cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.77p06
title: Data from: Multi-DICE: R package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes

description: Population genetic data from multiple taxa can address comparative
 phylogeographic questions about community-scale response to environmental
 shifts, and a useful strategy to this end is to employ hierarchical
 co-demographic models that directly test multi-taxa hypotheses within a
 single, unified analysis while benefiting in statistical power from
 aggregating datasets. This approach has been applied to classical
 phylogeographic datasets such as mitochondrial barcodes as well as
 reduced-genome polymorphism datasets that can yield 10,000s of SNPs,
 produced by emergent technologies such as RAD-seq and GBS. A strategy for
 the latter had been accomplished by adapting the site frequency spectrum
 to a novel summarization of population genomic data across multiple taxa
 called the aggregate site frequency spectrum (aSFS), which potentially can
 be deployed under various inferential frameworks including approximate
 Bayesian computation, random forest, and composite likelihood
 optimization. Here, we introduce the R package Multi-DICE, a wrapper
 program that exploits existing simulation software for straight-forward
 and flexible execution of hierarchical model-based inference using the
 aSFS, which is derived from genomic-scale data, as well as mitochondrial
 data. We validate several novel software features such as applying
 alternative inferential frameworks, enforcing a minimal threshold of time
 surrounding event pulses, and specifying flexible hyperprior
 distributions. In sum, Multi-DICE provides comparative analysis within the
 familiar R environment while allowing a high degree of user customization,
 and will thus serve as a valuable tool for comparative phylogeography and
 population genomics.
description: Testing Inferential
 FrameworksScript, parameter,
 result, and POD files for testing inferential frameworks simulation
 experiment.1 Testing Inferential
 Frameworks.zip2 Pulse Buffer on Prior
 Space and Truncating Hyperprior RangeScript and result files
 for pulse buffer on prior space and truncating hyperprior range simulation
 experiments.
DOI: 10.5061/dryad.dn357
title: Data from: Why close relatives make bad neighbors: phylogenetic conservatism in niche preferences and dispersal disproves Darwin’s Naturalization Hypothesis in the thistle tribe

description: The number of exotic plant species that have been introduced into the
 United States far exceeds that of other groups of organisms, and many of
 these have become invasive. As in many regions of the globe, invasive
 members of the thistle tribe, Cardueae, are highly problematic in the
 California Floristic Province, an established biodiversity hotspot. While
 Darwin's naturalization hypothesis posits that plant invaders closely
 related to native species would be at a disadvantage, evidence has been
 found that introduced thistles more closely related to native species are
 more likely to become invasive. To elucidate the mechanisms behind this
 pattern, we modelled the ecological niches of thistle species present in
 the province and compared niche similarity between taxa and their
 evolutionary relatedness, using fossil-calibrated molecular phylogenies of
 the tribe. The predicted niches of invasive species were found to have
 higher degrees of overlap with native species than noninvasive introduced
 species do, and pairwise niche distance was significantly correlated with
 phylogenetic distance, suggesting phylogenetic niche conservatism.
 Invasive thistles also displayed superior dispersal capabilities compared
 to noninvasive introduced species, and these capabilities exhibited a
 phylogenetic signal. By analysing the modelled ecological niches and
 dispersal capabilities of over a hundred thistle species, we demonstrate
 that exapted preferences to the invaded environment may explain why close
 exotic relatives may make bad neighbours in the thistle tribe.
description: Time Calibrated
 Phylogenetic Trees of Cardueae (Exponential Prior)1000 fossil calibrated
 trees of the tribe Cardueae generated from BEAST using exponential prior
 distributions.c200_EXPO2_1000.treesTime Calibrated Phylogenetic Trees of Cardueae (Lognormal Prior)1000 fossil calibrated trees of the tribe Cardueae generated from BEAST using lognormal prior distributions.new_CARD2014_random_1000.treesCombined Alignment File of CardueaeFasta file containing the combined alignments (ITS, matK, trnL) for the tribe Cardueae.ccN3+part3+Re-Realigned.nex.alter.fas.txt
DOI: 10.5061/dryad.5bc98
title: Data from: Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

description: Gastropods are a highly diverse clade of molluscs that includes many
 familiar animals, such as limpets, snails, slugs and sea slugs. It is one
 of the most abundant groups of animals in the sea and the only molluscan
 lineage that has successfully colonized land. Yet the relationships among
 and within its constituent clades have remained in flux for over a century
 of morphological, anatomical and molecular study. Here, we re-evaluate
 gastropod phylogenetic relationships by collecting new transcriptome data
 for 40 species and analysing them in combination with publicly available
 genomes and transcriptomes. Our datasets include all five main gastropod
 clades: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda
 and Heterobranchia. We use two different methods to assign orthology,
 subsample each of these matrices into three increasingly dense subsets,
 and analyse all six of these supermatrices with two different models of
 molecular evolution. All 12 analyses yield the same unrooted network
 connecting the five major gastropod lineages. This reduces deep gastropod
 phylogeny to three alternative rooting hypotheses. These results reject
 the prevalent hypothesis of gastropod phylogeny, Orthogastropoda. Our
 dated tree is congruent with a possible end-Permian recovery of some
 gastropod clades, namely Caenogastropoda and some Heterobranchia
 subclades.
description: Phylogenetic alignments,
 tree sets, and summary trees30 files corresponding
 the multiple sequence alignments, tree sets (bootstrap replicates and post
 burn-in posterior probabilities), and summary trees (maximum-likelihood
 trees and majority rule consensus trees) for multiple phylogenetic
 analyses.Zapata_et_al_Dryad.tar.gz
DOI: 10.5061/dryad.5pt57
title: Data from: Development and application of an alert system to detect cases of food poisoning in Japan

description: Recent public health concerns regarding commercial food products have
 increased the need to develop an automated method to detect food
 product-related health events. We developed and verified a method for the
 early detection of potentially harmful events caused by commercial food
 products. We collected data from daily internet-based questionnaires
 examining the presence or absence of symptoms and information about food
 purchased by the respondents. Using these data, we developed a method to
 detect possible health concerns regarding commercialized food products. To
 achieve this, we combined the signal detection method used in the
 reporting system of adverse effects of pharmaceutical products and the
 Early Aberration Reporting System (EARS) used by the United States Centers
 for Disease Control. Whiteleg shrimp (Litopenaeus vannamei), which had
 odds ratio and Odds(−) of 8.99 and 4.13, respectively, was identified as a
 possible causative food product for diarrhea and vomiting. In conclusion,
 this study demonstrated that food distributors can implement
 post-marketing monitoring of the safety of food products purchased via the
 internet.
description: Tokyo_Osaka_DataThe health and Food-purchasing survey. Exact date has been masked by a small variable to protect participant identity. The variables j1, j2, j3, etc. stand for the JAN code (Japan Article Number code) which is a barcode standard compatible with the EAN (European Article Number). The JAN code has been masked so as not to identify the individual food products.
DOI: 10.5061/dryad.qm30m
title: Data from: Mining from transcriptomes: 315 single-copy orthologous genes concatenated for the phylogenetic analyses of Orchidaceae

description: Phylogenetic relationships are hotspots for orchid studies with
 controversial standpoints. Traditionally, the phylogenies of orchids are
 based on morphology and subjective factors. Although more reliable than
 classic phylogenic analyses, the current methods are based on a few gene
 markers and PCR amplification, which are labor intensive and cannot
 identify the placement of some species with degenerated plastid genomes.
 Therefore, a more efficient, labor-saving and reliable method is needed
 for phylogenic analysis. Here, we present a method of orchid phylogeny
 construction using transcriptomes. Ten representative species covering
 five subfamilies of Orchidaceae were selected, and 315 single-copy
 orthologous genes extracted from the transcriptomes of these organisms
 were applied to reconstruct a more robust phylogeny of orchids. This
 approach provided a rapid and reliable method of phylogeny construction
 for Orchidaceae, one of the most diversified family of angiosperms. We
 also showed the rigorous systematic position of holomycotrophic species,
 which has previously been difficult to determine because of the
 degenerated plastid genome. We concluded that the method presented in this
 study is more efficient and reliable than methods based on a few gene
 markers for phylogenic analyses, especially for the holomycotrophic
 species or those whose DNA sequences have been difficult to amplify.
 Meanwhile, a total of 315 single-copy orthologous genes of orchids are
 offered and more informative loci could be used in the future orchid
 phylogenetic studies.
description: Unigenesingle_copy
DOI: 10.5061/dryad.gf39c8dc
title: Data from: Telling the whole story in a 10,000-genome world

description: BACKGROUND: Genome sequencing has revolutionized our view of the
 relationships among genomes, particularly in revealing the confounding
 effects of lateral genetic transfer (LGT). Phylogenomic techniques have
 been used to construct purported trees of microbial life. Although such
 trees are easily interpreted and allow the use of a subset of genomes as
 "proxies" for the full set, LGT and other phenomena impact the
 positioning of different groups in genome trees, confounding and
 potentially invalidating attempts to construct a phylogeny-based taxonomy
 of microorganisms. Network and graph approaches can reveal complex sets of
 relationships, but applying these techniques to large data sets is a
 significant challenge. Notwithstanding the question of what exactly it
 might represent, generating and interpreting a Tree or Network of All
 Genomes will only be feasible if current algorithms can be improved upon.
 RESULTS: Complex relationships among even the most-similar genomes
 demonstrate that proxy-based approaches to simplifying large sets of
 genomes are not alone sufficient to solve the analysis problem. A
 phylogenomic analysis of 1173 sequenced bacterial and archaeal genomes
 generated phylogenetic trees for 159,905 distinct homologous gene sets.
 The relationships inferred from this set can be heavily dependent on the
 inclusion of other taxa: for example, phyla such as Spirochaetes,
 Proteobacteria and Firmicutes are recovered as cohesive groups or split
 depending on the presence of other specific lineages. Furthermore, named
 groups such as Acidithiobacillus, Coprothermobacter and Brachyspira show a
 multitude of affiliations that are more consistent with their ecology than
 with small subunit ribosomal DNA-based taxonomy. Network and graph
 representations can illustrate the multitude of conflicting affinities,
 but all methods impose constraints on the input data and create challenges
 of construction and interpretation. CONCLUSIONS: These complex
 relationships highlight the need for an inclusive approach to genomic
 data, and current methods with minor alterations will likely scale to
 allow the analysis of data sets with 10,000 or more genomes. The main
 challenges lie in the visualization and interpretation of genomic
 relationships, and the redefinition of microbial taxonomy when subsets of
 genomic data are so evidently in conflict with one another, and with the
 "canonical" molecular taxonomy.
description: Beiko_trees.tar
DOI: 10.5061/dryad.1d7n9
title: Data from: SNP markers tightly linked to root knot nematode resistance in grapevine (Vitis cinerea) identified by a genotyping-by-sequencing approach followed by Sequenom MassARRAY validation

description: Plant parasitic nematodes, including root knot nematode Meloidogyne
 species, cause extensive damage to agriculture and horticultural crops. As
 Vitis vinifera cultivars are susceptible to root knot nematode parasitism,
 rootstocks resistant to these soils pests provide a sustainable approach
 to maintain grapevine production. Currently, most of the commercially
 available root knot nematode resistant rootstocks are highly vigorous and
 take up excess potassium, which reduces wine quality. As a result, there
 is a pressing need to breed new root knot nematode resistant rootstocks,
 which have no impact on wine quality. To develop molecular markers that
 predict root knot nematode resistance for marker assisted breeding, a
 genetic approach was employed to identify a root knot nematode resistance
 locus in grapevine. To this end, a Meloidogyne javanica resistant Vitis
 cinerea accession was crossed to a susceptible Vitis vinifera cultivar
 Riesling and results from screening the F1 individuals support a model
 that root knot nematode resistance, is conferred by a single dominant
 allele, referred as MELOIDOGYNE JAVANICA RESISTANCE1 (MJR1). Further, MJR1
 resistance appears to be mediated by a hypersensitive response that occurs
 in the root apical meristem. Single nucleotide polymorphisms (SNPs) were
 identified using genotyping-by-sequencing and results from association and
 genetic mapping identified the MJR1 locus, which is located on chromosome
 18 in the Vitis cinerea accession. Validation of the SNPs linked to the
 MJR1 locus using a Sequenom MassARRAY platform found that only 50% could
 be validated. The validated SNPs that flank and co-segregate with the MJR1
 locus can be used for marker-assisted selection for Meloidogyne javanica
 resistance in grapevine.
description: Smith et al SNP data
 setSNP data set for the
 PLOS ONE submitted manuscript "SNP markers tightly linked to root
 knot nematode resistance in grapevine (Vitis cinerea) identified by a
 genotyping-by-sequencing approach followed by Sequenom MassARRAY
 validation".
DOI: 10.5061/dryad.85pd5
title: Data from: Gene expression patterns associated with caste and reproductive status in ants: worker-specific genes are more derived than queen-specific ones

description: Variation in gene expression leads to phenotypic diversity and plays a
 central role in caste differentiation of eusocial insect species. In
 social Hymenoptera, females with the same genetic background can develop
 into queens or workers, which are characterized by divergent morphologies,
 behaviors and lifespan. Moreover, many social insects exhibit behaviorally
 distinct worker castes, such as brood-tenders and foragers. Researchers
 have just started to explore which genes are differentially expressed to
 achieve this remarkable phenotypic plasticity. Although the queen is
 normally the only reproductive individual in the nest, following her
 removal, young brood-tending workers often develop ovaries and start to
 reproduce. Here, we make use of this ability in the ant Temnothorax
 longispinosus and compare gene expression patterns in the queens and three
 worker castes along a reproductive gradient. We found the largest
 expression differences between the queen and the worker castes (~2,500
 genes), and the smallest differences between infertile brood-tenders and
 foragers (~300 genes). The expression profile of fertile workers is more
 worker-like, but to a certain extent intermediate between the queen and
 the infertile worker castes. In contrast to the queen, a high number of
 differentially expressed genes in the worker castes are of unknown
 function, pointing to the derived status of Hymenopteran workers within
 insects.
description: asm_TlongiContigsFB_IFB_Q_W-MIRAThe transcriptome of four T. longispinosus female castes was sequenced on an Illumina HiSeq 2000. After read trimming, caste specific contigs were assembled using the CLC software package. With these contigs as input a meta-assembly was conducted with MIRA to obtain the final contig set.
DOI: 10.5061/dryad.8546
title: Data from: Ancestral polyploidy in seed plants and angiosperms

description: Whole-genome duplication (WGD), or polyploidy, followed by gene loss and
 diploidization has long been recognized as an important evolutionary force
 in animals, fungi and other organisms1, 2, 3, especially plants. The
 success of angiosperms has been attributed, in part, to innovations
 associated with gene or whole-genome duplications4, 5, 6, but evidence for
 proposed ancient genome duplications pre-dating the divergence of monocots
 and eudicots remains equivocal in analyses of conserved gene order. Here
 we use comprehensive phylogenomic analyses of sequenced plant genomes and
 more than 12.6 million new expressed-sequence-tag sequences from
 phylogenetically pivotal lineages to elucidate two groups of ancient gene
 duplications—one in the common ancestor of extant seed plants and the
 other in the common ancestor of extant angiosperms. Gene duplication
 events were intensely concentrated around 319 and 192 million years ago,
 implicating two WGDs in ancestral lineages shortly before the
 diversification of extant seed plants and extant angiosperms,
 respectively. Significantly, these ancestral WGDs resulted in the
 diversification of regulatory genes important to seed and flower
 development, suggesting that they were involved in major innovations that
 ultimately contributed to the rise and eventual dominance of seed plants
 and angiosperms.
description: Analysis1 - alignments
 and trees of 9 sequenced genomesAnalysis1.zipAnalysis2 - alignments and trees when basal angiosperms are consideredAnalysis2.zipAnalysis3 - alignments and trees when gymnosperms are consideredAnalysis3.zipAnalysis4 - alignments and trees when basal angiosperms and gymnosperms are consideredAnalysis4.zip
DOI: 10.5061/dryad.1h46d
title: Data from: Vocalisations of killer whales (Orcinus orca) in the Bremer Canyon, Western Australia

description: To date, there has been no dedicated study in Australian waters on the
 acoustics of killer whales. Hence no information has been published on the
 sounds produced by killer whales from this region. Here we present the
 first acoustical analysis of recordings collected off the Western
 Australian coast. Underwater sounds produced by Australian killer whales
 were recorded during the months of February and March 2014 and 2015 in the
 Bremer Canyon in Western Australia. Vocalisations recorded included
 echolocation clicks, burst-pulse sounds and whistles. A total of 28 hours
 and 29 minutes were recorded and analysed, with 2376 killer whale calls
 (whistles and burst-pulse sounds) detected. Recordings of poor quality or
 signal-to-noise ratio were excluded from analysis, resulting in 142
 whistles and burst-pulse vocalisations suitable for analysis and
 categorisation. These were grouped based on their spectrographic features
 into nine Bremer Canyon (BC) “call types”. The frequency of the
 fundamental contours of all call types ranged from 600 Hz to 29 kHz. Calls
 ranged from 0.05 to 11.3 seconds in duration. Biosonar clicks were also
 recorded, but not studied further. Surface behaviours noted during
 acoustic recordings were categorised as either travelling or social
 behaviour. A detailed description of the acoustic characteristics is
 necessary for species acoustic identification and for the development of
 passive acoustic tools for population monitoring, including assessments of
 population status, habitat usage, migration patterns, behaviour and
 acoustic ecology. This study provides the first quantitative assessment
 and report on the acoustic features of killer whales vocalisations in
 Australian waters, and presents an opportunity to further investigate this
 little-known population.
description: All acoustic sound files
 of killer whale vocalisations analyzed for this
 manuscriptAll vocalisations
 analysed for this manuscript are included in this zip folder as .wav
 files. There are a total of 142 whistles and burst-pulse vocalisations
 that were analysed and categorized accordingly. There are also 2
 echolocation clicks that are discussed in this manuscript. Acoustic
 recordings were obtained with two devices. Primarily recordings were
 undertaken with a High Tech Inc. HTI-96-MIN hydrophone with built-in
 pre-amplifier (flat frequency response of 2 Hz to 30 kHz; sensitivity
 -164.1 dB re 1 V/µPa), fitted to a Sound Devices 722 digital recorder
 sampling at 96 kHz, 24-bit. Secondary to this, a SoundTrap (Ocean
 Instruments, New Zealand) —a self-contained underwater sound recorder—was
 rigged to a tow-line and deployed overside during an encounter when the
 vessel was travelling less than 5 knots. The SoundTrap sampled at 192 kHz,
 16-bit.CMST_Wellard_Orca_bioacoustic_data.zip
DOI: 10.5061/dryad.vr021gq
title: Data from: High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)

description: The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found
 across the Northern hemisphere. It occurs in coastal waters and inhabits
 basins that vary broadly in salinity, temperature, and food availability.
 These diverse habitats could drive subtle differentiation among
 populations, but examination of this would be best conducted with a robust
 reference genome. Here we report the first harbour porpoise genome,
 assembled de novo from an individual originating in the Kattegat Sea
 (Sweden). The genome is one of the most complete cetacean genomes
 currently available, with a total size of 2.39 Gb and 50% of the total
 length found in just 34 scaffolds. Using just 122 of the longest
 scaffolds, we were able to show high levels of synteny with the genome of
 the domestic cattle (Bos taurus). Our draft annotation comprises 22,154
 predicted genes, which we further annotated through matches to the NCBI
 nucleotide database, GO categorization, and motif prediction. Within the
 predicted genes we have confirmed the presence of &gt;20 genes or gene
 families that have been associated with adaptive evolution in other
 cetaceans. Overall, this genome assembly and draft annotation represent a
 crucial addition to the genomic resources currently available for the
 study of porpoises and Phocoenidae evolution, phylogeny, and conservation.
description: Autenrieth-MER-Pp_genome_annotationone annotation file for the harbour porpoise (phocoena phocoena) genome generated by the MAKER2 annotation. Format: gff Annotation statistics are given in the README