cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v3p3j
title: Data from: Molecular phylogeny of unikonts: new insights into the position of apusomonads and ancyromonads and the internal relationships of Opisthokontsí

description: The eukaryotic supergroup known as the Opisthokonta includes animals
 (Metazoa), fungi, choanoflagellates, as well as some poorly-studied
 unicellular eukaryotes, such as the Nucleariidea, Fonticula alba, the
 Ichthyosporea, the Filasterea and Corallochytrium limacisporum. Whereas
 the evolutionary positions of the well-known opisthokont lineages are
 mostly resolved, the specific phylogenetic relationships among those
 neglected opisthokont lineages is unsettled. Moreover, it remains unclear
 whether Amoebozoa or Apusozoa are the sister group to opisthokonts. Aiming
 at elucidating the evolutionary tree of the opisthokonts, we have produced
 a dataset with a large sampling of both organisms and number of genes,
 including representatives from all known opisthokont lineages. Moreover,
 we have generated new molecular data from an additional ichthyosporean
 (Creolimax fragrantissima) and a choanoflagellate (Codosiga botrytis). Our
 analyses show the Apusozoa as a paraphyletic assemblage with the
 Apusomonadida as sister group to Opisthokonta. Within the the Holozoa, the
 Ichthyosporea are shown as the first splitting group, followed by C.
 limacisporum, the Filasterea, the Choanoflagellata, and the Metazoa. With
 this taxon-rich opisthokont tree, it is possible to pinpoint the origin
 and evolution of morphological characters. As an example, we discuss cilia
 evolution under the evolutionary scenario here presented.
description: Concat12Concatenated alignment of the two ribosomal subunit rDNA genes (18S and 28S) and six protein coding genes: actin, elongation factor 1 alpha (EF1 alpha), alpha and beta tubulins, and the heat shock proteins 70 (hsp 70) and 90 (hsp 90)
DOI: 10.5061/dryad.k41qk
title: Data from: Speciation history of three closely related oak gall wasps, Andricus mukaigawae, A. kashiwaphilus, and A. pseudoflos (Hymenoptera: Cynipidae) inferred from nuclear and mitochondrial DNA sequences

description: The Andricus mukaigawae complex of oak gall wasps is composed of
 cyclically parthenogenetic species: A. mukaigawae and A. kashiwaphilus,
 and a parthenogenetic species, A. pseudoflos. The component species differ
 in life history, host plant, karyotype, and asexual gall shape, although
 little difference is found in the external morphology of asexual adults.
 To understand the speciation history of this species complex, DNA
 sequences of one mitochondrial region and nine nuclear gene regions were
 investigated. The genetic relationship among the species suggested that a
 loss of sex occurred after host shift. Unexpectedly, two or three distinct
 groups in the parthenogenetic species, A. pseudoflos, were revealed by
 both mitochondrial and nuclear DNA data. Gene flow in nuclear genes from
 the species not infected by Wolbachia (A. kashiwaphilus) to the species
 infected by it (A. mukaigawae) was suggested by a method based on
 coalescent simulations. On the other hand gene flow in mitochondrial genes
 was suggested to be in the opposite direction. These findings indicate
 possible involvement of Wolbachia infection in the speciation process of
 the A. mukaigawae complex.
description: 0_mtDNA_1_1055_1206210_mtDNA_1056_3272_1206211_AntSesB_1206202_RpL37_1206203_RpS18_1206204_Locus2_1107135_Locus4_1107136_COXlike_1107137_Locus5_1107138_RpL27A_F_1107138_RpL27A_R_1107139_LWRh_110722IMa2_AKAM110610_MitoIMa2_AKAM110722_9Nuc_MitoIMa2_AKAM110722_9Nucbpp_AMAKAP120508
DOI: 10.5281/zenodo.18391919
title: FIREWALL J2 data
DOI: 10.5281/zenodo.18391920
title: FIREWALL J2 data
DOI: 10.15468/6ecwt7
title: Natural History Museum of Utah Fungarium
DOI: 10.5061/dryad.4tf74
title: Data from: Migration strategy affects avian influenza dynamics in mallards (Anas platyrhynchos)

description: Studies of pathogen transmission typically overlook that wildlife hosts
 can include both migrant and resident populations when attempting to model
 circulation. Through the application of stable isotopes in flight
 feathers, we estimated the migration strategy of mallards (Anas
 platyrhynchos) - resident, intermediate-distance migrant or long-distance
 migrant, occurring on California wintering grounds. Our study demonstrates
 that mallards, a principal host of avian influenza virus (AIV) in nature,
 contribute differently to virus gene flow depending on migration strategy.
 No difference in AIV prevalence was detected between resident (9.6%),
 intermediate-distance (9.6%) and long-distance migrants (7.4%). Viral
 diversity among the three groups was also comparable, possibly owing to
 viral pool mixing when birds converge at wetlands during winter. These
 findings challenge the view that migratory animals are exposed to a higher
 number and diversity of pathogens. However, migrants and residents
 contributed differently to the virus gene pool at wintering wetlands.
 Migrants introduced virus from northern breeding grounds (Alaska and the
 NW Pacific Rim) into the wintering population, facilitating gene flow at
 continental scales, but circulation of imported virus appeared to be
 limited. In contrast, resident mallards acted as AIV reservoirs
 facilitating year-round circulation of limited subtypes (i.e. H5N2) at
 lower latitudes. This study supports a model of virus exchange in
 temperate regions driven by the convergence of wild birds with separate
 geographic origins and exposure histories.
description: Mallard_metadata
 Text_MEC-12-0355.R1Mallard_HA NA alignments
 Text_MEC-12-0355.R1
DOI: 10.15468/8dy35f
title: New York State Museum Mycology Collection

description: The fungus collection at the New York State Museum in Albany was initiated by Charles Peck from 1868 to 1913 during which time he amassed 33,600 mycological specimens. In the years following, the next State Botanist, Homer House, and other mycologists added to this number. The collection now contains more than 90,000 specimens. However, the importance of the collection is not in the number of specimens it contains, but, rather, in the type specimens of American fungi collected during the early years of American mycology. It is especially rich in Agarics and other larger fungi. Some of the other collectors represented in the herbarium of the New York State Museum are G. F. Atkinson, M. E. Banning, E. Bartholomew, M. J. Berkeley, E. A. Burt, G. W. Clinton, M. C. Cooke, M. A. Curtis, J. Dearness, J. B. Ellis, W. R. Gerard, E. C. Howe, J. H. Haines, H. W. Harkness, E. W. D. Holway, C. H. Kauffman, W. A. Murrill, P. A. Saccardo, S. J. Smith, and C. J. Sprague. In addition to specimens, the Museum holds numerous original drawings and paintings of fungi by Charles Peck, Mary Banning, and others plus an extensive file of correspondence covering the formative years of American mycology. Non-type specimens are available on loan to recognized scientific institutions for taxonomic research. Requests for samples of type specimens for genetic and morphological analyses are considered on a case-by-case basis.
DOI: 10.5061/dryad.478g5
title: Data from: Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis

description: Understanding the extent of local adaptation in natural populations and
 the mechanisms that allow individuals to adapt to their native environment
 is a major avenue in molecular ecology research. Evidence for the frequent
 occurrence of diverging ecotypes in species that inhabit multiple
 ecological habitats is accumulating, but experimental approaches to
 understanding the biological pathways as well as the underlying genetic
 mechanisms are still rare. Parasites are invoked as one of the major
 selective forces driving evolution and are themselves dependent on the
 ecological conditions in a given habitat. Immunological adaptation to
 local parasite communities is therefore expected to be a key component of
 local adaptation in natural populations. Here we use next generation
 sequencing technology to compare the transcriptome-wide response of
 experimentally infected three-spined sticklebacks from a lake and a river
 population, which are known to evolve under selection by distinct parasite
 communities. By comparing overall gene expression levels as well as the
 activation of functional pathways in response to parasite exposure, we
 identified potential differences between the two stickleback populations
 at several levels. Our results suggest locally adapted patterns of gene
 regulation in response to parasite exposure, which may reflect different
 local optima in the trade-off between the benefits and the disadvantages
 of mounting an immune response due to quantitative differences of the
 local parasite communities.
description: Lenz_SampleIdentificationTable with information on origin, treatment and attributes for each SuperSAGE library sample.Lenz_ESTmatrix_NormalizedSuperSAGE tag count data for each detected gene and sample library. Tags are filtered according to description in the manuscript and tag count is normalized to 1 Mio tags per library. See accompanying files for sample description. Gene IDs are from ENSEMBL. Ready for input into R.Lenz_24SuperSAGElibrariescontains the 24 individual libraries with sequenced SuperSAGE tags and their frequencies.Lenz_MappedAssembly.fastacontains the output of the mapping assembly of the normalized cDNA reads against the ENSEMBL transcriptsLenz_ParasiteDataParasite data for experimental fish. Tab-delimited and ready for input into R.
DOI: 10.5061/dryad.2sk59
title: Data from: Prediction of genetic values of quantitative traits with epistatic effects in plant breeding populations

description: Though epistasis has long been postulated to play a critical role in
 genetic regulation of important pathways as well as provide a major source
 of variation in the process of speciation, the importance of epistasis for
 genomic selection in the context of plant breeding is still being debated.
 In this paper, we report the results on the prediction of genetic values
 with epistatic effects for 280 accessions in the Nebraska Wheat Breeding
 Program using adaptive mixed LASSO. The development of adaptive mixed
 LASSO, originally designed for association mapping, for the context of
 genomic selection is reported. The results show that adaptive mixed LASSO
 can be successfully applied to the prediction of genetic values while
 incorporating both marker main effects and epistatic effects. Especially,
 the prediction accuracy is substantially improved by the inclusion of
 two-locus epistatic effects (more than one fold in some cases as measured
 by cross validation correlation coefficient), which is observed for
 multiple traits and planting locations. This points to significant
 potential in using non-additive genetic effects for genomic selection in
 crop breeding practices.
description: phenotypePhenotype data for 280 lines in the Nebraska Wheat Breeding Program measured in 2010 at nine testing sites.DartGenotGenotype data for DArT markers regarding 280 lines in the Nebraska Wheat Breeding Program.
DOI: 10.5061/dryad.mm54f
title: Data from: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

description: Bananas (Musa spp.), including dessert and cooking types, are giant
 perennial monocotyledonous herbs of the order Zingiberales, a sister group
 to the well-studied Poales, which include cereals. Bananas are vital for
 food security in many tropical and subtropical countries and the most
 popular fruit in industrialized countries1. The Musa domestication process
 started some 7,000 years ago in Southeast Asia. It involved hybridizations
 between diverse species and subspecies, fostered by human migrations2, and
 selection of diploid and triploid seedless, parthenocarpic hybrids
 thereafter widely dispersed by vegetative propagation. Half of the current
 production relies on somaclones derived from a single triploid genotype
 (Cavendish)1. Pests and diseases have gradually become adapted,
 representing an imminent danger for global banana production3, 4. Here we
 describe the draft sequence of the 523-megabase genome of a Musa acuminata
 doubled-haploid genotype, providing a crucial stepping-stone for genetic
 improvement of banana. We detected three rounds of whole-genome
 duplications in the Musa lineage, independently of those previously
 described in the Poales lineage and the one we detected in the Arecales
 lineage. This first monocotyledon high-continuity whole-genome sequence
 reported outside Poales represents an essential bridge for comparative
 genome analysis in plants. As such, it clarifies commelinid-monocotyledon
 phylogenetic relationships, reveals Poaceae-specific features and has led
 to the discovery of conserved non-coding sequences predating
 monocotyledon–eudicotyledon divergence.
description: Gene trees and
 alignments for Musa gene orthogroupsThese are the orthogroup
 gene trees and alignments that were used to phylogenetically place the
 polyploidy events suggested by the Musa acuminata genome. See the README
 files for a complete description.Musa_WGD.tar.bz2
DOI: 10.5061/dryad.3t19n
title: Data from: Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei:Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion

description: Squirrelfishes and soldierfishes (Holocentridae) are among the most
 conspicuous species in the nocturnal reef fish community. However, there
 is no clear consensus regarding their evolutionary relationships, which is
 reflected in a complicated taxonomic history. We collected DNA sequence
 data from multiple single copy nuclear genes and one mitochondrial gene
 sampled from over fifty percent of the recognized holocentrid species and
 infer the first species-level phylogeny of the Holocentridae. Our results
 strongly support the monophyly of the clades Myripristinae (soldierfishes)
 and Holocentrinae (squirrelfishes). The molecular phylogenies differ with
 regard to previous hypotheses of relationships within the Myriprisitinae,
 resolving a clade of cryptic reef associated and deep water non-reef
 dwelling lineages (Corniger+Plectrypops+Ostichthys) that is the sister
 lineage to a monophyletic Myripristis. Within Holocentrinae, Neoniphon and
 Sargocentron are strongly supported as paraphyletic, while Holocentrus is
 nested within Sargocentron. Using Bayesian ancestral state reconstruction
 methods, we demonstrate the taxonomically diagnostic characters for
 Neoniphon and Sargocentron likely represent character states with a
 complex evolutionary history that is not reflective of shared common
 ancestry. We propose a new classification for Holocentrinae, recognizing
 four lineages that are treated as genera: Sargocentron Fowler, 1904,
 Holocentrus Scopoli, 1777, Flameo Jordan and Evermann, 1898, and Neoniphon
 Castelnau, 1875.
description: All_holocentrid_MLAlignment of all data for maximum likelihood analysisAll_holocentrid_MB2Nexus file for mrBayes analysis with all gene data and partitioning strategy identified.UCLN_ALL_StarBEASTStarbeast input file for gene tree species tree analysisRLC_ALL_StarBEASTInput for gene tree species tree analysis using *beast and the RLC model.
DOI: 10.5061/dryad.gm2p8
title: Data from: The island-mainland species turnover relationship

description: Many oceanic islands are notable for their high endemism, suggesting that
 islands may promote unique assembly processes. However, mainland
 assemblages sometimes harbour comparable levels of endemism, suggesting
 that island biotas may not be as unique as often assumed. Here, we test
 the uniqueness of island biotic assembly by comparing the rate of species
 turnover among islands and the mainland, after accounting for distance
 decay and environmental gradients. We modeled species turnover as a
 function of geographic and environmental distance for mainland (M-M)
 communities of Anolis lizards and Terrarana frogs, two clades that have
 diversified extensively on Caribbean islands and the mainland Neotropics.
 We compared mainland-island (M–I) and island-island (I–I) species turnover
 to predictions of the M–M model. If island assembly is not unique, then
 the M–M model should successfully predict M–I and I–I turnover, given
 geographic and environmental distance. We found that M–I turnover and, to
 a lesser extent, I–I turnover were significantly higher than predicted for
 both clades. Thus, in the first quantitative comparison of mainland–island
 species turnover, we confirm the long-held but untested assumption that
 island assemblages accumulate biodiversity differently than their mainland
 counterparts.
description: Stuart_etal_dataframes.RDataThis R workspace image contains two dataframes, one for anoles and one for terraranans. Each data frame contains pairwise environmental dissimilarity and species turnover values for island and mainland sub regions. The columns are: | geo_dist: geographic distance between sampling areas | climelev.pc.dist: environmental distance between sampling areas from a pca on environmental variables and elevation | log.area.diff: the difference in log area between sampling areas | sor: Sorensen's index of species turnover | jac: jaccard's index | comp.type: Identifies measures as mainland-mainland (m.m), mainland-island (i.m), or island-island (i.i) | comp.nums: identifies the corresponding sampling areas, which are mapped in the accompanying ArcGIS grids in the Stuart_etal_sample_areas.zip fileStuart_etal_sample_areasStuart_etal_sample_areas.zip | This compressed folder contains two ArcGIS grids: ter_m_i_samp (Terraranans) and an_m_i_samp (anoles). Each grid shows the mainland range of the relevant clade (values of 1.0), mainland sampled areas (50xxx) and islands included in the analysis(60xxx)
DOI: 10.5061/dryad.r0t1q
title: Data from: Gene expression levels are correlated with synonymous codon usage, amino acid composition and gene architecture in the red flour beetle, Tribolium castaneum

description: Gene expression levels correlate with multiple aspects of gene sequence
 and gene structure in phylogenetically diverse taxa suggesting an
 important role of gene expression levels in the evolution of
 protein-coding genes. Here we present results of a genome-wide study of
 the influence of gene expression on synonymous codon usage, amino acid
 composition and gene structure in the red flour beetle, Tribolium
 castaneum. Consistent with the action of translational selection, we find
 that synonymous codon usage bias increases with gene expression. However,
 the correspondence between tRNA gene copy number and optimal codons is
 weak. At the amino acid level, translational selection is suggested by the
 positive correlation between tRNA gene numbers and amino acid usage which
 is stronger for highly expressed genes. In addition, there is a clear
 trend for increased use of metabolically cheaper, less complex, amino
 acids as gene expression increases. tRNA gene numbers also correlate
 negatively with amino acid size/complexity score indicating the coupling
 between translational selection and selection to minimize the use of
 large/complex amino acids. Interestingly, the correlation between tRNA
 gene numbers and amino acid size/complexity score appears to be widespread
 given our analyses of 10 additional genomes and might be explained by
 selection against negative consequences of protein misfolding. At the
 level of gene structure, three major trends are detected 1) CDS length
 increases across low and intermediate expression levels but decreases in
 highly expressed genes; 2) the average intron size shows the opposite
 trend, first decreasing with expression, followed by a slight increase in
 highly expressed genes and 3) intron density remains nearly constant
 across all expression levels. These changes in gene architecture are only
 in partial agreement with selection favoring reduced cost of biosynthesis.
description: ExpressionDataThe expression data from Tribolium castaneum whole body and reproductive tracts samples provided here is the output of ArrayStar gene expression software that was used to processes and normalize NimbleGen-generated raw expression data (Prince, Kirkland and Demuth 2010, Genome Biol Evol 2:336-346).
DOI: 10.5061/dryad.8363t
title: Data from: Shape variation in outline shapes

description: A general morphometric method for describing shape variation in a sample
 consisting of landmarks and multiple outline shapes is developed in this
 paper. A distance metric is developed for such data and is used to embed
 the data in a low-dimensional Euclidean space. The Euclidean space is used
 to generate summary statistics such as mean and principal shape variation
 which are implicitly represented in the original space using elements of
 the sample. A new distance metric for outline shapes is proposed based on
 Procrustes distance that does not require the extraction of discrete
 points along the curve. The outline distant metric can be naturally
 combined with distances between landmarks. A method for aligning outlines
 and multiple outlines is developed that minimises the distance metric. The
 method is compared to semi-landmarks on synthetic data and two real data
 sets. Conclusion: outline methods produce useful and valid results when
 suitably constrained by landmarks and are useful visualisation aids, but
 questions remain about their suitability for answering biological
 questions until appropriate distance metrics can be biologically
 validated.
description: appendicesThe appendices.mccane_shape_variation_dataThis contains all the markup data which is used in the paper.
DOI: 10.15468/hhnd4h
title: Chrysler Herbarium - Mycological Collection

description: The Chrysler Herbarium (CHRB) is the last internationally recognized herbarium still in existence in the state of New Jersey. Over 150,000 vascular plant and algal collections, about 7,000 moss and liverwort specimens, and 2,600 lichen specimens form are collection and are arranged and catalogued systematically. The collection is worldwide in scope, with an emphasis on New Jersey and the Mid-Atlantic area, and contains specimens back to the mid-1800s.
DOI: 10.5061/dryad.vs49s
title: Data from: The evolutionary root of flowering plants

description: Correct rooting of the angiosperm radiation is both challenging and
 necessary for understanding the origins and evolution of physiological and
 phenotypic traits in flowering plants. The problem is known to be
 difficult due to the large genetic distance separating flowering plants
 from other seed plants and the sparse taxon sampling among basal
 angiosperms. Here we provide further evidence for concern over
 substitution model misspecification in analyses of chloroplast DNA
 sequences. We show that support for Amborella as the sole representative
 of the most basal angiosperm lineage is founded on sequence site patterns
 poorly described by time reversible substitution models. Improving the fit
 between sequence data and substitution model identifies Trithuria,
 Nymphaeales and Amborella as surviving relatives of the most basal lineage
 of flowering plants. This finding indicates that aquatic and herbaceous
 species dominate the earliest extant lineage of flowering plants.
description: S1Gapped alignment of
 40553 positions in length used to produce the OV
 alignmentS2alignment of first and
 the second codon positions 25246 positions in lengthS3OV sorted version of the
 40553 pos. long alignmentS431674 positions long
 alignment, maintaining the reading frameS5NNet split networks for
 S1 and S4 alignmentsS6zip archive containing
 scripts used in the paper
DOI: 10.5281/zenodo.18390104
title: Filtering out euroskepticism: Media influence and interpersonal communication in an agent-based model of Brexit opinion dynamics

description: Data generated by the agent-based model described in “Filtering out Euroskepticism: Media Influence and Interpersonal Communication in an Agent-Based Model of Brexit Opinion Dynamics.”The datasets can be used to replicate the figures and results reported in the paper.