cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9jn6r
title: Data from: Buchnera has changed flatmate but the repeated replacement of co-obligate symbionts is not associated with the ecological expansions of their aphid hosts

description: Symbiotic associations with bacteria have facilitated important
 evolutionary transitions in insects and resulted in long-term obligate
 interactions. Recent evidence suggests that these associations are not
 always evolutionarily stable and that symbiont replacement and/or
 supplementation of an obligate symbiosis by an additional bacterium has
 occurred during the history of many insect groups. Yet, the factors
 favoring one symbiont over another in this evolutionary dynamic are not
 well understood; progress has been hindered by our incomplete
 understanding of the distribution of symbionts across phylogenetic and
 ecological contexts. While many aphids are engaged into an obligate
 symbiosis with a single Gammaproteobacterium, Buchnera aphidicola, in
 species of the Lachninae subfamily, this relationship has evolved into a
 “ménage à trois”, in which Buchnera is complemented by a co-symbiont,
 usually Serratia symbiotica. Using deep sequencing of 16S rRNA bacterial
 genes from 128 species of Cinara (the most diverse Lachninae genus), we
 reveal a highly dynamic dual symbiotic system in this aphid lineage. Most
 species host both Serratia and Buchnera but, in several clades,
 endosymbionts related to Sodalis, Erwinia or an unnamed member of the
 Enterobacteriaceae have replaced Serratia. Endosymbiont genome sequences
 from four aphid species confirm that these co-resident symbionts fulfill
 essential metabolic functions not ensured by Buchnera. We further
 demonstrate through comparative phylogenetic analyses that co-symbiont
 replacement is not associated with the adaptation of aphids to new
 ecological conditions. We propose that symbiont succession was driven by
 factors intrinsic to the phenomenon of endosymbiosis, such as rapid genome
 deterioration or competitive interactions between bacteria with similar
 metabolic capabilities.
description: bacterial16SMiseqCinarafastq1bacterial16SMiseqCinarafastq2Appendix 1Appendix 1 includes collection details for aphid samples and GenBank accession numbersMeseguer_etal-Appendix-1.xlsxAppendix 2Appendix 2 shows a contingency table reporting bacterial sequence occurrences across aphid samplesMeseguer_etal-Appendix-2.xlsxAppendix 3Appendix 3 includes a summary of the number of reads and unique sequences per sampleMeseguer_etal-Appendix-3.xlsx
DOI: 10.5061/dryad.t096s
title: Data from: Succession of arbuscular mycorrhizal fungi along a 52-year agricultural recultivation chronosequence

description: Arbuscular mycorrhizal (AM) fungi provide a range of functions in natural
 and managed ecosystems. However, the trajectory of AM fungal diversity
 after land degradation is poorly known. We studied the succession of AM
 fungi along an agricultural recultivation chronosequence after open-cast
 mining near Cologne, Germany. We used high-throughput sequencing of the
 large-subunit ribosomal RNA genes to characterize the soil AM fungal
 communities of 10 agricultural fields spanning 52 years of recultivation.
 During three years, soils are recultivated with a legume, and then
 converted to agriculture to be later returned to local farmers
 implementing conventional agriculture. Our data reveal a quick and strong
 recovery of AM fungal richness after a few years of recultivation, but
 also a rapid decline following years of conventional agriculture. The
 community structure was strongly correlated to mineral nitrogen and
 phosphorus, richness peaking at high N:P ratio. This work represents the
 first molecular data documenting temporal patterns of AM fungal
 communities in agriculture; it shows the deleterious effect of
 conventional agricultural practices on AM fungal communities developing
 over time. Nonetheless, the highly dynamic nature of AM fungal communities
 suggests strategies for site-level management for which considering N:P
 stoichiometry is crucial.
description: fastq.part1Raw sequences reads, demultiplexed paired-end fastq files, samples S1-S75fastq.part2Raw sequences reads, demultiplexed paired-end fastq files, samples S76-S150postprocessed_dataAll post-processed tables used for statistical analyses, including the OTUs contingency table (otu97_table.txt), the metadata associated with each sample (metadata_table.odt), and the idenitifed taxonomy of each OTU (otu97_taxo).
DOI: 10.5061/dryad.30k4v
title: Data from: Phylogenomics of Lophotrochozoa with consideration of systematic error

description: Phylogenomic studies have improved understanding of deep metazoan
 phylogeny and show promise for resolving incongruences among analyses
 based on limited numbers of loci. One region of the animal tree that has
 been especially difficult to resolve, even with phylogenomic approaches,
 is relationships within Lophotrochozoa (the animal clade that includes
 molluscs, annelids, and flatworms among others). Lack of resolution in
 phylogenomic analyses could be due to insufficient phylogenetic signal,
 limitations in taxon and/or gene sampling, or systematic error. Here, we
 investigated why lophotrochozoan phylogeny has been such a difficult
 question to answer by identifying and reducing sources of systematic
 error. We supplemented existing data with 32 new transcriptomes spanning
 the diversity of Lophotrochozoa and constructed a new set of
 Lophotrochozoa-specific core orthologs. Of these, 638 orthologous groups
 (OGs) passed strict screening for paralogy using a tree-based approach. In
 order to reduce possible sources of systematic error, we calculated
 branch-length heterogeneity, evolutionary rate, percent missing data,
 compositional bias, and saturation for each OG and analyzed increasingly
 stricter subsets of only the most stringent (best) OGs for these five
 variables. Principal component analysis of the values for each factor
 examined for each OG revealed that compositional heterogeneity and average
 patristic distance contributed most to the variance observed along the
 first principal component while branch-length heterogeneity and, to a
 lesser extent, saturation contributed most to the variance observed along
 the second. Missing data did not strongly contribute to either. Additional
 sensitivity analyses examined effects of removing taxa with heterogeneous
 branch lengths, large amounts of missing data, and compositional
 heterogeneity. Although our analyses do not unambiguously resolve
 lophotrochozoan phylogeny, we advance the field by reducing the list of
 viable hypotheses. Moreover, our systematic approach for dissection of
 phylogenomic data can be applied to explore sources of incongruence and
 poor support in any phylogenomic dataset.
description: Assembliesassemblies.zipPreliminary_BI_resultsML_resultsSupplementary TablesSupplementary_Tables.zipLophotrochozoa-Kocot_core_orthologsSupplementary FiguresSupplementary Figures 1-70.Supplementary_Figures.zip
DOI: 10.5061/dryad.m8t72
title: Data from: Female dietary bias towards large migratory moths in the European free-tailed bat (Tadarida teniotis)

description: In bats, sexual segregation has been described in relation to differential
 use of roosting and foraging habitats. It is possible that variation may
 also exist between genders in the use of different prey types. However,
 until recently this idea was difficult to test owing to poorly resolved
 taxonomy of dietary studies. Here, we use high-throughput sequencing to
 describe gender-related variation in diet composition of the European
 free-tailed bat (Tadarida teniotis), while controlling for effects of age
 and season. We analysed guano pellets collected from 143 individuals
 mist-netted from April to October 2012 and 2013, in northeast Portugal.
 Moths (Lepidoptera; mainly Noctuidae and Geometridae) were by far the most
 frequently recorded prey, occurring in nearly all samples and accounting
 for 96 out of 115 prey taxa. There were significant dietary differences
 between males and females, irrespective of age and season. Compared to
 males, females tended to consume larger moths and more moths of migratory
 behaviour (e.g. Autographa gamma). Our study provides the first example of
 gender-related dietary variation in bats, illustrating the value of novel
 molecular tools for revealing intraspecific variation in food resource use
 in bats and other insectivores.
description: Sequence Raw Data - Part
 1First part of a file
 containing the raw illumina sequencing data regarding Tadarida teniotis
 diet described in Mata et al.RawData_Mata_etal.part1.rarSequence Raw Data - Part 2Second part of a file containing the raw illumina sequencing data regarding Tadarida teniotis diet described in Mata et al.RawData_Mata_etal.part2.rarSequence Raw Data - Part 3Third part of a file containing the raw illumina sequencing data regarding Tadarida teniotis diet described in Mata et al.RawData_Mata_etal.part3.rarSequence Raw Data - Part 4Fourth part of a file containing the raw illumina sequencing data regarding Tadarida teniotis diet described in Mata et al.RawData_Mata_etal.part4.rarSample SheetSample sheet of the illumina sequencing data regarding Tadarida teniotis diet described in Mata et al.SampleSheet_Mata_etal.xlsxDiet analysis datasetData used for analysis. Contains all the prey identified in the diet per sample, as well as the characteristics of the prey and the samples.dataset_Mata.et.al.2016.xlsx
DOI: 10.5517/ccdc.csd.cc1p0z7x
title: CCDC 1550069: Experimental Crystal Structure Determination

description: Related Article: Volkmar Trommer, Fabian Fischer, Marko Hapke|2018|Monatsh.Chem.|149|755|doi:10.1007/s00706-017-2083-9
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1p70hf
title: CCDC 1555874: Experimental Crystal Structure Determination

description: Related Article: Lynn Ferres, Khai-Nghi Truong, Wolfgang Stahl, Ha Vinh Lam Nguyen|2018|ChemPhysChem|19|1781|doi:10.1002/cphc.201800115
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.0vm37
title: Data from: A genome for gnetophytes and early evolution of seed plants

description: Gnetophytes are an enigmatic gymnosperm lineage comprising three genera,
 Gnetum, Welwitschia and Ephedra, which are morphologically distinct from
 all other seed plants. Their distinctiveness has triggered much debate as
 to their origin, evolution and phylogenetic placement among seed plants.
 To increase our understanding of the evolution of gnetophytes, and their
 relation to other seed plants, we report here a high-quality draft genome
 sequence for Gnetum montanum, the first for any gnetophyte. By using a
 novel genome assembly strategy to deal with high levels of heterozygosity,
 we assembled &gt;4 Gb of sequence encoding 27,491 protein-coding
 genes. Comparative analysis of the G. montanum genome with other
 gymnosperm genomes unveiled some remarkable and distinctive genomic
 features, such as a diverse assemblage of retrotransposons with evidence
 for elevated frequencies of elimination rather than accumulation,
 considerable differences in intron architecture, including both length
 distribution and proportions of (retro) transposon elements, and
 distinctive patterns of proliferation of functional protein domains.
 Furthermore, a few gene families showed Gnetum-specific copy number
 expansions (for example, cellulose synthase) or contractions (for example,
 Late Embryogenesis Abundant protein), which could be connected with
 Gnetum’s distinctive morphological innovations associated with their
 adaptation to warm, mesic environments. Overall, the G. montanum genome
 enables a better resolution of ancestral genomic features within seed
 plants, and the identification of genomic characters that distinguish
 Gnetum from other gymnosperms.
description: READMEreadmeGmm.final.pepAmino acid FASTA format file of all gene coding sequences, with or without alternative splice variantsGmm.final.cdsNucleotide FASTA format file of all gene coding sequences, with or without alternative splice variantsGmm.final.gffGFF3 format representation of all mRNA sequences (UTR, CDS). Genomic coordinates are relative to the referenceall.repeat.gffrepeat gffGnetum.final.part01genome fa file (which was compressed into four files)Gnetum.final.part02genome fa file (which was compressed into four files)Gnetum.final.part03genome fa file (which was compressed into four files)Gnetum.final.part04genome fa file (which was compressed into four files)InterPro.resultFunctional annotation(InterPro)IPR2GO.resultFunctional annotation(IPR2GO)KEGG.resultFunctional annotation(KEGG)Swissprot.resultFunctional annotation(Swissprot)TrEMBL.resultFunctional annotation(TrEMBL)Wmi_unigene.cut200.faUnigene of Welwitschia mirabilisGmo_unigene.cut200.faUnigene of Gnetum montanumEeq_unigene.cut200.faUnigene of Ephedra equisetina
DOI: 10.5061/dryad.gm073
title: Data from: Increased power to dissect adaptive traits in global sorghum diversity using a nested association mapping population

description: Adaptation of domesticated species to diverse agroclimatic regions has led
 to abundant trait diversity. However, the resulting population structure
 and genetic heterogeneity confounds association mapping of adaptive
 traits. To address this challenge in sorghum [Sorghum bicolor (L.)
 Moench]—a widely adapted cereal crop—we developed a nested association
 mapping (NAM) population using 10 diverse global lines crossed with an
 elite reference line RTx430. We characterized the population of 2214
 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing.
 The population captures ∼70% of known global SNP variation in sorghum, and
 57,411 recombination events. Notably, recombination events were four- to
 fivefold enriched in coding sequences and 5′ untranslated regions of
 genes. To test the power of the NAM population for trait dissection, we
 conducted joint linkage mapping for two major adaptive traits, flowering
 time and plant height. We precisely mapped several known genes for these
 two traits, and identified several additional QTL. Considering all SNPs
 simultaneously, genetic variation accounted for 65% of flowering time
 variance and 75% of plant height variance. Further, we directly compared
 NAM to genome-wide association mapping (using panels of the same size) and
 found that flowering time and plant height QTL were more consistently
 identified with the NAM population. Finally, for simulated QTL under
 strong selection in diversity panels, the power of QTL detection was up to
 three times greater for NAM vs. association mapping with a diverse panel.
 These findings validate the NAM resource for trait mapping in sorghum, and
 demonstrate the value of NAM for dissection of adaptive traits.
description: SRX2999295Key file to the GBS data linked to NCBI database https://www.ncbi.nlm.nih.gov/sra/SRX2999295NAM_Key_file.txtRaw hapmap fileIllumina Hi-Seq datanam_raw.hmp.txt.zipSorghum GenomeCurrent genome version of sorghum (v3)nam_composite2017.hmp.txtnam_compositenam_composite.mapgenotypes_lubbockgenotypes_weslacogenotypes_gringeno_grin60K.csvgeno_sap60Kgeno_nam60Kgeno_grin60Kscript_simulationdiv_imputed.hmp.txtdiv_raw.hmp.txtmap.compositediv_rec_dist.chr_defheterozygosityrecombinationinfo_marker_genemonomorphismprop_Tx430_distorsion
DOI: 10.5061/dryad.6524f
title: Data from: HiMAP: robust phylogenomics from highly multiplexed amplicon sequencing

description: High-throughput sequencing has fundamentally changed how molecular
 phylogenetic datasets are assembled, and phylogenomic datasets commonly
 contain 50-100-fold more loci than those generated using traditional
 Sanger-based approaches. Here, we demonstrate a new approach for building
 phylogenomic datasets using single tube, highly multiplexed amplicon
 sequencing, which we name HiMAP (Highly Multiplexed Amplicon-based
 Phylogenomics), and present bioinformatic pipelines for locus selection
 based on genomic and transcriptomic data resources and post-sequencing
 consensus calling and alignment. This method is inexpensive and amenable
 to sequencing a large number (hundreds) of taxa simultaneously, requires
 minimal hands-on time at the bench (&lt;1/2 day), and data analysis
 can be accomplished without the need for read mapping or assembly. We
 demonstrate this approach by sequencing 878 amplicons in single reactions
 for 82 species of tephritid fruit flies across seven genera (384
 individuals), including some of the most economically-important
 agricultural insect pests. The resulting filtered dataset (&gt;150,000
 bp concatenated alignment, ~20% missing character sites across all
 individuals and amplicons) contained &gt;40,000 phylogenetically
 informative characters, and although some discordance was observed between
 analyses, it provided unparalleled resolution of many phylogenetic
 relationships in this group. Most notably, we found high support for the
 generic status of Zeugodacus and the sister relationship between Dacus and
 Zeugodacus. We discuss HiMAP, with regard to its molecular and
 bioinformatic strengths, and the insight the resulting dataset provides
 into relationships of this diverse insect group.
description: amplicon_alignments_ntamplicon alignments in nucleotide spaceamplicon_alignments_pepamplicon alignments in peptide spaceASTRAL_INPUT_all_raxml_genetreesinput trees for ASTRAL analysisASTRAL_INPUT_CONFIG_spp_indsRmvdconfig file for ASTRAL analysisEXABAYES_INPUT_CONFIG_configconfig file for EXABAYES analysisFigureS1-S6Supplemental figures S1-S6Full_HiMAP_part01_inputfull input for HiMAP part01Full_HiMAP_part02_inputfull input for HiMAP part02OrthoMCL_inputfull input for OrthoMCLPARTITIONFINDER_INPUT_CONFIG_partition_finder_ntconfig file for PartitionFinder (nucleotide space)PARTITIONFINDER_INPUT_CONFIG_partition_finder_pepconfig file for PartitionFinder (peptide space)POMO_INPUT_Teph3_878genes_cutInds100_cutGenes200input file for POMO analysisSVDQUARTETS_INPUT_Teph3_878genes_cutInds100_cutGenes200_svdq_noLoginput file for SVDquartets analysisTables_S1-S5Supplemental tables S1-S5Teph3_878genes_cutInds100_cutGenes200_Peptidesconcatenated alignment (peptide space)Teph3_878genes_cutInds100_cutGenes200concatenated alignment (nucleotide space)Dupuis_10.5061_dryad.6524f
DOI: 10.5061/dryad.2h3f2
title: Data from: Species interactions in occurrence data for a community of tick-transmitted pathogens

description: Interactions between species of ticks, their realised range of hosts, the
 pathogens they carry and transmit, as well as the geographical
 distribution of species in the Western Palearctic, have been obtained
 based on evidence published between 1970–2014. These relationships were
 linked to remotely-sensed features of temperature and vegetation and used
 to extract the network of interactions among the organisms. The resulting
 datasets were focussed on niche overlap among ticks and hosts, species
 interactions and the fraction of the environmental niche where tick-borne
 pathogens may circulate, as a result of interactions and environmental
 trait overlap. The presented datasets provide a valuable resource for
 researchers of tick-borne pathogens, as they conciliate the abiotic and
 biotic sides of their niche, allowing exploration of the importance of
 each species of vertebrate reservoir in the circulation of
 tick-transmitted pathogens at intervals of the environmental niche.
description: Dataset of records of
 ticks, hosts, and pathogens (with climate and coordinates) in Western
 PalearcticThis file contains a
 description of the data package contents for Estrada-Peña and de la Fuente
 (2016) "Species interactions in occurrence data for a community of
 tick-transmitted pathogens"description_of_dataPackage_contents.rtfEnvironmental variablesCoordinates of HostsCoordinates of hosts.zipCoordinates of ticks with hosts recordsMaps of predicted distribution of hostsMaps of distribution of hosts.zipMaps of predicted distribution of ticksData for networksCalculating CwHOFourier coefficients
DOI: 10.5061/dryad.sf654
title: Data from: A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat)

description: One common goal in evolutionary biology is the identification of genes
 underlying adaptive traits of evolutionary interest. Recently
 next-generation sequencing techniques have greatly facilitated such
 evolutionary studies in species otherwise depauperate of genomic
 resources. Kangaroo rats (Dipodomys sp.) serve as exemplars of adaptation
 in that they inhabit extremely arid environments, yet require no drinking
 water because of ultra-efficient kidney function and osmoregulation. As a
 basis for identifying water conservation genes in kangaroo rats, we
 conducted a priori bioinformatics searches in model rodents (Mus musculus
 and Rattus norvegicus) to identify candidate genes with known or suspected
 osmoregulatory function. We then obtained 446,758 reads via 454
 pyrosequencing to characterize genes expressed in the kidney of
 banner-tailed kangaroo rats (Dipodomys spectabilis). We also determined
 candidates a posteriori by identifying genes that were overexpressed in
 the kidney. The kangaroo rat sequences revealed nine different a priori
 candidate genes predicted from our Mus and Rattus searches, as well as 32
 a posteriori candidate genes that were overexpressed in kidney. Mutations
 in two of these genes, Slc12a1 and Slc12a3, cause human renal diseases
 that result in the inability to concentrate urine. These genes are likely
 key determinants of physiological water conservation in desert rodents.
description: Trimmed_Kidney_ReadsThese are the trimmed fasta and qual files for each of the individual kidney libraries and all of the individual libraries together in a whole tissue fileTrimmed_Spleen_ReadsTrimmed .fasta and .qual files for each individual spleen library and for the total tissue libraryKidney_contigsThese are the .fasta and .ace files for all of the contigs from individual kidney assemblies as well as all of the kidney libraries assembled into one total 'kidney' assembly as described in the paper.Spleen_contigsThis file contains all of the spleen .fasta and .ace files for the contigs of all assemblies of individual spleen libraries as well as a total tissue 'spleen' libraryIndividual_Kidney_libraries_raw_readsIndividual .sff files for each of four individuals, for kidneySpleen_indiv_libraries_raw_readsIndividual .sff files for each of four individuals, for spleenTotal_kidney_raw_readsSingle .sff file with all reads from the four individual kidney libraries concatenated into one total tissue fileSpleen_total_raw_readsSingle .sff file with all reads from the four individual spleen libraries concatenated into one total tissue file