cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4kt16
title: Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

description: Africa is renowned for its biodiversity and endemicity, yet little is
 known about the factors shaping them across the continent. African Agama
 lizards (45 species) have a pan-continental distribution, making them an
 ideal model for investigating biogeography. Many species have evolved
 conspicuous sexually dimorphic traits, including extravagant breeding
 coloration in adult males, large adult male body sizes, and variability in
 social systems among colorful versus drab species. We present a
 comprehensive time-calibrated species tree for Agama, and their close
 relatives, using a hybrid phylogenetic-phylogenomic approach that combines
 traditional Sanger sequence data from five loci for 57 species (146
 samples) with anchored phylogenomic data from 215 nuclear genes for 23
 species. The Sanger data are analyzed using coalescent-based species tree
 inference using *BEAST, and the resulting posterior distribution of
 species trees is attenuated using the phylogenomic tree as a backbone
 constraint. The result is a time-calibrated species tree for Agama that
 includes 95% of all species, multiple samples for most species, strong
 support for the major clades, and strong support for most of the initial
 divergence events. Diversification within Agama began approximately 23
 million years ago (Ma), and separate radiations in Southern, East, West,
 and Northern Africa have been diversifying for &gt; 10 Myr. A suite of
 traits (morphological, coloration, and sociality) are tightly correlated
 and show a strong signal of high morphological disparity within clades,
 whereby the subsequent evolution of convergent phenotypes has accompanied
 diversification into new biogeographic areas.
description: Sanger Sequence
 DataMitochondrial and
 nuclear loci in nexus format, with data partitioning.SangerData.nexSequence Capture LociSequence capture loci (a.k.a. anchored phylogenomics data). The data are in Nexus format (partitioned).SequenceCaptureLoci.nexHybrid PhylogenyThe final hybrid species tree for African Agama lizards (Newick format). The Sanger data (mtDNA and four nuclear genes) were used to estimate a time-calibrated species tree using *BEAST. This posterior distribution of species trees was then filtered using the anchored phylogenomics tree as a backbone constraint.HybridPhylogeny.treSequence Capture Gene TreesMaximum likelihood (ML) trees for each sequence capture gene used for species tree analyses. ML analyses were run with RAxML.SequenceCaptureGeneTrees.tre
DOI: 10.5061/dryad.v53h1
title: Data from: The deep phylogeny of jumping spiders (Araneae, Salticidae)

description: In order to resolve better the deep relationships among salticid spiders,
 we compiled and analyzed a molecular dataset of 169 salticid taxa (and 7
 outgroups) and 8 gene regions. This dataset adds many new taxa to previous
 analyses, especially among the non-salticoid salticids, as well as two new
 genes – wingless and myosin heavy chain. Both of these genes, and
 especially the better sampled wingless, confirm many of the relationships
 indicated by other genes. The cocalodines are placed as sister to
 lapsiines, in a broader clade with the spartaeines. Cocalodines,
 lapsiines, and spartaeines are each supported as monophyletic, though the
 first two have no known morphological synapomorphies. The lyssomanines
 appear to be non-monophyletic, of three separate groups: (1) Lyssomanes
 plus Chinoscopus, (2) Onomastus, and (3) the remainder of Old World
 species. Several previously-inferred relationships continue to be
 supported: hisponines as sister to the Salticoida, Amycoida as sister to
 the remaining Salticoida, and Saltafresia as monophyletic. The
 relationship of Salticus with Philaeus and relatives is now considered
 well enough corroborated to move the latter into the subfamily Salticinae.
 A new clade consisting of the Plexippoida + Aelurilloida + Leptorchesteae
 + Salticinae is recognized. Nungia is found to be an astioid, and
 Echeclus, Gedea and Diplocanthopoda to be hasariines. The euophryines are
 corroborated as monophyletic. The agoriines Agorius and Synagelides are
 salticoids, within the sister group to amycoids, but their further
 placement is problematical, perhaps because of their nuclear ribosomal
 genes’ high GC bias, as also seen in the similarly problematic Eupoa.
description: Maddison et al.
 2014-Deep salticid phylogenyContains alignments for
 8 genes for different samples of taxa, and corresponding
 treesMaddisonEtAl2014-DeepSalticidPhylogeny-MatricesAndTrees.nex
DOI: 10.5061/dryad.6n890
title: Data from: Cenozoic latitudinal response curves: individualistic changes in the latitudinal distributions of marine bivalves and gastropods

description: We use a Gaussian logistic regression model to characterize epoch-to-epoch
 and stage-tostage changes in the latitudinal response curves of Cenozoic
 marine bivalve and gastropod genera along the global latitudinal gradient,
 and analyze these changes to understand the mode and tempo of changes in
 latitudinal distribution. A ubiquitous ‘‘hollow curve’’ pattern is
 apparent, wherein smaller changes in response-curve parameters are much
 more common than larger changes. Curves are strikingly consistent in terms
 of the average level of change exhibited, despite the many unique
 environmental and biological changes documented between each of these
 intervals. This implies that the pace and magnitude of changes in the
 latitudinal distribution of marine mollusks are not controlled, in
 aggregate, by time-period-specific conditions. Additionally, we find no
 evidence for long-term migration from tropical to extratropical latitudes.
 Our results instead favor a model of either equatorward migration or no
 general trend. This likely reflects the tendency of genera to maintain
 their highest concentrations in the tropics even if their ranges become
 extended out of the tropics over time.
description: Pleistocene Data
 (Raw)The Pleistocene data
 from the Paleobiology Database (www.paleobiodb.org), downloaded
 10-09-2013. Please note that this is raw data, un-culled. See the
 manuscript for a discussion of the culled elements.Pleistocene.csvPliocene Data (Raw)The Pliocene data from the Paleobiology Database (www.paleobiodb.org), downloaded 10-09-2013. Please note that this is raw data, un-culled. See the manuscript for a discussion of the culled elements.Pliocene.csvMiocene Data (Raw)The Pleistocene data from the Paleobiology Database (www.paleobiodb.org), downloaded 10-09-2013. Please note that this is raw data, un-culled. See the manuscript for a discussion of the culled elements.Miocene.csvOligocene Data (Raw)The Oligocene data from the Paleobiology Database (www.paleobiodb.org), downloaded 10-09-2013. Please note that this is raw data, un-culled. See the manuscript for a discussion of the culled elements.Oligocene.csvEocene Data (Raw)The Eocene data from the Paleobiology Database (www.paleobiodb.org), downloaded 10-09-2013. Please note that this is raw data, un-culled. See the manuscript for a discussion of the culled elements.Eocene.csvPaleocene Data (Raw)The Paleocene data from the Paleobiology Database (www.paleobiodb.org), downloaded 10-09-2013. Please note that this is raw data, un-culled. See the manuscript for a discussion of the culled elements.Paleocene.csvSUPPLEMENTARY FIGURESThe supplementary figures. For further details see the manuscript.
DOI: 10.5061/dryad.j9v4p
title: Data from: Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon

description: The genes of the major histocompatibility complex (MHC) are an important
 component of the vertebrate immune system and can provide insights into
 the role of pathogen-mediated selection in wild populations. Here we
 examined variation at the MHC class II peptide binding region in 27
 populations of sockeye salmon (Oncorhynchus nerka), distributed among
 three distinct spawning ecotypes, from a complex of interconnected rivers
 and lakes in southwestern Alaska. We also obtained genotypes from 90
 putatively neutral SNPs for each population to compare the relative roles
 of demography and selection in shaping the observed MHC variation. We
 found that MHC divergence was generally partitioned by spawning ecotype
 (lake beaches, rivers, and streams) and was 30 times greater than
 variation at neutral markers. Additionally, we observed substantial
 differences in modes of selection and diversity among ecotypes, with beach
 populations displaying higher levels of directional selection and lower
 MHC diversity than the other two ecotypes. Finally, the level of MHC
 differentiation in our study system was comparable to that observed over
 much larger geographic ranges, suggesting that MHC variation does not
 necessarily increase with increasing spatial scale and may instead be
 driven by fine-scale differences in pathogen communities or pathogen
 virulence. The low levels of neutral structure and spatial proximity of
 populations in our study system indicates that MHC differentiation can be
 maintained through strong selective pressure even when ample opportunities
 for gene flow exist.
description: genotypes for 90 neutral
 SNPs for 27 populationsA genepop file
 containing the genotypes for 88 neutral SNPs from 27 populations. Three
 mitochondrial SNPs (One_CO1, One_Cytb_17, and One_Cytb_26) were phenotyped
 according to the methods of Habicht et al. (2010). SNP names correspond to
 those found in Dann et al. (2012,
 http://www.adfg.alaska.gov/FedAidpdfs/sp12-12.pdf). Population codes are
 found in the readme file.wr_88_snps_27_pops_genepop.txtMHC genotypes for 27 populationsGenepop file of MHC genotypes for 27 populations. Genotypes are coded as haplotypes 1-27 based on the order they were discovered. For example haplotype L1-16 in the manuscript would be coded with a 16 in this file. A description of the haplotypes including their sequence can be found in Table S1 of the manuscript. The readme file for this data file includes information on population abbreviations.MHC_genotypes_WR_27_pops_genepop.txt
DOI: 10.5061/dryad.22v18
title: Data from: Genome sequence and virulence variation-related transcriptome profiles of Curvularia lunata, an important maize pathogenic fungus

description: Background: Curvularia lunata is an important maize foliar fungal pathogen
 that distributes widely in maize growing area in China. Genome sequencing
 of the pathogen will provide important information for globally
 understanding its virulence mechanism. Results: We report the genome
 sequences of a highly virulent C. lunata strain. Phylogenomic analysis
 indicates that C. lunata was evolved from Bipolaris maydis (Cochliobolus
 heterostrophus). The highly virulent strain has a high potential to evolve
 into other pathogenic stains based on analyses on transposases and
 repeat-induced point mutations. C. lunata has a smaller proportion of
 secreted proteins as well as B. maydis than entomopathogenic fungi. C.
 lunata and B. maydis have a similar proportion of protein-encoding genes
 highly homologous to experimentally proven pathogenic genes from
 pathogen-host interaction database. However, relative to B. maydis, C.
 lunata possesses not only many expanded protein families including MFS
 transporters, G-protein coupled receptors, protein kinases and proteases
 for transport, signal transduction or degradation, but also many
 contracted families including cytochrome P450, lipases, glycoside
 hydrolases and polyketide synthases for detoxification, hydrolysis or
 secondary metabolites biosynthesis, which are expected to be crucial for
 the fungal survival in varied stress environments. Comparative
 transcriptome analysis between a lowly virulent C. lunata strain and its
 virulence-increased variant induced by resistant host selection reveals
 that the virulence increase of the pathogen is related to pathways of
 toxin and melanin biosynthesis in stress environments, and that the two
 pathways probably have some overlaps. Conclusions: The data will
 facilitate a full revelation of pathogenic mechanism and a better
 understanding of virulence differentiation of C. lunata.
description: Alignments of
 orthologous proteinsFirstly, 1328
 orthologous proteins were screened out among Curvualria lunata and other
 11 close fungi including Bipolaris maydis, Setosphaeria turcica,
 Pyrenophora tritici-repentis, Phaeosphaeria nodorum, Cercospora zea-madis,
 Aspergillus flavus, Magnaporthe oryzae, Fusarium graminearum,
 Saccharomyces cerevisiae, and Ustilago maydis with a cutoff E value of
 1e-20. Secondly, these orthologous proteins were aligned using Clustal W
 2.1. Lastly, the aligned proteins were concatenatedorthologous_proteins_align.fastaPhylogenetic treeThe concatenated amino acid sequences were used to create a neighbor-joining tree using TREE-PUZZLE program with the Dayhoff model. The divergence time between species was estimated using r8s software with the Langley-Fitch medel by calibrating with the origin of the Ascomycota at 500-650 million years ago.phylogenetic tree.txt
DOI: 10.5061/dryad.4158c
title: Data from: Microhabitat differences impact phylogeographic concordance of co-distributed species: genomic evidence in montane sedges (Carex L.) from the Rocky Mountains

description: By selecting co-distributed, closely related montane sedges from the Rocky
 Mountains that are similar in virtually all respects but one – their
 microhabitat affinities – we test predictions about how patterns of
 genetic variation are expected to differ between Carex nova, an inhabitant
 of wetlands, and Carex chalciolepis, an inhabitant of drier meadows,
 slopes, and ridges. Although contemporary populations of the taxa are
 similarly isolated, the distribution of glacial moraines suggests
 thattheirpast population connectedness would have differed. Sampling of
 co-distributed population pairs from different mountain ranges combined
 with the resolution provided by over 24,000 SNP loci
 supportsmicrohabitat-mediated differences in the sedges’ patterns of
 genetic variation that are consistent with their predicted differences in
 the degree of isolation of ancestral source populations.Our results
 highlight how microhabitat preferences may interact with glaciations to
 produce fundamental differences in the past distributions of presently
 co-distributed species. We discuss the implications of these findings for
 generalizing the impacts of climate-induced distributional shifts for
 communities, as well as for the prospects of gaining insights about
 species-specific deterministic processes, not just deterministic community
 level responses, from comparative phylogeographic study.
description: Carex chalciolepis
 distribution pointsThis file contains the
 latitude and longitude for populations from throughout this species'
 range. The data are gathered from verified voucher specimens at the Rocky
 Mountain Herbarium and personal field work. This information was used for
 Maxent distribution modeling.chal.txtCarex nova distribution pointsThis file contains the latitude and longitude for populations from throughout this species' range. The data are gathered from verified voucher specimens at the Rocky Mountain Herbarium and personal field work. This information was used for Maxent distribution modeling.nova.txtQC script for cleaning raw Illumina dataThis script was used to filter low quality reads from the raw Illumina data.thin_illumina_fastq_based_on_quality_singleEnd.pyQC script for removing adaptorsThis script was used for removing portions of the Illumina reads that were not needed.remove_adaptors_illumina_reads.pychal_structureThis file contains the data for Carex chalciolepis that was used for Structure and PCA analyses.nova_structureThis file contains the data for Carex nova that was used for Structure and PCA analyses.
DOI: 10.5061/dryad.f2h6r
title: Data from: Atolchelys lepida, a new side-necked turtle from the Early Cretaceous of Brazil and the age of crown Pleurodira

description: We report a new pleurodiran turtle from the Barremian Morro do Chaves
 Formation, Sergipe-Alagoas Basin, Brazil. We tested the phylogenetic
 position of Atolchelys lepida gen. et sp. nov. by including it in a
 comprehensive cladistic analysis of pleurodires. The new species is a
 basal member of Bothremydidae and simultaneously the oldest unambiguous
 crown Pleurodira. The biogeographic and chronostratigraphic significance
 of the finding has implications for the calibration of molecular clocks
 studies by pushing back the minimum age of crown Pleurodira by more than
 12 Ma (ca 125 Ma). The reanalysis of Pelomedusoides relationships provides
 evidence that the early evolution and relationships among the main
 lineages of side-necked turtles can be explained, at least partially, by a
 sequence of vicariance events.
description: Electronic Supplementary
 MaterialElectronic Supplementary
 Material of the paper "Atolchelys lepida, a new side-necked turtle
 from the Early Cretaceous of Brazil and the age of crown
 Pleurodira"Romano_RSBL-2014-0290.R1_ESM_10-07-14_final.pdf
DOI: 10.5061/dryad.4m5b5
title: Data from: Size, shape, and systematics of the Silurian trilobite Aulacopleura koninckii

description: A new dataset of the highest quality specimens of fully articulated,
 juvenile and mature exoskeletons of the Czech middle Silurian trilobite
 Aulacopleura koninckii offers improved resolution of original morphology
 by all measures considered. The degree of variation in both size and shape
 among later meraspid instars was constant, and suggesting targeted growth
 in both attributes. Size-related changes in the shape of the dorsal
 exoskeleton and of the segment-invariant cephalon were detected in the
 meraspid stage, but in the holaspid phase marked allometry was detected
 only in the trunk region, with the pygidium showing notable expansion in
 relative size. Meraspid cranidial allometry was subtle, with significant
 changes in instar form detectable only after several molts. This trilobite
 developed gradually throughout meraspid and holaspid ontogeny, with the
 synchronous cessation of trunk segment appearance and release at the onset
 of the holaspid phase. Precise development of shape and size occurs in the
 context of marked variability in the number of trunk segments at maturity,
 illustrating complex patterns of character variation within a species. A
 new systematic description establishes the synonymy of several subspecies
 with A. koninckii.
description: Supplemental
 DataSupplemental
 DataSupplemental.docx
DOI: 10.5061/dryad.bt963
title: Data from: Morphological, cellular and molecular evidences of chromosome random elimination in vivo upon haploid induction in maize

description: The mechanism of maternal in vivo haploid induction is not fully
 understood. In this study, the young embryos were identified by
 morphology, cytology and simple sequence repeat (SSR) markers at different
 developmental stages in the cross HZ514 (sweet corn) × HZI1 (inducer). The
 results indicated that the low seed setting rate was determined by the
 inducer pollen during the process of fertilization. The mosaic endosperm
 kernels and the different percentages of aneuploidy, mixploidy, lagged
 chromosome, micronuclei, chromosomal bridge and ring chromosome were found
 in the cross; 7.37% of the haploid embryos carried chromosome segments
 from HZI1. About 1% twin seedlings resulted from the cross and were
 analyzed by cytology and SSR markers. Four pairs of twin seedlings had
 different chromosome numbers (2n = 20 and 2n = 10–20) and there were some
 chromosome fragments from HZI1. Aneuploidy, mixploidy and the abnormal
 chromosomes occurred in the in vivo haploid induction by HZI1, which is
 the cytological basis for haploid induction and indicates that the
 inducer's chromosomes are prone to be lost during mitotic and meiotic
 divisions. Morphological, cellular and molecular evidences reveal that
 complete or partial chromosome elimination from inducer HZI1 controls the
 maize in vivo haploid induction.
description: Phenotype and cytology
 raw data for CPB paperPhenotype and cytology
 raw data for the paper "Morphological, cellular and molecular
 evidences of chromosome random elimination in vivo upon haploid induction
 in maize".raw data for
 cpb.docxthe sequence of SSR
 markersthe sequence of SSR
 markers for polymorphism analysis in the manuscript and some markers were
 used for haploid genotype analysis.
DOI: 10.5061/dryad.q6h4n
title: Data from: The effects of the avoidance of infectious hosts on infection risk in an insect-pathogen interaction

description: In many animal host-pathogen interactions, uninfected hosts either avoid
 or are attracted to infected conspecifics, but understanding how such
 behaviors affect infection risk is difficult. In experiments, behaviors
 are often eliminated entirely, which allows demonstration that a behavior
 affects risk but makes it impossible to quantify effects of individual
 behaviors. In models, host behaviors have been studied using ordinary
 differential equations, which can be easily analyzed but cannot be used to
 relate individual behaviors to risk. For many insect baculoviruses,
 however, quantifying effects of behavior on risk is straightforward
 because transmission occurs when host larvae accidentally consume
 virus-contaminated foliage. Moreover, increases in computing power have
 made it possible to fit complex models to data. We therefore used
 experiments to quantify the behavior of gypsy moth larvae feeding on oak
 leaves contaminated with virus-infected cadavers, and we tested for
 effects of cadaver-avoidance behavior by fitting stochastic simulation
 models to our data. The models that best explain the data include cadaver
 avoidance, and comparison of models that do and do not include cadaver
 avoidance shows that this behavior substantially reduces infection risk.
 Our work demonstrates that host behaviors that affect exposure risk play a
 key role in baculovirus transmission and adds to the growing consensus
 that host behavior can strongly alter pathogen transmission rates.
description: Discretized images of
 virus-contaminated leaves fed on by gypsy mothsLeaf grids used for
 analyses and simulations. These grids are discretized images of red oak
 leaves that were used in an experiment in which individual gypsy moth
 larvae were allowed to feed on single leaves for 24h. Each leaf was
 infected with at least one infectious cadaver of a first-instar larva
 killed by a baculovirus. Healthy fourth-instar larvae were then allowed to
 feed on the leaves (one leaf per larva) for 24 hours. The grids show the
 leaf area, as well as the location of the cadaver(s) and each larva's
 feeding history. The infection outcome for each larva is also recorded.
 Also included is an index file labeled
 'Eakin_et_al_2014_leaf_grids.dat', which contains the file name
 for each leaf grid, the dimension of the grid (in pixels), the infection
 outcome for the larva (0=uninfected, 1 = infected), and the predicted
 probability of infection calculated using the infection model in the
 associated article. Lastly, there is also some R code titled
 'visualize_leaf_grids.R' that will create a visual
 representation of the numerical leaf grids. See the README file for more
 details.LeafGrids.zip