cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6d3v0
title: Data from: Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa

description: A sequestered germline in Metazoa has been argued to be an obstacle to
 lateral gene transfer (LGT), though few studies have specifically assessed
 this claim. Here we test the hypothesis that the origin of a sequestered
 germline reduced LGT events in Bilateria (i.e. triploblast lineages) as
 compared to early-diverging Metazoa (i.e. Ctenophora, Cnidaria, Porifera,
 and Placozoa). We analyze single-gene phylogenies generated with over 900
 species, sampled from among Bacteria, Archaea and Eukaryota to identify
 well-supported interdomain LGTs. We focus on interdomain LGT (i.e. those
 between prokaryotes and Metazoa) as systematic errors in single gene tree
 reconstruction create uncertainties for interpreting
 eukaryote-to-eukaryotes transfers. The breadth of the sampled Metazoa
 enables us to estimate the timing of LGTs, and to examine the pattern
 before vs. after the evolution of a sequestered germline. We identified 58
 LGTs found only in Metazoa and prokaryotes (i.e. bacteria and/or archaea),
 and 7 genes transferred from prokaryotes into Metazoa plus one other
 eukaryotic clade. Our analyses indicate that more interdomain transfers
 occurred before the development of a sequestered germline, consistent with
 the hypothesis that this feature is an obstacle to LGT.
description: OG# to Protein
 ListAn excel file listing
 the protein name, abbreviation, found KEGG function (if known), and the
 corresponding OG5 number of the alignment for all 58 presence/absence
 lateral gene transfers found. Each animo acid sequence alignment file is
 labeled with a unique OG5#.OG_to_Protein_List.xlsxTopologies with two LGT EventsSingle gene trees in Newick format for the seven genes found with topologies consistent with two lateral gene transfers.Double_event_topologies.zipPresence/absence alignmentsAll 58 laterally transferred presence/absence animo acid sequence alignments found. Files are in text format.Presence_absence_alignments.zip
DOI: 10.5061/dryad.pq742
title: Data from: Indirect genetic effects and the genetic bases of social dominance: evidence from cattle

description: Genetic studies of social behaviour have currently received new impetus
 from models including indirect genetic effects (IGEs) of social partners.
 This study aimed at investigating the contribution of conspecifics in
 social dominance, considered as response of dyadic interaction that is,
 winning (dominant individual) or losing (subordinate). A genetic
 correlation of −1 is expected between the attitude to win and the attitude
 to loose, and because a population always accounts for half winners and
 half losers, the heritability of the dominant status should be close to
 zero. Specifically, social dominance was studied in Aosta Chestnut and
 Aosta Black Pied (Bos taurus) breeds, alpine rustic cattle famous for
 traditional tournaments where pairs of cows assess dominant status in
 bloodless fights. The outcomes of 25 590 dyadic interactions performed by
 8159 individuals in 11 years were analysed by applying a classical
 quantitative model and models including indirect effects. Data were
 analysed via Bayesian approach on a threshold trait. The assessment of
 variances revealed a genetic correlation of −0.976 between direct and
 indirect genetic components. The heritability measured on a liability
 scale was 0.122 for direct phenotype, but decreased to 0.014 when the
 total heritable variance (TBV) was considered. The trend of estimated
 breeding values showed that the total TBV was constant over the years,
 even though its direct component increased and the indirect part
 decreased. This result confirms the relevance of IGEs on social behaviour
 and the assumption that the mean individual social dominance cannot evolve
 within a population, due to the evolutionary constraints imposed by the
 ‘social environment’.
description: DataData utilized in the
 study. The zip folder contains the following files: Dataset, Pedigree,
 EBVs, ReadMe. More information on data are provided in the ReadMe file
 (within the zip folder or below).
DOI: 10.5061/dryad.q68m1
title: Data from: Prevalence and severity of asthmatic symptoms in Grenadian school children: the Grenada National Asthma Survey

description: Objective: The goal of this study was to determine the prevalence of
 asthma in school children in the tri-island Caribbean nation of Grenada.
 Setting, participants and outcomes: This was a self-report study provided
 to the guardians of all primary school children between ages 6 and 7
 throughout Grenada, Carriacou and Petite Martinique in 2013. Of the 2362
 surveys provided, 1374 were returned, resulting in a response rate of
 58.2%. Only responders listing birthdays between 1 January 2006 and 31
 December 2007 were included in the analysis, resulting in 1165 qualifying
 responders. Asthma diagnosis was based on previous physician diagnosed
 asthma and/or self-reported presence of wheeze in the past 12 months
 (current wheeze). Severity of asthma, medication usage, environmental
 exposures, physician and emergency department visits were compared among
 respondents. Results: The prevalence of wheezing in the past year was
 30.5±1.8%, and of these 68.4% were previously diagnosed with asthma. Of
 the current wheeze participants, 39.9±9.2% reported moderate to severe
 asthma symptoms and increased exposure to cigarette smoke, excessive dust,
 burning brush and landfills. Carriacou and Petite Martinique, the two
 smaller islands, had a lower incidence of current wheeze (14.1±7.7%) and
 exposure rates to cigarette smoke and burning brush as compared to the
 larger, denser island of Grenada. Although 65.7% of respondents diagnosed
 with asthma reported taking medication, the number of annual doctor and
 emergency department visits were high (2.82 and 0.86, respectively).
 Respondents with the most severe asthma symptoms reported the most
 emergency department visits with an average of 1.05 visits annually,
 whereas respondents with moderate asthma symptoms had the most doctor
 visits with an average of 3.33 visits annually. Conclusions: This study
 indicates that the prevalence of childhood asthma in Grenada is very high
 and warrants policy consideration in public health and education to
 decrease its morbidity.
description: Data from the first
 national asthma survey for the country of Grenada, West
 Indies.The data contains the
 self-reported, digitized, de-identified asthma survey results from parents
 on behalf of Grenadian school children between the ages of 6-7 from
 October to December 2013. The survey was based on the ISAAC study and thus
 designed to aid in cross-comparison with other countries and/or
 communities. Along with the data, please refer to a copy of the survey
 uploaded as the ReadMe file. Please address any questions to Mark Clunes,
 PhD (mclunes@sgu.edu).Grenada Asthma Survey
 Data.xlsx
DOI: 10.5061/dryad.t4p013r
title: Data from: Clade-limited colonization in brood parasitic finches (Vidua spp.)

description: The African brood parasitic finches (Vidua spp.) are host specialists that
 mimic the songs and nestling mouth markings of their finch hosts (family
 Estrildidae). Although recent molecular analyses suggest rapid speciation
 associated with host switches in some members of this group, the
 association of different Vidua lineages with particular host genera
 suggests the possibility of cospeciation at higher levels in the host and
 parasite phylogenies. We compared a phylogeny of all Vidua species with a
 phylogeny of their estrildid finch hosts and compared divergence time
 estimates for the two groups. Basal divergences among extant members of
 the Vidulidae and among Vidua species are more recent than those among
 host genera and species, respectively, allowing a model of cospeciation to
 be rejected at most or all levels of the Vidua phylogeny. Nonetheless,
 some tests for cospeciation indicated significant congruence between host
 and parasite tree topologies. This result may be an artifact of
 clade-limited colonization. Host switches in parasitic finches have most
 often involved new hosts in the same or a closely related genus, an effect
 that increases the apparent congruence of host and parasites trees.
description: Estrilid
 dataSorenson_EstVidPlo.nexVidua dataSorenson_Vidua.nex
DOI: 10.5061/dryad.q30rt
title: Data from: Genetic relationships of extant brown bears (Ursus arctos) and polar bears (Ursus maritimus)

description: Polar bears (Ursus maritimus) and brown bears (Ursus arctos) are closely
 related species for which extensive mitochondrial and nuclear phylogenetic
 genetic comparisons have been made. We used previously-published genotype
 data for 8 microsatellite DNA loci from 930 brown bears in 19 populations
 and 473 polar bears in 16 populations to compare the population genetic
 relationships of extant populations of the species. Genetic distances (Nei
 standard distance = 1.157), the proportion of private alleles (52% of
 alleles are not shared by the species), and Bayesian cluster analysis are
 consistent with morphological and life history characteristics that
 distinguish polar bears and brown bears as different species with little
 or no gene flow among extant populations.
description: Bear microsats for Paper
 For Dryad ArchiveThe file contains
 diploid genotypes for eight microsatellite DNA locifor three species of
 bears that were first reported in previous
 publications.
DOI: 10.5061/dryad.34dn2
title: Data from: Activity and migratory flights of individual free-flying songbirds throughout the annual cycle: method and first case study

description: We describe a method and device (&lt; 1.2 g) for recording, processing
 and storing data about activity and location of individuals of free-living
 songbirds throughout the annual cycle. Activity level was determined every
 five minutes from five 100 ms samples of accelerometer data with 5 s
 between the sampling events. Activity levels were stored on an hourly
 basis throughout the annual cycle, allowing periods of resting/sleep,
 continuous flight and intermediate activity (foraging, breeding) to be
 distinguished. Measurements from a light sensor were stored from
 preprogrammed key stationary periods during the year to provide control
 information about geographic location. Successful results, including
 annual actogram, were obtained for a red-backed shrike Lanius collurio
 carrying out its annual loop migration between northern Europe and
 southern Africa. The shrike completed its annual migration by performing
 &gt; 66 (max. 73) nocturnal migratory flights (29 flights in autumn
 and &gt; 37, max. 44, in spring) adding up to a total of &gt; 434
 (max. 495) flight hours. Migratory flights lasted on average 6.6 h with
 maximum 15.9 h. These flights were aggregated into eight travel episodes
 (periods of 4–11 nights when flights took place on the majority of
 nights). Daytime resting levels were much higher during the winter period
 compared to breeding and final part of spring migration. Daytime resting
 showed peaks during days between successive nocturnal flights across
 Sahara, continental Africa and the Arabian Peninsula, indicating that the
 bird was mostly sleeping between these long migratory flights. Annual
 activity and flight data for free-living songbirds will open up many new
 research possibilities. Main topics that can be addressed are e.g.
 migratory flight performance (total flight investment, numbers and
 characteristics of flights), timing of stationary periods, activity
 patterns (resting/sleep, activity level) in different phases of the annual
 cycle and variability in the annual activity patterns between and within
 individuals.
description: SuppInfo_accelerometer_data_dryadDatafile in plain text containing detailed accelerometer data. First two columns are Date/Time. Act0 means number of sequences that scored 0 during the preceding hour (12 measurement sequences). Next columns Act1 to Act5 follow the same way. Column "check" is the sum of all activity counts and should be 12 if all sampling worked as intended. See doi: 10.1111/jav.01068 for details on data collection and compilation.
DOI: 10.5061/dryad.7st32
title: Data from: Species traits and abundances predict metrics of plant–pollinator network structure, but not pairwise interactions

description: Plant–pollinator mutualistic networks represent the ecological context of
 foraging (for pollinators) and reproduction (for plants and some
 pollinators). Plant–pollinator visitation networks exhibit highly
 conserved structural properties across diverse habitats and species
 assemblages. The most successful hypotheses to explain these network
 properties are the neutrality and biological constraints hypotheses, which
 posit that species interaction frequencies can be explained by species
 relative abundances, and trait mismatches between potential mutualists
 respectively. However, previous network analyses emphasize the prediction
 of metrics of qualitative network structure, which may not represent
 stringent tests of these hypotheses. Using a newly documented temporally
 explicit alpine plant–pollinator visitation network, we show that metrics
 of both qualitative and quantitative network structure are easy to
 predict, even by models that predict the identity or frequency of species
 interactions poorly. A variety of phenological and morphological
 constraints as well as neutral interactions successfully predicted all
 network metrics tested, without accurately predicting species observed
 interactions. Species phenology alone was the best predictor of observed
 interaction frequencies. However, all models were poor predictors of
 species pairwise interaction frequencies, suggesting that other aspects of
 species biology not generally considered in network studies, such as
 reproduction for dipterans, play an important role in shaping
 plant–pollinator visitation network structure at this site. Future
 progress in explaining the structure and dynamics of mutualistic networks
 will require new approaches that emphasize accurate prediction of species
 pairwise interactions rather than network metrics, and better reflect the
 biology underlying species interactions.
description: SM_A2_rawdata_fullExcel file with separate worksheets including: Raw visitation data, aggregate network, plant densities, and morphology classification matrices for plants and pollinators.SM_A3_Rcode_rquantwebsR code for the algorithm used to generate random interaction frequency matrices from the different probability models used in the study.
DOI: 10.5061/dryad.r98g7
title: Data from: Novel R pipeline for analyzing Biolog phenotypic microarray data

description: Data produced by Biolog Phenotype MicroArrays are longitudinal
 measurements of cells’ respiration on distinct substrates. We introduce a
 three-step pipeline to analyze phenotypic microarray data with novel
 procedures for grouping, normalization and effect identification. Grouping
 and normalization are standard problems in the analysis of phenotype
 microarrays defined as categorizing bacterial responses into active and
 non-active, and removing systematic errors from the experimental data,
 respectively. We expand existing solutions by introducing an important
 assumption that active and non-active bacteria manifest completely
 different metabolism and thus should be treated separately. Effect
 identification, in turn, provides new insights into detecting differing
 respiration patterns between experimental conditions, e.g. between
 different combinations of strains and temperatures, as not only the main
 effects but also their interactions can be evaluated. In the effect
 identification, the multilevel data are effectively processed by a
 hierarchical model in the Bayesian framework. The pipeline is tested on a
 data set of 12 phenotypic plates with bacterium Yersinia enterocolitica.
 Our pipeline is implemented in R language on the top of opm R package and
 is freely available for research purposes.
description: Biolog
 dataIntensity values
 produced by the Biolog's OmniLog Incubator/Reader. Cells of the
 Bacterium Yersinia enterocolitica (strains 53/03 and 8081c) were cultured
 on Biolog's PM1 plate and incubated for 48 hours at 28 and 37 degrees
 Celcius. Each of the four strain/temperature combinations was replicated
 three times.exampleData.zip
DOI: 10.5061/dryad.dt7mh
title: Data from: Contrasting patterns in species and functional-trait diversity of bees in an agricultural landscape

description: Land-use change frequently reduces local species diversity. Species losses
 will often result in loss of trait diversity, with likely consequences for
 community functioning. However, the converse need not be generally true:
 management approaches that succeed in retaining species richness could
 nevertheless fail to maintain trait diversity. We evaluated this
 possibility using bee communities in a California agroecosystem. We
 examined among-site patterns in bee species diversity and functional-trait
 diversity in a landscape composed of a mosaic of semi-natural habitat,
 organic farms, and conventional farms. We sampled bees from all three
 habitat types, and compiled a database of life-history (“functional”)
 traits for each species. Although species richness was higher on organic
 farms than conventional farms, functional diversity was lower in both farm
 types than in natural habitat. Nesting location (below-ground vs.
 above-ground) was the primary trait contributing to differences in
 functional diversity between farms and natural habitat, reflecting
 observed differences in availability of nesting substrates among habitat
 types. Other traits, including phenology and sociality, were also
 associated with species’ occurrences or dominance in particular site
 types. These patterns suggest that management practices common to all
 farms act as environmental filters that cause similarly low functional
 diversity in their bee communities. Synthesis and applications. Although
 our results support the value of organic farming in maintaining abundant
 and species-rich bee communities, components of bee functional diversity
 are not well supported in farmed landscapes, regardless of farming
 practice. Maintenance of natural habitat, and/or the addition of
 natural-habitat elements to farms, is therefore important for the
 retention of functionally diverse bee assemblages in agroecosystems.
description: Bee specimen
 dataPlease consult the
 ReadMe file.KW_handnet_2002_female_bees.txtNesting habitat data (quadrats)Please consult the ReadMe file.KW_nesting_habitat_quadrats.txtNesting habitat data (transects)Please consult the ReadMe file.KW_nesting_habitat_transects.txt
DOI: 10.5061/dryad.7p160
title: Data from: Repeatability, heritability, and age-dependence in the aggressiveness reaction norms of a wild passerine bird

description: Labile characters allow individuals to flexibly adjust their phenotype to
 changes in environmental conditions. There is growing evidence that
 individuals can differ both in average expression and level of plasticity
 in this type of character. Both of these aspects are studied in
 conjunction within a reaction norm framework. Theoreticians have
 investigated the factors promoting variation in reaction norm intercepts
 (average phenotype) and slopes (level of plasticity) of a key labile
 character: behaviour. A general prediction from their work is that
 selection will favour the evolution of repeatable individual variation in
 level of plasticity only under certain ecological conditions. While
 factors promoting individual repeatability of plasticity have thus been
 identified, empirical estimates of this phenomenon are largely lacking for
 wild populations. We assayed aggressiveness of individual male great tits
 (Parus major) twice during their egg-laying stage and twice during their
 egg-incubation stage to quantify each male's level of seasonal
 plasticity. This procedure was applied during six consecutive years; all
 males breeding in our plots during those years were assayed, resulting in
 repeated measures of individual reaction norms for any individual breeding
 in multiple years. We quantified among- and within-individual variation in
 reaction norm components, allowing us to estimate repeatability of
 seasonal plasticity. Using social pedigree information, we further
 partitioned reaction norm components into their additive genetic and
 permanent environmental counterparts. Cross-year individual repeatability
 for the intercepts (average aggressiveness) and slopes (level of seasonal
 plasticity) of the aggressiveness reaction norms were 0·574 and 0·516
 respectively. The mean of the posterior distributions suggested modest
 heritabilities (h2 = 0·260 for intercepts; h2 = 0·266 for slopes), but
 these estimates were relatively uncertain. Males behaved more aggressively
 in areas with higher breeding densities, and became less aggressive and
 less plastic with increasing age; plasticity thus varied within
 individuals and was multidimensional in nature. This empirical study
 quantified cross-year individual repeatability, heritability and
 age-related reversible plasticity in behaviour. Acknowledging such
 patterns of multi-level variation is important not only for testing
 behavioural ecology theory concerning the evolution of repeatable
 differences in behavioural plasticity but also for predicting how
 reversible plasticity may evolve in natural populations.
description: Data for the multi-level
 reaction norm analysisGreat tits aggressive
 response towards simulated territorial intrusions.data.csv