cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.71qt7
title: Data from: Molecular characterization of resistance to soybean rust (Phakopsora pachyrhizi Syd. & Syd.) in soybean cultivar DT 2000 (PI 635999)

description: Resistance to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd.
 & Syd., has been identified in many soybean germplasm accessions
 and is conferred by either dominant or recessive genes that have been
 mapped to six independent loci (Rpp1 –Rpp6), but No U.S. cultivars are
 resistant to SBR. The cultivar DT 2000 (PI 635999) has resistance to P.
 pachyrhizi isolates and field populations from the United States as well
 as Vietnam. A F6:7 recombinant inbred line (RIL) population derived from
 Williams 82 × DT 2000 was used to identify genomic regions associated with
 resistance to SBR in the field in Ha Noi, Vietnam, and in Quincy, Florida,
 in 2008. Bulked segregant analysis (BSA) was conducted using the soybean
 single nucleotide polymorphism (SNP) USLP 1.0 panel along with simple
 sequence repeat (SSR) markers to detect regions of the genome associated
 with resistance. BSA identified four BARC_SNP markers near the Rpp3 locus
 on chromosome (Chr.) 6. Genetic analysis identified an additional genomic
 region around the Rpp4 locus on Chr. 18 that was significantly associated
 with variation in the area under disease progress curve (AUDPC) values and
 sporulation in Vietnam. Molecular markers tightly linked to the DT 2000
 resistance alleles on Chrs. 6 and 18 will be useful for marker-assisted
 selection and backcrossing in order to pyramid these genes with other
 available SBR resistance genes to develop new varieties with enhanced and
 durable resistance to SBR.
description: Will82xDT2000-Soybean
 Rust-Genotypic DataGenetic marker data
 generated in an RIL mapping population derived from a Williams 82 x DT2000
 cross. No. of lines: 240 No. of polymorphic markers:
 504Will82xDT2000-Soybean
 Rust-Phenotypic DataField phenotypic data
 collected in an RIL mapping population derived from a Williams 82 x DT2000
 cross. No. of lines: 240 No. of traits studied: 4
DOI: 10.5061/dryad.4g87s
title: Data from: An adaptable but threatened big cat: density, diet and prey selection of the Indochinese leopard (Panthera pardus delacouri) in eastern Cambodia

description: We studied the Indochinese leopard (Panthera pardus delacouri) in eastern
 Cambodia, in one of the few potentially remaining viable populations in
 Southeast Asia. The aims were to determine the: (i) current leopard
 density in Srepok Wildlife Sanctuary (SWS) and (ii) diet, prey selection
 and predation impact of leopard in SWS. The density, estimated using
 spatially explicit capture–recapture models, was 1.0 leopard/100 km2, 72%
 lower than an estimate from 2009 at the same site, and one of the lowest
 densities ever reported in Asia. Dietary analysis of 73 DNA confirmed
 scats showed leopard consumed 13 prey species, although ungulates
 comprised 87% of the biomass consumed (BC). The overall main prey (42% BC)
 was banteng (Bos javanicus), making this the only known leopard population
 whose main prey had adult weight greater than 500 kg. Consumption of wild
 pig (Sus scrofa) was also one of the highest ever reported (22% BC),
 indicating leopard consistently predated on ungulates with some of the
 largest adult weights in SWS. There were important differences in diet and
 prey selection between sexes, as males consumed mostly banteng (62% BC) in
 proportion to availability, but few muntjac (Muntiacus vaginalis; 7% BC),
 whereas females selectively consumed muntjac (56% BC) and avoided banteng
 (less than 1% BC). Predation impact was low (0.5–3.2% of populations) for
 the three ungulate species consumed. We conclude that the Indochinese
 leopard is an important apex predator in SWS, but this unique population
 is declining at an alarming rate and will soon be eradicated unless
 effective protection is provided.
description: READMEFile describing the
 datasets accompanying the above publicationLeopard
 DietFile containing the raw
 data used to determine the diet of leopard in Srepok Wildlife Sanctuary,
 Cambodia. Only confirmed leopard scats were used for the analysis and are
 shown here.Individual Leopard
 GenotypeFile containing the
 genotype data from each individual leopardLine
 TransectsFile containing the data
 collected for banteng, wild pig, and muntjac in 2014Camera
 TrapDates camera trap
 stations were set, checked, and collectedUngulates
 DensityFile containing the
 density, estimated using Distance 6.2, of banteng, wild pig, and muntjac
 in the inner core zone (450 km2) of Srepok Wildlife Sanctuary during
 2014Ungulates Detection
 FunctionsFile containing the
 Detection Functions produced in Distance 6.2 for banteng (A), wild pig
 (B), and muntjac (C) for line-transect data collected during 2014 in the
 Eastern Plains Landscape, Cambodia
DOI: 10.5061/dryad.9238j7f
title: Data from: Experimental evolution across different thermal regimes yields genetic divergence in recombination fraction but no divergence in temperature-associated plastic recombination

description: Phenotypic plasticity is pervasive in nature. One mechanism underlying the
 evolution and maintenance of such plasticity is environmental
 heterogeneity. Indeed, theory indicates that both spatial and temporal
 variation in the environment should favor the evolution of phenotypic
 plasticity under a variety of conditions. The frequency of recombination
 in the model system Drosophila melanogaster has long been known to exhibit
 phenotypic plasticity in response to temperature. Here were use a panel of
 replicated experimental evolution populations of D. melanogaster to test
 whether variable environments favor enhanced plasticity in recombination
 rate in response to temperature. In contrast to expectation, we find no
 evidence for enhanced plasticity in recombination in the variable
 environment lines. Our data confirm a role of temperature in mediating
 recombination fraction in D. melanogaster, and indicate that recombination
 is genetically and plastically depressed under lower temperatures. Our
 data further suggest that the genetic architectures underlying plastic
 recombination and population-level variation in recombination rate are
 likely to be distinct.
description: PlasticityRecombinatioRawThis is the raw data file from this experiment. We report the number of each phenotype for each replicate at each temperature.
DOI: 10.5061/dryad.p3878
title: Data from: The contribution of maternal effects to selection response: an empirical test of competing models

description: Maternal effects can dramatically influence the evolutionary process, in
 some cases facilitating and in others hindering adaptive evolution.
 Maternal effects have been incorporated into quantitative genetic models
 using two theoretical frameworks: the variance-components approach, which
 partitions variance into direct and maternal components, and the
 trait-based approach, which assumes that maternal effects are mediated by
 specific maternal traits. Here, we demonstrate parallels between these
 models and test their ability to predict evolutionary change. First, we
 show that the two approaches predict equivalent responses to selection in
 the absence of maternal effects mediated by traits that are themselves
 maternally influenced. We also introduce a correction factor that may be
 applied when such cascading maternal effects are present. Second, we use
 several maternal effect models, as well as the standard breeder's
 equation, to predict evolution in response to artificial selection on
 flowering time in American bellflower, Campanulastrum americanum. Models
 that included maternal effects made much more accurate predictions of
 selection response than the breeder's equation. Maternal effect
 models differed somewhat in their fit, with a version of the trait-based
 model providing the best fit. We recommend fitting such trait-based models
 when possible and appropriate to make the most accurate evolutionary
 predictions.
description: Table 1, Fig 2 - Model
 comparisonContains the observed
 and predicted population means for each selection line. Includes a key
 identifying the variables.Table S2 - Selection
 gradientsContains the raw data
 for calculating selection gradients for each generation, as well as the
 population mean for each generation. Includes a key identifying the
 variables.Supplement - ASReml data
 and pedigree from Galloway et al 2009Contains the raw data
 for calculating the results of Galloway et al. (2009, New Phytologist 183:
 826–838), which were used extensively in the current paper. This includes
 the M matrix in Table S1, the G matrices in Table S3-S4, and the various
 matrices used here and originally reported in Galloway et al. (2009).
 Includes a key identifying the variables.
DOI: 10.5061/dryad.3c025
title: Data from: Phylogeny suggests non-directional and isometric evolution of sexual size dimorphism in argiopine spiders

description: Sexual dimorphism describes substantial differences between male and
 female phenotypes. In spiders, sexual dimorphism research almost
 exclusively focuses on size, and recent studies have recovered steady
 evolutionary size increases in females, and independent evolutionary size
 changes in males. Their discordance is due to negative allometric size
 patterns caused by different selection pressures on male and female size
 (converse Rensch's rule). Here, we investigated macroevolutionary
 patterns of sexual size dimorphism (SSD) in Argiopinae, a global lineage
 of orb weaving spiders with varying degrees of SSD. We devised a Bayesian
 and maximum likelihood molecular species level phylogeny, then used it to
 reconstruct sex specific size evolution, to examine general hypotheses and
 different models of size evolution, to test for sexual size coevolution,
 and to examine allometric patterns of SSD. Our results, revealing
 ancestral moderate sizes and SSD, failed to reject the Brownian motion
 model, which suggests a non-directional size evolution. Contrary to
 predictions, male and female sizes were phylogenetically correlated, and
 SSD evolution was isometric. We interpret these results to question the
 classical explanations of female-biased SSD via fecundity, gravity, and
 differential mortality. In argiopines, SSD evolution may be driven by
 these or additional selection mechanisms, but perhaps at different
 phylogenetic scales.
description: Sequences data matrix
 and treesThe original molecular
 data, and the results from ML, BI and BEAST analyses.Appendix
 S2.nexBody_length_ArgThe original body size data matrix
DOI: 10.5061/dryad.c4018
title: Data from: Phenotypic selection exerted by a seed predator is replicated in space and time and among prey species

description: Although consistent phenotypic selection arising from biotic interactions
 is thought to be the primary cause of adaptive diversification, studies
 documenting such selection are relatively few. Here we analyze 12 episodes
 of phenotypic selection exerted by a predispersal seed predator, the red
 crossbill (Loxia curvirostra complex), on five species of pines (Pinus).
 We find that even though the intensity of selection for some traits
 increased with the strength of the interaction (i.e., proportion of seeds
 eaten), the relative strength of selection exerted by crossbills on cone
 and seed traits is replicated across space, time, and among species. Such
 selection (1) can account for repeated patterns of conifer cone evolution,
 and escalation in seed defenses with time, and (2) suggests that variation
 in selection is less the result of variation intrinsic to pairwise biotic
 interactions than, for example, variation in relative densities of the
 interacting species, community context, and abiotic factors.
description: Phenotypic selection
 dataMean pine cone traits
 and the proportion of seeds consumed by crossbills at 11 sites/years. Each
 row represents data for one tree, and the rows are ordered by
 site/year.DataforDryad.xls
DOI: 10.15468/dl.9xu86k
title: Occurrence Download

description: A dataset containing 1643 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 "TaxonKey is one of (Dermoptera [GBIF Backbone Taxonomy])"
 ]
}

 The dataset includes 1643 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000658-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k0218
title: Data from: Sylleptic branching in winter-headed apple (Malus × domestica) trees: accession-dependent responses and their relationships with other tree architectural characteristics

description: Well-feathered apple trees are essential for commercial orchards to
 optimize yields. However, most cultivars do not form these sylleptic
 branches readily in commercial nurseries due to high apical dominance.
 Several treatments exist to promote their formation in the nurseries, one
 of which is heading. However, not all cultivars are expected to react
 similarly to these treatments. We studied the branching response of 155
 genotypes following heading and its relation to other architectural traits
 as a function of the cultivar’s genetic background. Trees were grown for
 two consecutive years after grafting in a nursery, and the main axes were
 headed in the winter following growth in year 1. After heading, a single
 shoot was retained when growth resumed in the second year. Plant
 architectural traits such as growth of the main shoot, internode length,
 sylleptic branching, etc. were measured before and after heading and were
 statistically compared using a mixed model. This model showed the effect
 of heading for all architectural traits studied. In addition significant
 genotype and genotype × treatment interactions were found. In general,
 genotypes that showed a more vigorous growth during the first year also
 reacted more vigorously to heading. Accounting for the genetic
 substructure of this collection, no clear distinction in tree response
 could be found except in a small group of individuals that belonged to an
 F1 mapping population. This study shows that heading is not favorable for
 all genotypes to promote sufficient sylleptic branching and that other
 methods are needed to promote branching in these accessions.
description: Headed apple
 architecture data year 1 and 2Phenotypic data of
 1-year-old and 2-year-old headed trees from a germplasm collection modern
 cultivars and older local varieties
DOI: 10.5061/dryad.v5007p45
title: Data from: Do animals living in larger groups experience greater parasitism? A meta-analysis

description: Parasitism is widely viewed as the primary cost of sociality and a
 constraint on group size, yet studies report varied associations between
 group size and parasitism. Using the largest database of its kind, we
 performed a meta-analysis of 69 studies of the relationship between group
 size and parasite risk, as measured by parasitism and immune defenses. We
 predicted a positive correlation between group size and parasitism with
 organisms that show contagious and environmental transmission, and a
 negative correlation for searching parasites, parasitoids, and possibly
 vector-borne parasites (based on the encounter-dilution effect). Overall,
 we found a positive effect of group size (r=0.187) that varied in
 magnitude across transmission modes and measures of parasite risk, with
 only weak indications of publication bias. Among different groups of
 hosts, we found a stronger relationship between group size and parasite
 risk in birds than in mammals, which may be driven by ecological and
 social factors. A meta-regression showed that effect sizes increased with
 maximum group size. Phylogenetic meta-analyses revealed no evidence for
 phylogenetic signal in the strength of the group size-parasitism
 relationship. We conclude that group size is a weak predictor of parasite
 risk except in species that live in large aggregations, such as colonial
 birds, where effect sizes are larger.
description: Effect sizes and study
 identitiesAn Excel spreadsheet of
 the effect sizes (Hedges G) included in our study. Note: Missing
 Hedges' G indicates that sample size was too small to estimate effect
 size or direction was not provided in original paper.Final Tree
 usedThe phylogenetic tree
 used in our analysis. This tree is fully dichotomous, includes branch
 lengths, and has no non-zero branch-lengths. Tree structure and branch
 lengths were collected from the literature and estimated as described in
 the methods. The tree was edited in R and Notepad.Final data
 usedThe data used for the
 phylogenetic meta-analysis in Phylometa. The data file is formatted in
 accordance with the instructions in the Phylometa manual: it is
 tab-delimited and the columns are taxon name, taxon-specific effect size,
 effect size variance, and moderator grouping. In moderator grouping,
 0=arachnid, lizard or fish, 1=mammal, 2=bird, and
 3=insect.Supplementary
 methodsDescribes statistical
 methods omitted from paper because they were not relevant to the results
 presented.
DOI: 10.5061/dryad.82d5f33
title: Data from: Completing the hybridization triangle: the inheritance of genetic incompatibilities during homoploid hybrid speciation in ragworts (Senecio).

description: A new homoploid hybrid lineage needs to establish a degree of reproductive
 isolation from its parent species if it is to persist as an independent
 entity, but the role hybridization plays in this process is known in only
 a handful of cases. The homoploid hybrid ragwort species, Senecio
 squalidus, (Oxford ragwort) originated following the introduction of
 hybrid plants to the UK approximately 320 years ago. The source of the
 hybrid plants was from a naturally occurring hybrid zone between S.
 aethnensis and S. chrysanthemifolius on Mount Etna, Sicily. Previous
 studies of the parent species found evidence for multiple incompatibility
 loci causing transmission ratio distortion of genetic markers in their
 hybrid progeny. This study closes the hybridization triangle by reporting
 a genetic mapping analysis of the remaining two paired cross combinations
 between S. squalidus and its parents. Genetic maps produced from F2
 mapping families were generally collinear but with half of the linkage
 groups showing evidence of genomic reorganization between genetic maps.
 The new maps produced from crosses between S. squalidus and each parent
 showed multiple incompatibility loci distributed across the genome, some
 of which co-locate with previously reported incompatibility loci between
 the parents. These findings suggest that this young homoploid hybrid
 species has inherited a unique combination of genomic rearrangements and
 incompatibilities from its parents that contribute to its reproductive
 isolation.
description: F2AScodominantgenotypesCodominant marker genotypes for an F2 Senecio aethnensis x S. squalidus mapping familyF2CScodominantgenotypesCodominant marker genotypes for an F2 Senecio chrysanthemifolius x S. squalidus mapping familyF2ASdominantgenotypesDominant marker genotypes for an F2 Senecio aethnensis x S. squalidus mapping familyF2CSdominantgenotypesDominant marker genotypes for an F2 Senecio chrysanthemifolius x S. squalidus mapping familyF2genotypesnotesNotes explaining the data files: F2AScodominantgenotypes, F2ASdominantgenotypes, F2CScodominantgenotypes, and F2CSdominantgenotypesF2ASjoinmapJoinmap formatted input file for an F2 S. aethnensis x S. squalidus mapping familyF2CSjoinmapJoinmap formatted input file for an F2 S. chrysanthemifolius x S. squalidus mapping familyF2joinmapnotesNotes for F2ASjoinmap and F2CSjoinmap data filesF2ASmapGenetic linkage map for an F2 S. aethnensis x S. squalidus mapping familyF2CSmapGenetic linkage map for an F2 S. chrysanthemifolius x S. squalidus mapping familyF2mapnotesNotes for F2ASmap and F2CSmap data files
DOI: 10.5061/dryad.82ms3
title: Data from: Vectored dispersal of Symbiodinium by larvae of a Caribbean gorgonian octocoral

description: The ability of coral reefs to recover from natural and anthropogenic
 disturbance is difficult to predict, in part due to uncertainty regarding
 the dispersal capabilities and connectivity of their reef inhabitants. We
 developed microsatellite markers for the broadcast spawning gorgonian
 octocoral Eunicea (Plexaura) flexuosa (four markers) and its
 dinoflagellate symbiont, Symbiodinium B1 (five markers), and used them to
 assess genetic connectivity, specificity and directionality of gene flow
 among sites in Florida, Panama, Saba and the Dominican Republic. Bayesian
 analyses found that most E. flexuosa from the Florida reef tract,
 Saba and the Dominican Republic were strongly differentiated from many
 E. flexuosa in Panama, with the exception of five colonies from
 Key West that clustered with colonies from Panama. In contrast,
 Symbiodinium B1 was more highly structured. At least seven populations
 were detected that showed patterns of isolation by distance. The symbionts
 in the five unusual Key West colonies also clustered with symbionts from
 Panama, suggesting these colonies are the result of long-distance
 dispersal. Migration rate tests indicated a weak signal of northward
 immigration from the Panama population into the lower Florida Keys. As
 E. flexuosa clonemates only rarely associated with the same
 Symbiodinium B1 genotype (and vice versa), these data suggest a dynamic
 host–symbiont relationship in which E. flexuosa is relatively
 well dispersed but likely acquires Symbiodinium B1 from highly structured
 natal areas prior to dispersal. Once vectored by host larvae, these
 symbionts may then spread through the local population, and/or host
 colonies may acquire different local symbiont genotypes over time.
description: Pflex_structureData file with alleles for 4 microsatellite markers used to run analyses in the program STRUCTURE for Plexaura flexuosa.singlehaps_structureData file with alleles for 5 haploid microsatellite markers used to run analyses in the program STRUCTURE for Symbiodinium.totalmatrix_structureData file with presence/absence matrix for multiple alleles in Symbiodinium. Used for analyses with the program STRUCTURE.Pflex_createFile used to generate program-specific input files for Plexaura flexuosa dataset using CREATE (https://bcrc.bio.umass.edu/pedigreesoftware/node/2). Example files created include those for Genepop, Arlequin, and Bayesass.singlehaps_createFile used to generate program-specific input files for Symbiodinium "singlehaps" dataset using CREATE (https://bcrc.bio.umass.edu/pedigreesoftware/node/2). Example files created include those for Genepop and Arlequin.