and may
 feedback on community dynamics.
description: dataall.csv contains the
 results of cross-inoculation experiments; each line is a specific parasite
 * host combination. The column "Virulence" is infectivity (0 or
 1) Variables_dynamique.xlsx contains host and parasite population sizes
 population_sizes_dynamics contains R code to analyse the dynamics of host
 and parasite populations correlations_and_nestedness contains R code to
 analyse the infectivity matrices (analyses ii to iv in the paper)
 temporal_trends_infectivity contains R code to analyse temporal trends in
 infectivity (analysis v in the paper)
DOI: 10.5061/dryad.md712
title: Data from: Linking phenological events in migratory passerines with a changing climate: 50 years in the Laurel Highlands of Pennsylvania

description: Advanced timing of both seasonal migration and reproduction in birds has
 been strongly associated with a warming climate for many bird species.
 Phenological responses to climate linking these stages may ultimately
 impact fitness. We analyzed five decades of banding data from 17 migratory
 bird species to investigate 1) how spring arrival related to timing of
 breeding, 2) if the interval between arrival and breeding has changed with
 increasing spring temperatures, and 3) whether arrival timing or breeding
 timing best predicted local productivity. Four of 17 species, all mid- to
 long-distance migrants, hatched young earlier in years when migrants
 arrived earlier to the breeding grounds (~1:1 day advancement). The
 interval between arrival on breeding grounds and appearance of juveniles
 shortened with warmer spring temperatures for 12 species (1-6 days for
 every 1ºC increase) and over time for seven species (1-8 days per decade),
 suggesting that some migratory passerines adapt to climate change by
 laying more quickly after arrival or reducing the time from laying to
 fledging. We found more support for the former, that the rate of
 reproductive advancement was higher than that for arrival in warm years.
 Timing of spring arrival and breeding were both poor predictors of avian
 productivity for most migrants analyzed. Nevertheless, we found evidence
 that fitness benefits may occur from shifts to earlier spring arrival for
 the multi-brooded Song Sparrow. Our results uniquely demonstrate that
 co-occurring avian species are phenologically plastic in their response to
 climate change on their breeding grounds. If migrants continue to show a
 weaker response to temperatures during migration than breeding, and the
 window between arrival and optimal breeding shortens further, biological
 constraints to plasticity may limit the ability of species to adapt
 successfully to future warming.
description: McDermott and DeGroote
 raw data PLOS ONEData were collected at a
 bird banding station in Pennsylvania and are summarized by year. Species
 codes are standard four letter abbreviations
 (http://www.birdpop.org/docs/misc/Alpha_codes_eng.pdf). Variables
 beginning with X are temperature means in three week intervals (see
 manuscript text). The following 3 numbers correspond to the month and day
 at the beginning of the interval. The other column headings are explained
 in the Methods section.
DOI: 10.5061/dryad.jb3tc
title: Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus)

description: Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys
 a worldwide distribution. While black rats and the house mouse tracked the
 regional development of human agricultural settlements, brown rats did not
 appear in Europe until the 1500s, suggesting their range expansion was a
 response to relatively recent increases in global trade. We inferred the
 global phylogeography of brown rats using 32 k SNPs, and detected 13
 evolutionary clusters within five expansion routes. One cluster arose
 following a southward expansion into Southeast Asia. Three additional
 clusters arose from two independent eastward expansions: one expansion
 from Russia to the Aleutian Archipelago, and a second to western North
 America. Westward expansion resulted in the colonization of Europe from
 which subsequent rapid colonization of Africa, the Americas and
 Australasia occurred, and multiple evolutionary clusters were detected. An
 astonishing degree of fine-grained clustering between and within sampling
 sites underscored the extent to which urban heterogeneity shaped genetic
 structure of commensal rodents. Surprisingly, few individuals were recent
 migrants, suggesting that recruitment into established populations is
 limited. Understanding the global population structure of R. norvegicus
 offers novel perspectives on the forces driving the spread of zoonotic
 disease, and aids in development of rat eradication programmes.
description: Puckett_etal_RatPhylogeog_SNPs.tarSNPs (l=32,127) discovered from a ddRAD-Seq project with Rattus norvegicus (n=314) and Rattus rattus (n=33) samples from around the world. SNPs are aligned to the Rattus norvegicus Rnor_6.0 genome and provided as binary PLINK files (.bed, .bim, .fam). See Tables S1 and S2 of the manuscript for locations for each sample name.Puckett_etal-RatPhylogeog-MitoHaplotypesMitochondrial SNP haplotypes produced from ddRAD-Seq data. We identified 104 haplotypes in 144 brown rat (Rattus norvegicus) samples, that group into 10 clades. SNP positions found in Table S3 of the manuscript. Geographic distribution of haplotypes in Table S4 of the manuscript.
DOI: 10.5061/dryad.j316c
title: Data from: A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution

description: Gracillariidae are one of the most diverse families of internally feeding
 insects, and many species are economically important. Study of this family
 has been hampered by lack of a robust and comprehensive phylogeny. In the
 present paper, we sequenced up to 22 genes in 96 gracillariid species,
 representing all previously recognized subfamilies and genus groups, plus
 20 outgroups representing other families and superfamilies. Following
 objective identification and removal of two rogue taxa, two datasets were
 constructed: dataset 1, which included 12 loci totalling 9927 bp for 94
 taxa, and dataset 2, which supplemented dataset 1 with 10 additional loci
 for 10 taxa, for a total of 22 loci and 16 167 bp. Maximum likelihood
 analyses strongly supported the monophyly of Gracillariidae and most
 previously recognized subfamilies and genus groups. On this basis, we
 propose a new classification consisting of eight subfamilies, four of
 which are newly recognized or resurrected: Acrocercopinae Kawahara
 & Ohshima subfam. n.; Gracillariinae Stainton; Lithocolletinae
 Stainton; Marmarinae Kawahara & Ohshima subfam. n.;
 Oecophyllembiinae Réal & Balachowsky; Parornichinae Kawahara
 & Ohshima subfam. n.; Ornixolinae Kuznetzov & Baryshnikova
 stat. rev.; and Phyllocnistinae Zeller. The subfamily Gracillariinae is
 restricted to the monophyletic group comprising Gracillaria Haworth and
 closely related genera. We also formally transfer Acrocercops scriptulata
 Meyrick to Ornixolinae and use the name Diphtheroptila Vári, creating
 Diphtheroptila scriptulata comb. n. An exploratory mapping of larval
 host-use traits on the phylogeny shows strong conservation of modes of
 leaf mining but much higher lability of associations with host plant
 orders and families, suggesting that host shifts could play a significant
 role in gracillariid diversification.
description: 10genes_nt12312genes_degen112genes_nt12322genes_degen122genes_nt123
DOI: 10.5061/dryad.4c3g9
title: Data from: PrimerMiner: an R package for development and in silico validation of DNA metabarcoding primers

description: 1. DNA metabarcoding is a powerful tool to assess biodiversity by
 amplifying and sequencing a standardized gene marker region. Its success
 is often limited due to variable binding sites that introduce
 amplification biases. Thus the development of optimized primers for
 communities or taxa under study in a certain geographic region and/or
 ecosystems is of critical importance. However, no tool for obtaining and
 processing of reference sequence data in bulk that can serve as a backbone
 for primer design is currently available. 2. We developed the R package
 PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD
 and NCBI databases for specified target taxonomic groups and then applies
 sequence clustering into operational taxonomic units (OTUs) to reduce
 biases introduced by the different number of available sequences per
 species. Additionally, PrimerMiner offers functionalities to evaluate
 primers in silico, which are in our opinion more realistic then the
 strategy employed in another available software for that purpose, ecoPCR.
 3. We used PrimerMiner to download cytochrome c oxidase subunit I (COI)
 sequences for 15 important freshwater invertebrate groups, relevant for
 ecosystem assessment. By processing COI markers from both databases, we
 were able to increase the amount of reference data 249-fold on average,
 compared to using complete mitochondrial genomes alone. Furthermore, we
 visualized the generated OTU sequence alignments and describe how to
 evaluate primers in silico using PrimerMiner. 4. With PrimerMiner we
 provide a useful tool to obtain relevant sequence data for targeted primer
 development and evaluation. The OTU based reference alignments generated
 with PrimerMiner can be used for manual primer design, or processed with
 bioinformatic tools for primer development.
description: COI Folmer
 regionReference OTU sequence
 alignments of the Folmer COI barcoding region for 15 relevant freshwater
 taxa (Downloaded with PrimerMiner April 2015)COI Primer
 bindReference OTU sequence
 alignments of the HCO / LCO Folmer primer binding regions barcoding region
 for 15 relevant freshwater taxa (Downloaded with PrimerMiner February
 2015, 26 bp trimming applied to sequences before
 clustering)
DOI: 10.34810/data2518
title: Partitura i enregistrament [partitura y grabación] Sonata en Re menor / D minor, d'autor anònim / de autor anónimo [ca. 1780-1790]

description: &lt;br&gt;[CAT] Sota el marc del projecte Estudi i Recuperació de Patrimoni Musical que està desenvolupant la UB i el CSIC, juntament amb el CRAI Biblioteca de Fons Antic de la Universitat de Barcelona, el Grup per a l'Estudi del Patrimoni Musical (GEPAM), el Grup de Recerca Patrimoni Musical Històric de la Institució Milà i Fontanals d'Investigació en Humanitats del CSIC, l'Arquebisbat de Barcelona, la Catedral de Barcelona, l'Arxiu de l'Església de Santa Maria del Pi i l'Oratori de Sant Felip Neri de Barcelona, ha recuperat una peça musical de Carles Baguer (1768-1808) que es troba al manuscrit MS. 1378 del fons musical del CRAI Biblioteca de Fons Antic de la Universitat de Barcelona. 
Aquest conjunt de dades conté dos arxius:

&lt;br&gt;- Transcripció de la Sonata en Re menor, d'autor anònim, del manuscrit Ms. 1378.

&lt;br&gt;- Enregistrament del so de la peça interpretada per: Roger Illa Prats, amb un piano A. Walter de 1803 (còpia moderna de Paul Poletti).

&lt;br&gt;[ESP]El proyecto Estudio y Recuperación del Patrimonio Musical que desarrollan la UB y el CSIC, junto con el CRAI Biblioteca de Fons Antic de la Universitat de Barcelona, el Grupo de Investigación Patrimonio Musical Histórico de la Institución Milá y Fontanals de Investigación en Humanidades del CSIC, la Archidiócesis de Barcelona, la Catedral de Barcelona, el Arxiu de l'Església de Santa Maria del Pi y el Oratorio de Sant Felip Neri de Barcelona, ha recuperado Patrimonio musical: pieza musical de Carles Baguer (1768-1808) que se encuentra en el manuscrito Ms.1378 de la colección de música del CRAI Biblioteca de Fons Antic de la Universitat de Barcelona. 
Este conjunto de datos contiene dos archivos:

&lt;br&gt;- Transcripción de la Sonata en Re menor, d'autor anónimo, del manuscrito Ms. 1378.

&lt;br&gt;- Grabación sonora de la pieza interpretada por: Roger Illa Prats, con un piano A. Walter de 1803 (copia moderna de Paul Poletti).
DOI: 10.5061/dryad.92h5d
title: Data from: Tensor analysis reveals distinct population structure that parallels the different computational roles of areas M1 and V1

description: Cortical firing rates frequently display elaborate and heterogeneous
 temporal structure. One often wishes to compute quantitative summaries of
 such structure—a basic example is the frequency spectrum—and compare with
 model-based predictions. The advent of large-scale population recordings
 affords the opportunity to do so in new ways, with the hope of
 distinguishing between potential explanations for why responses vary with
 time. We introduce a method that assesses a basic but previously
 unexplored form of population-level structure: when data contain responses
 across multiple neurons, conditions, and times, they are naturally
 expressed as a third-order tensor. We examined tensor structure for
 multiple datasets from primary visual cortex (V1) and primary motor cortex
 (M1). All V1 datasets were ‘simplest’ (there were relatively few degrees
 of freedom) along the neuron mode, while all M1 datasets were simplest
 along the condition mode. These differences could not be inferred from
 surface-level response features. Formal considerations suggest why tensor
 structure might differ across modes. For idealized linear models,
 structure is simplest across the neuron mode when responses reflect
 external variables, and simplest across the condition mode when responses
 reflect population dynamics. This same pattern was present for existing
 models that seek to explain motor cortex responses. Critically, only
 dynamical models displayed tensor structure that agreed with the empirical
 M1 data. These results illustrate that tensor structure is a basic feature
 of the data. For M1 the tensor structure was compatible with only a subset
 of existing models.
description: Tensor
 dataMATLAB data structure
 containing all analyzed data.datastruct.mat
DOI: 10.5061/dryad.jm654
title: Data from: Development of Diversity Arrays Technology markers as a tool for rapid genomic assessment in Nile tilapia, Oreochromis niloticus

description: The development of genomic markers is described for Nile tilapia,
 Oreochromis niloticus, using the Diversity Arrays Technology (DArT)
 genotype-by-sequencing platform. A total of 13 215 single nucleotide
 polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were
 identified from broodstock of two selective breeding programs [Genetically
 Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain
 from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985
 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa
 strains respectively. We demonstrate the potential utility of these
 markers for rapid genomic screening and use in breeding programs.
description: SNP genotypes,
 silicoDArT genotypes, and respective metadata of GIFT and Abbassa strains
 of Nile tilapiaData file containing
 13,215 SNP and 12,490 silicoDArT genotype scores and respective marker
 sequence and metadata information for 188 Nile tilapia (Oreochromis
 niloticus). Samples are taken from the GIFT strain and the Abbassa strain
 selective breeding program nucleus populations managed and run by
 WorldFish in Malaysia and Egypt, respectively.DRYAD-Report-DTi15-1800-recoded.xlsx
DOI: 10.5061/dryad.52mt5
title: Data from: Effectiveness of complementary food supplement and dietary counseling on anemia and stunting in children aged 6-23 months in poor areas in Qinghai Province, China: a controlled interventional study

description: Objective: To assess the effectiveness of dietary counseling and
 complementary food supplements on anemia and stunting prevalence in
 children aged 6-23 months. Design: A controlled intervention study with
 measurements of height and hemoglobin levels, and cross-sectional surveys
 in August 2012 (baseline) and 2013 and 2014 (end-line). Setting: One
 intervention and control county in rural Qinghai Province, China.
 Intervention: Complementary food supplements (containing protein, fat,
 carbohydrate, vitamin A, B1, B2, B12, D3, folic acid, iron, zinc, and
 calcium) and complementary feeding counseling were given in the
 intervention county. Participants: Caregivers and their children aged 6-23
 months. Primary and secondary outcomes measures: The effect of the
 interventions on anemia (hemoglobin&lt; 110g/L) and stunting (z-score
 of height-for-age&lt; -2.0) prevalence(controlled for differences
 between the counties), and infant feeding practices. Results: The surveys
 were conducted among 1804, 2187, and 2186 child aged 6-23 months in the
 intervention county in August 2012, 2013 and 2014 respectively, and 804,
 680 and 790 children in the control county respectively. Between baseline
 and end-line, anemia prevalence decreased more in the intervention county
 compared to the control county (71.1% to 47.8% vs 86.3% to 75.3%,
 respectively; P&lt;0.0001). There was no difference in the decrease in
 stunting prevalence between the counties (9.7% to 7.1% vs 17.0% to 15.0%;
 P=0.7954). The proportions of children given iron-rich or -fortified food,
 introduced (semi-) solid food at 6-8 months, and given food with minimum
 dietary diversity increased from 43.2% to 88.8% (P&lt;0.0001), 81.4%
 to 96% (P=0.0470), and 53.0% to 59.8% (P&lt;0.0001), respectively.
 Conclusions: We found much higher anemia prevalence in poor rural areas of
 Qinghai Province compared to national data. Community-based complementary
 food supplements combined with dietary counseling can improve feeding
 practices and reduce anemia prevalence. Future studies should use longer
 follow-up to assess the effects on stunting.
description: Data of YYB
 surveysIncluding all related
 data in the paper
DOI: 10.5061/dryad.92tn2
title: Data from: Nonlinear scaling of foraging contacts with rodent population density

description: Density-dependent shifts in population processes like territoriality,
 reproduction, dispersal, and parasite transmission are driven by changes
 in contacts between individuals. Despite this, surprisingly little is
 known about how contacts change with density, and thus the mechanisms
 driving density-dependent processes. A simple linear contact-density
 function is often assumed, but this is not based on a sound basis of
 empirical data. We addressed this question using a replicated,
 semi-natural experiment in which we measured contacts at feeding stations
 between multimammate mice, Mastomys natalensis, across ten distinct,
 linearly increasing densities between 10 and 272 animals/ha. Unexpectedly,
 unique contacts increased not linearly but sigmoidally with density, which
 we attribute to the species’ scramble competition mating system,
 small-scale dominance/avoidance and absence of territoriality. These
 results provide new insights into how species’ characteristics can relate
 to density-dependent changes in contacts, and the unexpected shape of the
 contact-density function warrants that density-dependence in ecological
 models, such as parasite transmission models, must be parameterized with
 care.
description: Borremans2015_VisitationDataBorremans2015_AttributeData
DOI: 10.5061/dryad.78qq7
title: Data from: QTL analysis of soft scald in two apple populations

description: The apple (Malus×domestica Borkh.) is one of the world’s most widely grown
 and valuable fruit crops. With demand for apples year round, storability
 has emerged as an important consideration for apple breeding programs.
 Soft scald is a cold storage-related disorder that results in sunken,
 darkened tissue on the fruit surface. Apple breeders are keen to generate
 new cultivars that do not suffer from soft scald and can thus be marketed
 year round. Traditional breeding approaches are protracted and labor
 intensive, and therefore marker-assisted selection (MAS) is a valuable
 tool for breeders. To advance MAS for storage disorders in apple, we used
 genotyping-by-sequencing (GBS) to generate high-density genetic maps in
 two F1 apple populations, which were then used for quantitative trait
 locus (QTL) mapping of soft scald. In total, 900 million DNA sequence
 reads were generated, but after several data filtering steps, only 2% of
 reads were ultimately used to create two genetic maps that included 1918
 and 2818 single-nucleotide polymorphisms. Two QTL associated with soft
 scald were identified in one of the bi-parental populations originating
 from parent 11W-12-11, an advanced breeding line. This study demonstrates
 the utility of next-generation DNA sequencing technologies for QTL mapping
 in F1 populations, and provides a basis for the advancement of MAS to
 improve storability of apples.
description: dryad_McClure_et_al_sept2016Data to accompany "QTL analysis of soft scald in two apple populations" published online 14 September 2016 in Horticulture Research, by McClure et al. (doi:10.1038/hortres.2016.43)