cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7334t
title: Data from: High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens

description: The study of arid palaeoenvironments is often frustrated by the poor or
 non-existent preservation of plant and animal material, yet these
 environments are of considerable environmental importance. The analysis of
 pollen and macrofossils isolated from herbivore middens has been an
 invaluable source of information regarding past environments and the
 nature of ecological fluctuations within arid zones. The application of
 ancient DNA (aDNA) techniques to hot, arid zone middens remains
 unexplored. This paper attempts to retrieve and characterise aDNA from
 four Southern Hemisphere fossil middens; three located in hot, arid
 regions of Australia and one sample from South Africa’s Western Cape
 province. The middens are dated to between 30,490 (±380) and 710 (±70) cal
 yr BP. The Brockman Ridge midden in this study is potentially the oldest
 sample from which aDNA has been successfully extracted in Australia. The
 application of high-throughput sequencing approaches to profile the biotic
 remains preserved in midden material has not been attempted to date and
 this study clearly demonstrates the potential of such a methodology. In
 addition to the taxa previously detected via macrofossil and palynological
 analyses, aDNA analysis indentified unreported plant and animal taxa, some
 of which are locally extinct or endemic. The survival and preservation of
 DNA in hot, arid environments is a complex and poorly understood process
 that is both sporadic and rare, but the survival of DNA through
 desiccation may be important. Herbivore middens now present an important
 source of material for DNA metabarcoding studies of hot, arid
 palaeoenvironments and can potentially be used to analyse middens in these
 environments throughout Australia, Africa, the Americas and the Middle
 East.
description: CR_plant_trnLPlant trnL sequences from the midden located at Cavenagh Range, Western AustraliaTK_plant_trnLPlant trnL sequences from the midden located at Truitjes Kraal, Western Cape, South AfricaYR_plant_trnLPlant trnL sequences from the midden located at Young Range, Western AustraliaBR_mammal_16SMammalian 16S sequences from the midden located at Brockman Ridge, Western AustraliaBR_plant_trnLPlant trnL sequences from the midden located at Brockman Ridge, Western AustraliaCR_mammal_16SMammalian 16S sequences from the midden located at Cavenagh Range, Western AustraliaTK_mammal_16SMammalian 16S sequences from the midden located at Truitjes Kraal, South AfricaYR_mammal_16SMammalian 16S sequences from the midden located at Young Range, Western AustraliaBR_mammal_12SMammalian 12S sequences from the midden located at Brockman Ridge, Western AustraliaCR_mammal_12SMammalian 12S sequences from the midden located at Cavenagh Range, Western AustraliaTK_mammal_12SMammalian 12S sequences from the midden located at Truitjes Kraal, South AfricaYR_mammal_12SMammalian 12S sequences from the midden located at Young Range, Western Australia
DOI: 10.5061/dryad.rh7f4
title: Data from: Direct sequencing of haplotypes from diploid individuals through a modified emulsion PCR-based single-molecule sequencing approach

description: While standard DNA sequencing approaches readily yield genotypic sequence
 data, haplotype information is often of greater utility for population
 genetic analyses. However, obtaining individual haplotype sequences can be
 costly and time consuming, and sometimes requires statistical
 reconstruction approaches that are subject to bias and error. Advancements
 have recently been made in determining individual chromosomal sequences in
 large-scale genomic studies, yet few options exist for obtaining this
 information from large numbers of highly polymorphic individuals in a cost
 effective manner. As a solution, we developed a simple PCR-based method
 for obtaining sequence information from individual DNA strands using
 standard laboratory equipment. The method employs a water-in-oil emulsion
 to separate the PCR mixture into thousands of individual microreactors.
 PCR within these small vesicles results in amplification from only a
 single starting DNA template molecule, and thus a single haplotype. We
 improved upon previous approaches by including SYBR Green I and a melted
 agarose solution in the PCR reaction, allowing easy identification and
 separation of individually amplified DNA molecules. We demonstrate the use
 of this method on a highly polymorphic estuarine population of the copepod
 Eurytemora affinis for which current molecular and computational methods
 for haplotype determination have been inadequate.
description: Emulsion PCR derived
 Haplotype SequencesHaplotypes derived by
 single molecule sequencing using emulsion PCR. Samples are from
 populations of E. affinis, either collected from Racine Harbor (R) in Lake
 Michigan or from Saint-Jean Port Joli (J) in Quebec. Numbers after the
 letter indicate sample number within the laboratory. Samples with only a
 single letter/number combination are single individuals. Samples with
 multiple letter/number combinations are mixtures of individuals. Samples
 derived from traditional, non-emulsion PCR and sequencing are indicated
 (NE). Samples derived from emulsion PCR and sequencing are numbered to
 indicate independent amplifications. All samples were sequenced in both
 directions.Metzger et al.
 MER.tar
DOI: 10.5061/dryad.27d0g
title: Data from: Lateral gene transfer from the dead

description: In phylogenetic studies, the evolution of molecular sequences is assumed
 to have taken place along the phylogeny traced by the ancestors of extant
 species. In the presence of lateral gene transfer (LGT), however, this may
 not be the case, because the species lineage from which a gene was
 transferred may have gone extinct or not have been sampled. Because it is
 not feasible to specify or reconstruct the complete phylogeny of all
 species, we must describe the evolution of genes outside the represented
 phylogeny by modelling the speciation dynamics that gave rise to the
 complete phylogeny. We demonstrate that if the number of sampled species
 is small compared to the total number of existing species, the
 overwhelming majority of gene transfers involve speciation to, and
 evolution along extinct or unsampled lineages. We show that the evolution
 of genes along extinct or unsampled lineages can to good approximation be
 treated as those of independently evolving lineages described by a few
 global parameters. Using this result, we derive an algorithm to calculate
 the probability of a gene tree and recover the maximum likelihood
 reconciliation given the phylogeny of the sampled species. Examining 473
 near universal gene families from 36 cyanobacteria, we find that nearly a
 third of transfer events − 28% – appear to have topological signatures of
 evolution along extinct species, but only approximately 6% of transfers
 trace their ancestry to before the common ancestor of the sampled
 cyanobacteria.
description: alnsThe dataset was
 constructed for near universal single copy genes from all 36
 cyanobacterial genomes found in version 5 the HOGENOM database. For each
 family sequences were aligned using MUSCLE with default parameters. The
 multiple alignment was subsequently cleaned using GBLOCKS as described in
 the Appendix.treesFor each of the 473
 families we inferred a gene topology G that maximizes the joint likelihood
 given by the product of the likelihood of observing the unrooted gene tree
 topology G according to the exODT model developed in the manuscript and
 the classic Felsenstein likelihood of the alignment. All trees are in
 Newick format.
DOI: 10.5061/dryad.2rk39
title: Data from: Generic recircumscriptions of Oncidiinae (Orchidaceae: Cymbidieae) based on maximum likelihood analysis of combined DNA datasets

description: Phylogenetic relationships within the orchid subtribe Oncidiinae sensu
 Chase were inferred using maximum likelihood analyses of single and
 multilocus DNA sequence data sets. Analyses included both nuclear
 ribosomal internal transcribed spacer DNA and plastid regions (matK exon,
 trnH-psbA intergenic spacer and two portions of ycf1 exon) for 736
 individuals representing approximately 590 species plus seven outgroup
 taxa. Based on the well resolved and highly supported results, we
 recognize 61 genera in Oncidiinae. Mimicry of oil-secreting Malpighiaceae
 and other floral syndromes evolved in parallel across the subtribe, and
 many clades exhibit extensive variation in pollination-related traits.
 Because previous classifications heavily emphasized these floral features,
 many genera recognized were not monophyletic. Our classification based on
 monophyly will facilitate focused monographs and clarifies the evolution
 of morphological and biochemical traits of interest within this highly
 diverse subtribe.
description: Oncidiinae Neubig et al
 5 regionNexus file of DNA
 sequence data of five combined DNA regionsOncidiinae Neubig et al
 7 regionNexus file of DNA
 sequence data of 7 DNA regions of Oncidiinae
DOI: 10.5061/dryad.rs4k0
title: Data from: The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq

description: Few studies have investigated the causes of evolutionary rate variation
 among plant nuclear genes, especially in recently diverged species still
 capable of hybridizing in the wild. The recent advent of Next Generation
 Sequencing (NGS) permits investigation of genome wide rates of protein
 evolution and the role of selection in generating and maintaining
 divergence. Here, we use individual whole-transcriptome sequencing
 (RNAseq) to refine our understanding of the population genomics of a wild
 species of sunflowers (Helianthus spp.) and the factors that affect rates
 of protein evolution. We aligned 35 GB of transcriptome sequencing data
 and identified 433,257 polymorphic sites (SNPs) in a reference
 transcriptome comprising 16,312 genes. Using SNP markers, we identified
 strong population clustering largely corresponding to the three species
 analyzed here (Helianthus annuus, H. petiolaris, H. debilis), with one
 distinct early generation hybrid. Then, we calculated the proportions of
 adaptive substitution fixed by selection (alpha) and identified gene
 ontology categories with elevated values of alpha. The “response to biotic
 stimulus” category had the highest mean alpha across the three
 interspecific comparisons, implying that natural selection imposed by
 other organisms plays an important role in driving protein evolution in
 wild sunflowers. Finally, we examined the relationship between protein
 evolution (dN/dS ratio) and several genomic factors predicted to co-vary
 with protein evolution (gene expression level, divergence and specificity,
 genetic divergence [FST], and nucleotide diversity [pi]). We find that
 variation in rates of protein divergence was correlated with gene
 expression level and specificity, consistent with results from a broad
 range of taxa and timescales. This would in turn imply that these factors
 govern protein evolution both at a microevolutionary and macroevolutionary
 timescale. Our results contribute to a general understanding of the
 determinants of rates of protein evolution and the impact of selection on
 patterns of polymorphism and divergence.
description: reference
 transcriptomefasta file containing
 reference transcriptome (16312 contigs) described in the method
 section.TranscriptomeRef_mar30.fasnp_tableTable containing genotypes for all 433,257 SNPs. First column contains contig name were the SNP is found, second column the reference allele, third column the position of the SNP within the contig, last three columns Fst values for the three comparisons (annuus-debilis, annuus-petiolaris, debilis-petiolaris). Species identification of individuals can be found in table 4. File was compressed (.zip).raw read count per geneNumber of reads aligned, per contig, per individuals. Column one contains contig name, column two length of the contig.raw_read_counts
DOI: 10.15159/phytop.157
title: Aheru

description: Phytoplankton biomass, diversity and abundance in samples collected from Lake Aheru during the period 1952-2005.
DOI: 10.5061/dryad.sp6p0
title: Data from: Dryness is accelerating degradation of vulnerable shrublands in semiarid Mediterranean environments

description: Semiarid Mediterranean regions are highly susceptible to desertification
 processes. This study investigated the influence of increasing climate
 aridity in explaining the decline in vegetation cover in highly vulnerable
 gypsum semiarid shrublands of the Mediterranean region. For this purpose,
 we have used time series of the percentage of vegetation coverage obtained
 from remote sensing imagery (Landsat satellites). We found a dominant
 trend toward decreased vegetation cover, mainly in summer and in areas
 affected by the most severe water stress conditions (low precipitation,
 higher evapotranspiration rates and sun-exposed slopes). We show that past
 human management and current climate trends interact with local
 environmental conditions to determine the occurrence of vegetation
 degradation processes. The results suggest that degradation could be a
 consequence of the past overexploitation that has characterized this area
 (and many others in the Mediterranean region), but increased aridity,
 mainly related to global warming, may be triggering and/or accelerating
 the degradation processes. The observed pattern may be an early warning of
 processes potentially affecting more areas of the Mediterranean, according
 to the most up to date climate change models for the 21st century.
description: vegetation coverage of
 the Ebro basinSeries of vegetation
 coverage obtained from landsat imagery, a digital terrain model and
 climate data.data-degradation-shrublands
 .zip
DOI: 10.5061/dryad.qq846
title: Data from: Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea

description: The family Melanotaeniidae (rainbowfishes) represents the largest
 monophyletic group of freshwater fishes found in Australia and New Guinea.
 The family consists of seven genera and a total of 81 species, which are
 broadly distributed throughout the region. We conducted a phylogenetic
 analysis of Melanotaeniidae based on nearly complete taxonomic sampling of
 all species. We sequenced seven protein coding mitochondrial genes and the
 first two introns of the nuclear S7 gene, for a total of 6827 base pairs.
 Our goal was to use the phylogeny to infer the biogeographic history of
 rainbowfishes in this region, to provide a framework for the timing of
 divergence within the family, and to test for possible introgression
 between species. We found strong support for the monophyly of
 Melanotaeniidae. Three species-poor genera-Cairnsichthys, Rhadinocentrus
 and Iriatherina-were all resolved as early branching lineages within the
 family. The three species-rich genera-Melanotaenia, Chilatherina and
 Glossolepis-did not form a single monophyletic group, but instead formed
 three monophyletic groups endemic to discrete geographic regions: western
 New Guinea, northern New Guinea, and southern New Guinea plus Australia,
 respectively. All three geographic regions also contained three to four
 additional lineages that were separated by large genetic divergences and
 were frequently sympatric (except in western New Guinea). Our molecular
 clock results provide much older estimates of divergence than some aspects
 of the present geological setting. For instance, the formation of the
 present day Central Highlands, the integration of the Birds Head region
 with the rest of New Guinea, and the present proximate position of Waigeo
 and Batanta islands relative to the Birds Head, are all younger than the
 rainbowfishes living there based on our molecular clock estimates. We also
 identified ten species that have likely experienced historical
 introgression. Most introgression events were between different groups
 within the northern New Guinea lineage and the Southern New
 Guinea/Australian lineages. Finally, we identified nearly 20 undescribed
 species within Melanotaeniidae, demonstrating that much work remains in
 describing freshwater fish diversity in this region.
description: rain.phylo.labeled.relabeled.concatNexus file used to generate phylogeny.rain.phylo.labeled.005XML file used in the BEAST molecular clock analysis.
DOI: 10.5061/dryad.8p2f7
title: Data from: Marked host specificity and lack of phylogeographic population structure of Campylobacter jejuni in wild birds

description: Zoonotic pathogens often infect several animal species, and gene flow
 among populations infecting different host species may affect the
 biological traits of the pathogen including host specificity,
 transmissibility and virulence. The bacterium Campylobacter jejuni is a
 widespread zoonotic multihost pathogen, which frequently causes
 gastroenteritis in humans. Poultry products are important transmission
 vehicles to humans, but the bacterium is common in other domestic and wild
 animals, particularly birds, which are a potential infection source.
 Population genetic studies of C. jejuni have mainly investigated isolates
 from humans and domestic animals, so to assess C. jejuni population
 structure more broadly and investigate host adaptation, 928 wild bird
 isolates from Europe and Australia were genotyped by multilocus sequencing
 and compared to the genotypes recovered from 1366 domestic animal and
 human isolates. Campylobacter jejuni populations from different wild bird
 species were distinct from each other and from those from domestic animals
 and humans, and the host species of wild bird was the major determinant of
 C. jejuni genotype, while geographic origin was of little importance. By
 comparison, C. jejuni differentiation was restricted between more
 phylogenetically diverse farm animals, indicating that domesticated
 animals may represent a novel niche for C. jejuni and thereby driving the
 evolution of those bacteria as they exploit this niche. Human disease is
 dominated by isolates from this novel domesticated animal niche.
description: Wild_bird_isolates_concatenated_alignmentA fasta-file alignment containing the concatenated MLST sequences from each wild bird C. jejuni isolate presented in the article.
DOI: 10.5061/dryad.3b7g5
title: Data from: Properties of spontaneous mutational variance and covariance for wing size and shape in Drosophila melanogaster

description: We estimated mutational variance-covariance matrices, M, for wing shape
 and size in two genotypes of Drosophila melanogaster after 192 generations
 of mutation accumulation. We characterized 21 potentially independent
 aspects of wing shape and size using geometric morphometrics, and analyzed
 the data using a likelihood-based factor- analytic approach. We implement
 a previously unused analysis that describes those directions with the
 greatest difference in evolvability between pairs of matrices. There are
 significant mutational effects on 19 of 21 possible aspects of wing form,
 consistent with the high dimensionality of standing genetic variation for
 wing shape previously identified in D. melanogaster. Mutations have
 partially recessive effects, consistent with average dominance around
 0.25. Sex-specific matrices are relatively similar, although male-specific
 matrices are slightly larger, as expected due to dosage compensation on
 the X chromosome. Genotype–specific matrices are quite different. Matrices
 may differ both because of sampling error based on small samples of
 mutations with large phenotypic effects, and due to the mutational
 properties of the genotypes. Genotypic differences are likely to be
 involved, as the two genotypes have different molecular mutation rates and
 properties.
description: MAdataData on wing shape
 gathered from mutatation accumulation lines, and
 controls.
DOI: 10.15468/dl.c5k5j2
title: Occurrence Download

description: A dataset containing 97534 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liquidambar styraciflua"
 ]
}

 The dataset includes 97534 records from 577 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001564-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6k1p6
title: Data from: Polypyrimidine tract-binding protein homologues from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes

description: Alternative splicing (AS) generates transcript variants by variable
 exon/intron definition and massively expands transcriptome diversity.
 Changes in AS patterns have been found to be linked to manifold biological
 processes, yet fundamental aspects such as the regulation of AS and its
 functional implications largely remain to be addressed. In this work,
 widespread AS regulation by Arabidopsis Polypyrimidine tract-binding
 protein homologues (PTBs) was revealed. In total 452 AS events derived
 from 307 distinct genes were found to be responsive to the levels of the
 splicing factors PTB1 and PTB2, which predominantly triggered splicing of
 regulated introns, inclusion of cassette exons, and usage of upstream 5’
 splice sites. In contrast, no major AS regulatory function of the
 distantly related PTB3 was found. Dependent on their position within the
 mRNA, PTB-regulated events can both modify the untranslated regions and
 give rise to alternative protein products. We find that PTB-mediated AS
 events are connected to diverse biological processes, and the functional
 implications of selected instances were further elucidated. Specifically,
 PTB misexpression changes AS of PHYTOCHROME INTERACTING FACTOR 6,
 coinciding with altered rates of abscisic acid-dependent seed germination.
 Furthermore, AS patterns as well as the expression of key flowering
 regulators were massively changed in an PTB1/2 level-dependent manner.
description: Supplemental Data
 Set1Computational analysis
 of transcriptome-wide AS patterns in AtPTB1/2 misexpression
 lines.Supplemental Data Set
 2Computational analysis
 of transcriptome-wide AS patterns in AtPTB3 misexpression
 lines.Supplemental Data Set2 AtPTB3
 regulated events.xlsxSupplemental Data Set
 3Detailed list of GO
 terms. Based on the MapMan software, AtPTB1/2-regulated genes as well as
 all genes from TAIR10 were categorized into different functional groups
 based on their respective GO annotations. Certain groups were combined as
 listed in tab ‘combination of GO-terms’. A detailed list of the genes
 belonging to the GO term “RNA” for the AtPTB1/2-regulation targets is
 provided.Supplemental Data Set3 GO term
 analysis.xlsx