cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q760h
title: Data from: Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue

description: RNA biomarkers discovered by RT-PCR-based gene expression profiling of
 archival formalin-fixed paraffin-embedded (FFPE) tissue form the basis for
 widely used clinical diagnostic tests; however, RT-PCR is practically
 constrained in the number of transcripts that can be interrogated. We have
 developed and optimized RNA-Seq library chemistry as well as
 bioinformatics and biostatistical methods for whole transcriptome
 profiling from FFPE tissue. The chemistry accommodates low RNA inputs and
 sample multiplexing. These methods both enable rediscovery of RNA
 biomarkers for disease recurrence risk that were previously identified by
 RT-PCR analysis of a cohort of 136 patients, and also identify a high
 percentage of recurrence risk markers that were previously discovered
 using DNA microarrays in a separate cohort of patients, evidence that this
 RNA-Seq technology has sufficient precision and sensitivity for biomarker
 discovery. More than two thousand RNAs are strongly associated with breast
 cancer recurrence risk in the 136 patient cohort (FDR &lt; 10%). Many
 of these are intronic RNAs for which corresponding exons are not also
 associated with disease recurrence. A number of the RNAs associated with
 recurrence risk belong to novel RNA networks. It will be important to test
 the validity of these novel associations in whole transcriptome RNA-Seq
 screens of other breast cancer cohorts.
description: gene_countsCounts of trimmed 36 bp reads that mapped uniquely to consolidated exons of genes annotated in RefSeq for 136 patients.IntronsCounts of trimmed 36 bp reads that mapped uniquely to consolidated introns of genes annotated in RefSeq for 136 patients.linc_KhalilGenesCounts of trimmed 36 bp reads that mapped uniquely to the coordinates of 2509 well-documented long-intergenic non-coding lincRNAs (Khalil et al., Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106: 11667-11672, 2009).intergenicsCounts of trimmed 36 bp reads that mapped uniquely to clusters in intergenic regions of the genome as described in Supplemental Methods.recurrenceTime to recurrence or censure for 136 patients. VSCode column contains a recurrence flag (1=recurrence, 0=no recurrence). Years column is the time to recurrence or censuring (ie., end of observation without a recurrence).
DOI: 10.5061/dryad.q8758
title: Data from: Evolution of eye morphology and rhodopsin expression in the Drosophila melanogaster species subgroup

description: A striking diversity of compound eye size and shape has evolved among
 insects. The number of ommatidia and their size are major determinants of
 the visual sensitivity and acuity of the compound eye. Each ommatidium is
 composed of eight photoreceptor cells that facilitate the discrimination
 of different colours via the expression of various light sensitive
 Rhodopsin proteins. It follows that variation in eye size, shape, and
 opsin composition is likely to directly influence vision. We analyzed
 variation in these three traits in D. melanogaster, D. simulans and D.
 mauritiana. We show that D. mauritiana generally has larger eyes than its
 sibling species, which is due to a combination of larger ommatidia and
 more ommatidia. In addition, intra- and inter-specific differences in eye
 size among D. simulans and D. melanogaster strains are mainly caused by
 variation in ommatidia number. By applying a geometric morphometrics
 approach to assess whether the formation of larger eyes influences other
 parts of the head capsule, we found that an increase in eye size is
 associated with a reduction in the adjacent face cuticle. Our shape
 analysis also demonstrates that D. mauritiana eyes are specifically
 enlarged in the dorsal region. Intriguingly, this dorsal enlargement is
 associated with enhanced expression of rhodopsin 3 in D. mauritiana. In
 summary, our data suggests that the morphology and functional properties
 of the compound eyes vary considerably within and among these closely
 related Drosophila species and may be part of coordinated morphological
 changes affecting the head capsule.
description: Body
 size_Wing_TibiaSpreadsheet of wing and
 tibia sizes of D. mauritiana (TAM16), D. simulans (yvf) and D.
 melanogaster (M36).DV_measurementsMeasurements of dorsal, ventral and total eye areas from D. mauritiana (TAM16), D. simulans (yvf), and D. melanogaster (M36).Eye_size_measurements_extHead, eye, face and wing measurements from extended data set of D. mauritiana and D. simulans strains.Eye_size_measurements_mainEye, face and tibia measurements of focal strains of D. mauritiana, D. simulans, and D. melanogaster.FaceTradeOffData for ratio of eye and face sizes for female D. mauritiana (TAM16), D. simulans (yvf), and D. melanogaster (M36).Ommatidia counts_sizeOmmatidia counts for focal strains of D. mauritiana, D. simulans, and D. melanogaster.Opsin_qPCRMeasurements of opsin expression in D. mauritiana, D. simulans, and D. melanogaster.
DOI: 10.5061/dryad.c2401
title: Data from: Analysis and visualization of H7 inﬂuenza using genomic, evolutionary and geographic information in a modular web service

description: We have reported previously on use of a web-based application, Supramap
 (http://supramap.org) for the study of biogeographic, genotypic, and
 phenotypic evolution. Using Supramap we have developed maps of the spread
 of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and
 coronaviruses such as SARS. Here we report on another zoonotic pathogen,
 H7 influenza, and provide an update on the implementation of Supramap as a
 web service. We find that the emergence of pathogenic strains of H7 is
 labile with many transitions from high to low pathogenicity, and from low
 to high pathogenicity. We use Supramap to put these events in a temporal
 and geospatial context. We identify several lineages of H7 influenza with
 biomarkers of high pathogenicity in regions that have not been reported in
 the scientific literature. The original implementation of Supramap was
 built with tightly coupled client and server software. Now we have
 decoupled the components to provide a modular web service for POY
 (http://poyws.org) that can be consumed by a data provider to create a
 novel application. To demonstrate the web service, we have produced an
 application, Geogenes (http://geogenes.org). Unlike in Supramap, in which
 the user is required to create and upload data files, in Geogenes the user
 works from a graphical interface to query an underlying dataset. Geogenes
 demonstrates how the web service can provide underlying processing for any
 sequence and metadata database.
description: Table of accession
 numbers, cleavage site, latitude, longitude for H7 HA
 segmentsData file from: Analysis
 and visualization of H7 inﬂuenza using genomic, evolutionary, and
 geographic information in a modular web service. In press Cladistics 2012.
 Daniel A. Janies, Laura W. Pomeroy, Jacob M. Aaronson, Samuel Handelman,
 Jori Hardman, Kevin Kawalec, Thomas Bitterman and Ward C. Wheeler. Excel
 file with the following fields: GISAID accession, cleavage site motif,
 number of basic amino acids, pathogenicity, latitude,
 longitude.ALLphenogeographicDec6accsort.xlsxKeyhole Markup Language (KML) file of the spread of H7 inﬂuenza lineages of various pathogenicity.Data file from: Analysis and visualization of H7 inﬂuenza using genomic, evolutionary, and geographic information in a modular web service. In press Cladistics 2012. Daniel A. Janies, Laura W. Pomeroy, Jacob M. Aaronson, Samuel Handelman, Jori Hardman, Kevin Kawalec, Thomas Bitterman and Ward C. Wheeler. KML file for Google Earth (TM) or other geospatial browser be sure to select the statusesdna878126-colored.kml "places" in the panel to the left. Red lines depict high pathogenic lineages, green lines show low pathogenic lineages, and purple lines represent lineages in a borderline state of pathogenicity. Color changes represent evolutionary changes in pathogenicity.statusesdna878126-colored.kmz
DOI: 10.5061/dryad.d54cc
title: Data from: Global honey bee viral landscape altered by a parasitic mite

description: Emerging diseases are among the greatest threats to honey bees.
 Unfortunately, where and when an emerging disease will appear are almost
 impossible to predict. The arrival of the parasitic Varroa mite into the
 Hawaiian honey bee population allowed us to investigate changes in the
 prevalence, load, and strain diversity of honey bee viruses. The mite
 increased the prevalence of a single viral species, deformed wing virus
 (DWV), from ~10 to 100% within honey bee populations, which was
 accompanied by a millionfold increase in viral titer and a massive
 reduction in DWV diversity, leading to the predominance of a single DWV
 strain. Therefore, the global spread of Varroa has selected DWV variants
 that have emerged to allow it to become one of the most widely distributed
 and contagious insect viruses on the planet.
description: DRYAD Fig.
 1Map
 of Hawaii showing the general locations of the 35 sites that from which
 honeybees where sampled.DRYAD Table
 1TaqMan® CT values (mean
 and standard deviation) for the EF1 control gene and five honeybee viruses
 (DWV, KBV, ABPV, IAPV, SPV).DRYAD Table
 2Estimated DWV copy
 number per honeybee in 2009 and 2010 from the four different Hawaiian
 Islands. All values have been normalised to each individual
 run.
DOI: 10.5061/dryad.26530
title: Data from: Macroevolutionary and morphofunctional patterns in theropod skulls: a morphometric approach

description: Theropod dinosaurs are one of the most remarkable lineages of terrestrial
 vertebrates in the Mesozoic, showing high taxonomic and ecological
 diversity. We investigate the cranial diversity of non-avian theropods and
 some basal birds, using geometric morphometrics to obtain insights into
 the evolutionary modifications of the skull. Theropod skulls mostly vary
 in the shape of the snout and length of the postorbital region (PC 1),
 with further variation in orbit shape, depth of the postorbital region,
 and position of the jaw joint (PC 2 and PC 3). These results indicate that
 the cranial shape of theropods is closely correlated with phylogeny and
 dietary preference. Skull shapes of non-carnivorous taxa differ
 significantly from carnivorous taxa, suggesting that dietary preference
 affects skull shape. Furthermore, we found a significant correlation
 between the first three PC axes and functional proxies (average maximum
 stress and an indicator of skull strength). Interestingly, basal birds
 occupy a large area within the morphospace, indicating a high cranial, and
 thus also ecological, diversity. However, we could include only a small
 number of basal avialan species, because their skulls are fragile and
 there are few good skull reconstructions. Taking the known diversity of
 basal birds from the Jehol biota into account, the present result might
 even underestimate the morphological diversity of basal avialans.
description: Theropod_Skull_morphoJMorphoJFoth_Rauhut_Theropod-skull_MorphoJTheropod_skull_ProCoorPASTFoth_Rauhut_Theropod_ProCoor_PASTParaves_skull_ProCoorPASTFoth_Rauhut_Paraves_ProCoor_PASTFoth_Rauhut_CLUSTER-Topologies
DOI: 10.5061/dryad.s808f
title: Data from: Comparison of non-Gaussian quantitative genetic models for migration and stabilizing selection

description: The balance between stabilizing selection and migration of maladapted
 individuals has formerly been modeled using a variety of quantitative
 genetic models of increasing complexity, including models based on a
 constant expressed genetic variance and models based on normality. The
 infinitesimal model can accommodate non-normality and a non-constant
 genetic variance as a result of linkage disequilibrium. It can be seen as
 a parsimonious one-parameter model which approximates the underlying
 genetic details well when a large number of loci are involved. Here, the
 performance of this model is compared to several more realistic explicit
 multilocus models, with either two, several or a large number of alleles
 per locus with unequal effect sizes. Predictions for the deviation of the
 population mean from the optimum are highly similar across the different
 models, so that the non-Gaussian infinitesimal model forms a good
 approximation. It does however generally estimate a higher genetic
 variance than the multilocus models, with the difference decreasing with
 an increasing number of loci. The difference between multilocus models
 depends more strongly on the effective number of loci, accounting for
 relative contributions of loci to the variance, than on the number of
 alleles per locus.
description: Simulation
 codeSimulation code in R and
 C, which can be opened in any text editor, and some simulated data. See
 README file and comments in .r files for details.Huisman_Evolution_non-Gaussian_Models_Scripts.zip
DOI: 10.5061/dryad.r3j5d
title: Data from: Grains of connectivity: analysis at multiple spatial scales in landscape genetics

description: Landscape genetic analyses are typically conducted at one spatial scale.
 Considering multiple scales may be essential for identifying landscape
 features influencing gene flow. We examined landscape connectivity for
 woodland caribou (Rangifer tarandus caribou) at multiple spatial scales
 using a new approach based on landscape graphs that creates a Voronoi
 tessellation of the landscape. To illustrate the potential of the method,
 we generated five resistance surfaces to explain how landscape pattern may
 influence gene flow across the range of this population. We tested each
 resistance surface using a raster at the spatial grain of available
 landscape data (200 m grid squares). We then used our method to produce up
 to 127 additional grains for each resistance surface. We applied a causal
 modelling framework with partial Mantel tests, where evidence of landscape
 resistance is tested against an alternative hypothesis of
 isolation-by-distance, and found statistically significant support for
 landscape resistance to gene flow in 89 of the 507 spatial grains
 examined. We found evidence that major roads as well as the cumulative
 effects of natural and anthropogenic disturbance may be contributing to
 the genetic structure. Using only the original grid surface yielded no
 evidence for landscape resistance to gene flow. Our results show that
 using multiple spatial grains can reveal landscape influences on genetic
 structure that may be overlooked with a single grain, and suggest that
 coarsening the grain of landcover data may be appropriate for
 highly-mobile species. We discuss how grains of connectivity and related
 analyses have potential landscape genetic applications in a broad range of
 systems.
description: Habitat
 rasterA raster in ArcASCII
 format giving the habitat feature classes in the study area
 (Smoothstone-Wapeweka caribou range, Saskatchewan,
 Canada)habitat.ascGenotype dataGenotypes for 95 boreal woodland caribou at 10 microsatellite loci.microsat.csv
DOI: 10.5061/dryad.rn30d
title: Data from: Weak disruptive selection and incomplete phenotypic divergence in two classic examples of sympatric speciation: Cameroon crater lake cichlids

description: Recent documentation of a few compelling examples of sympatric speciation
 led to a proliferation of theoretical models. Unfortunately, plausible
 examples from nature have rarely been used to test model predictions, such
 as the initial presence of strong disruptive selection. Here I estimated
 the form and strength of selection in two classic examples of sympatric
 speciation: radiations of Cameroon cichlids restricted to lakes Barombi
 Mbo and Ejagham. I measured five functional traits and relative growth
 rates in over 500 individuals within incipient species complexes from each
 lake. Disruptive selection was prevalent in both groups on single and
 multivariate trait axes, but weak relative to stabilizing selection on
 other traits and most published estimates of disruptive selection.
 Furthermore, despite genetic structure, assortative mating, and bimodal
 species-diagnostic coloration, trait distributions were unimodal in both
 species complexes, indicating the earliest stages of speciation. Long
 waiting times or incomplete sympatric speciation may result when
 disruptive selection is initially weak. Alternatively, I present evidence
 of additional constraints in both species complexes, including weak
 linkage between coloration and morphology, reduced morphological variance
 aligned with nonlinear selection surfaces, and minimal ecological
 divergence. While other species within these radiations show complete
 phenotypic separation, morphological and ecological divergence in these
 species complexes may be slow or incomplete outside optimal parameter
 ranges, in contrast to rapid divergence of their sexual coloration.
description: complete
 datasetField data on fitness
 (growth rates estimated from scale circuli spacing), standard length, five
 morphological traits, species-diagnostic coloration, and stable isotope
 ratios for two species complexes of Cameroon cichlids: Barombi Mbo
 Stomatepia and Ejagham Tilapia.standardized and
 size-corrected fitness and trait dataStandardized and
 size-corrected estimates of fitness and five morphological traits used for
 measuring selection on two species complexes of Cameroon cichlids: Barombi
 Mbo Stomatepia and Ejagham Tilapia.
DOI: 10.5061/dryad.d0t63
title: Data from: Reproduction and dispersal in an ant-associated root aphid community

description: Clonal organisms with occasional sex are important for our general
 understanding of the costs and benefits that maintain sexual reproduction.
 Cyclically parthenogenetic aphids are highly variable in their frequency
 of sexual reproduction and studies have mostly focused on free-living
 aphids above ground, whereas dispersal constraints and dependence on
 ant-tending may differentially affect the costs and benefits of sex in
 subterranean aphids. Here, we studied reproductive mode and dispersal in a
 community of root aphids that are obligatorily associated with the ant
 Lasius flavus. We assessed the genetic population structure of four
 species (Geoica utricularia, Tetraneura ulmi, Forda marginata and F.
 formicaria) in a Dutch population and found that all species reproduce
 predominantly if not exclusively asexually, so that populations consist of
 multiple clonal lineages. We show that population viscosity is high and
 winged aphids rare, consistent with infrequent horizontal transmission
 between ant host colonies. The absence of the primary host shrub
 (Pistacia) may explain the absence of sex in three of the studied species,
 but elm trees (Ulmus) that are primary hosts of the fourth species (T.
 ulmi), occured within a few km of the study population. We discuss the
 extent to which obligate ant-tending and absence of primary hosts may have
 affected selection for permanent parthenogenesis and we highlight the need
 for further study of these aphids in Southern Europe where primary hosts
 may occur close to Lasius flavus populations, so that all four root aphid
 species would have realistic opportunities for completing their sexual
 life-cycle.
description: Geoica-datamicrosatellite data files for Geoica samples. Includes geographic coordinates, sampling details, (raw) microsatellite data and a description of the software used and how to proceed to analyzeForda-datamicrosatellite data files for Forda samples. Includes geographic coordinates, sampling details, (raw) microsatellite data and a description of the software used and how to proceed to analyzeTetraneura-datamicrosatellite data files for Tetraneura samples. Includes geographic coordinates, sampling details, (raw) microsatellite data and a description of the software used and how to proceed to analyze
DOI: 10.5061/dryad.2g12q
title: Data from: Take this broken tail and learn to jump: the ability to recover from reduced in-air stability in tailless green anole lizards (Anolis carolinensis [Squamata: Dactyloidae])

description: Locomotion is involved in various fitness related tasks, such as foraging,
 acquiring mates and escaping from predators. Despite the importance of
 locomotor performance in determining fitness, animals often encounter
 situations in nature during which their locomotor performance is severely
 compromised. For animals that actively discard appendages as an
 antipredator strategy, the loss of appendages can cause a severe reduction
 in locomotor performance. However, whether animals can compensate for the
 impact on locomotor performance after autotomy is still unclear. A
 previous study has shown that tailless green anole lizards suffered from
 reduced in-air stability during jumping. In this study, we monitored jump
 kinematics in three groups of Anolis carolinensis for five consecutive
 weeks to test two hypotheses. First, whether tailless green anoles can
 recover from reduced in-air stability before their tails can regenerate.
 Second, whether gaining locomotor experience facilitates locomotor
 recovery. Our results revealed extensive individual variation in the
 ability to compensate for reduced in-air stability. Some individuals did
 improve in-air stability during the study period, whereas others showed no
 sign of improvement. Moreover, the acquisition of locomotor experience did
 not facilitate the recovery process. Our findings suggested that tail
 autotomy in green anoles likely imposes a long-term fitness disadvantage.
 The utility of other compensatory mechanisms, such as altering behavior,
 might play a role in natural populations to minimize the impact of
 autotomy on individual fitness. Our findings also shed some light on the
 independent evolutionary losses of the ability to autotomize within
 lizards. Comparative studies which test whether species that autotomize
 more frequently/easily can better compensate for the effect of autotomy
 would be a fruitful direction of future research.
description: locomotor
 recovery_original