cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.493b7
title: Data from: Xenacoelomorpha is the sister group to Nephrozoa

description: The position of Xenacoelomorpha in the tree of life remains a major
 unresolved question in the study of deep animal relationships.
 Xenacoelomorpha, comprising Acoela, Nemertodermatida, and Xenoturbella,
 are bilaterally symmetrical marine worms that lack several features common
 to most other bilaterians, for example an anus, nephridia, and a
 circulatory system. Two conflicting hypotheses are under debate:
 Xenacoelomorpha is the sister group to all remaining Bilateria
 (= Nephrozoa, namely protostomes and deuterostomes) or is a clade inside
 Deuterostomia. Thus, determining the phylogenetic position of this clade
 is pivotal for understanding the early evolution of bilaterian features,
 or as a case of drastic secondary loss of complexity. Here we show robust
 phylogenomic support for Xenacoelomorpha as the sister taxon of Nephrozoa.
 Our phylogenetic analyses, based on 11 novel xenacoelomorph transcriptomes
 and using different models of evolution under maximum likelihood and
 Bayesian inference analyses, strongly corroborate this result. Rigorous
 testing of 25 experimental data sets designed to exclude data partitions
 and taxa potentially prone to reconstruction biases indicates that
 long-branch attraction, saturation, and missing data do not influence
 these results. The sister group relationship between Nephrozoa and
 Xenacoelomorpha supported by our phylogenomic analyses implies that the
 last common ancestor of bilaterians was probably a benthic, ciliated
 acoelomate worm with a single opening into an epithelial gut, and that
 excretory organs, coelomic cavities, and nerve cords evolved after
 xenacoelomorphs separated from the stem lineage of Nephrozoa.
description: hamstr_all_taxaAligned phylip file for dataset 'HaMStR all taxa'hamstr_best_coverage_taxaAligned phylip file for data matrix 'HaMStR best coverage taxa'proteinorthoAligned phylip file for dataset 'ProteinOrtho'taxon_pruning_datasetsExperimental datasets with alternative taxon sampling and corresponding partition information filestrespex_datasetsExperimental phylogenomic datasets partitioned according to statistical tests implemented in program TreSpexmatrix_occupancy_datasetsPhylogenomic datasets generated to maximize overal matrix coverage and corresponding partition informationribosomal_or_non_ribosomal_gene_datasetsDatasets with only non-ribosomal protein genes or only ribosomal protein genessupplementary mrbayes filesMrBayes alignment files and run scriptssupplementarymrbayesfiles.zipBMGE_trimmingPhylip alignment for dataset 'BMGE trimming'
DOI: 10.5061/dryad.kp0rc5s
title: Data from: Transcriptome response of the foundation plant Spartina alterniflora to the Deepwater Horizon oil spill

description: Despite the severe impacts of the Deepwater Horizon oil spill, the
 foundation plant species Spartina alterniflora proved resilient to heavy
 oiling, providing an opportunity to identify mechanisms of response to the
 anthropogenic stress of crude oil exposure. We assessed plants from oil
 affected and unaffected populations using a custom DNA microarray to
 identify genome-wide transcription patterns and gene expression networks
 that respond to crude oil exposure. Additionally, we used T-DNA insertion
 lines of the model grass Brachypodium distachyon to assess the
 contribution of four novel candidate genes to crude oil response.
 Responses in S. alterniflora to hydrocarbon exposure across the
 transcriptome as well as xenobiotic specific response pathways had little
 overlap with those previously identified in the model plant Arabidopsis
 thaliana. Among T-DNA insertion lines of B. distachyon, we found
 additional support for two candidate genes, one (ATTPS21) involved in
 volatile production, and the other (SUVH5) involved in epigenetic
 regulation of gene expression, that may be important in the response to
 crude oil. The architecture of crude oil response in S. alterniflora is
 unique from that of the model species A. thaliana, suggesting that
 xenobiotic response may be highly variable across plant species. In
 addition, further investigations of regulatory networks may benefit from
 more information about epigenetic response pathways.
description: DWHZip file containing all
 R scripts and original data files (including site coordinates) used in the
 publication of Alvarez, et al. 2018.
DOI: 10.5061/dryad.5t8d9
title: Data from: Novel loci underlie natural variation in vitamin E levels in maize grain

description: Tocopherols, tocotrienols and plastochromanols (collectively termed
 tocochromanols) are lipid-soluble antioxidants synthesized by all plants.
 Their dietary intake, primarily from seed oils, provides vitamin E and
 other health benefits. Tocochromanol biosynthesis has been dissected in
 the dicot Arabidopsis thaliana, which has green, photosynthetic seeds, but
 our understanding of tocochromanol accumulation in major crops, whose
 seeds are non-photosynthetic, remains limited. To understand the genetic
 control of tocochromanols in grain, we conducted a joint linkage and
 genome-wide association study in the 5,000-line U.S. maize (Zea mays)
 nested association-mapping panel. Fifty-two quantitative trait loci (QTL)
 for individual and total tocochromanols were identified, and of the 14
 resolved to individual genes, six encode novel activities affecting
 tocochromanols in plants. These include two chlorophyll biosynthetic
 enzymes that explain the majority of tocopherol variation, which was not
 predicted, given that, like most major cereal crops, maize grain is
 non-photosynthetic. This comprehensive assessment of natural variation in
 vitamin E levels in maize establishes the foundation for improving
 tocochromanol and vitamin E content in seeds of maize and other major
 cereal crops.
description: README.txtREADME for Dryad Digital Repository Deposit associated with " Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain" by Diepenbrock et al. in The Plant Cell, 2017filtered_SNP_matrix_AGPv2_vitamaize_Jan_2016.zipSingle nucleotide polymorphisms derived from mRNAseq of a kernel developmental timecourse from the NAM parents.FPKM_gene_matrix_Jan_30_2016.txt.gzExpression abundances (FPKMs) of a kernel developmental timecourse of the NAM parents for the AGPv2 genes.FPKM_transcript_matrix_Jan_30_2016.txt.gzExpression abundances (FPKMs) of a kernel developmental timecourse of the NAM parents for the AGPv2 transcripts.
DOI: 10.5061/dryad.2jj16
title: Data from: Ecological legacies of civil war: 35-year increase in savanna tree cover following wholesale large-mammal declines

description: 1. Large mammalian herbivores (LMH) exert strong effects on plants in
 tropical savannas, and many wild LMH populations are declining. However,
 predicting the impacts of these declines on vegetation structure remains
 challenging. 2. Experiments suggest that tree cover can increase rapidly
 following LMH exclusion. Yet it is unclear whether these results scale up
 to predict ecosystem-level impacts of LMH declines, which often alter fire
 regimes, trigger compensatory responses of other herbivores, and accompany
 anthropogenic land-use changes. Moreover, theory predicts that grazers and
 browsers should have opposing effects on tree cover, further complicating
 efforts to forecast the outcomes of community-wide declines. 3. We used
 the near-extirpation of grazing and browsing LMH from Gorongosa National
 Park during the Mozambican Civil War (1977-1992) as a natural experiment
 to test whether megafaunal collapse increased tree cover. We classified
 herbaceous and tree cover in satellite images taken (a) at the onset of
 war in 1977 and (b) in 2012, two decades after hostilities ceased. 4.
 Throughout the 3620-km2 park, proportional tree cover increased by 34%
 (from 0.29 to 0.39)—an addition of 362 km2. Four of the park's five
 major habitat zones (including miombo woodland, Acacia-Combretum-palm
 savanna, and floodplain grassland) showed even greater increases in tree
 cover (51–134%), with an average increase of 94% in ecologically critical
 Rift Valley habitats. Only in the eastern Cheringoma Plateau, which had
 historically low wildlife densities, did tree cover decrease (by 5%). 5.
 The most parsimonious explanation for these results is that reduced
 browsing pressure enhanced tree growth, survival, and/or recruitment; we
 found no directional trends in rainfall or fire that could explain
 increased tree cover. 6. Synthesis: Catastrophic large-herbivore die-offs
 in Mozambique's flagship national park were followed by 35 years of
 woodland expansion, most severely in areas where pre-war wildlife biomass
 was greatest. These findings suggest that browsing release supersedes
 grazer-grass-fire feedbacks in governing ecosystem-level tree cover,
 consistent with smaller-scale experimental results, although the
 potentially complementary effect of CO2 fertilization cannot be
 definitively ruled out. Future work in Gorongosa will reveal whether
 recovering LMH populations reverse this trend, or alternatively whether
 woody encroachment hinders ongoing restoration efforts.
description: Data
 ArchiveDataArchive.zip
DOI: 10.5061/dryad.hd922
title: Data from: The role of transcriptome resilience in resistance of corals to bleaching

description: Wild populations increasingly experience extreme conditions as climate
 change amplifies environmental variability. How individuals respond to
 environmental extremes determines the impact of climate change overall.
 The variability of response from individual to individual can represent
 the opportunity for natural selection to occur as a result of extreme
 conditions. Here, we experimentally replicated the natural exposure to
 extreme temperatures of the reef lagoon at Ofu Island (American Samoa),
 where corals can experience severe heat stress during midday low tide. We
 investigated the bleaching and transcriptome response of 20 Acropora
 hyacinthus colonies 5 and 20 h after exposure to control (29 °C) or heated
 (35 °C) conditions. We found a highly dynamic transcriptome response: 27%
 of the coral transcriptome was significantly regulated 1 h postheat
 exposure. Yet 15 h later, when heat-induced coral bleaching became
 apparent, only 12% of the transcriptome was differentially regulated. A
 large proportion of responsive genes at the first time point returned to
 control levels, others remained differentially expressed over time, while
 an entirely different subset of genes was successively regulated at the
 second time point. However, a noteworthy variability in gene expression
 was observed among individual coral colonies. Among the genes of which
 expression lingered over time, fast return to normal levels was associated
 with low bleaching. Colonies that maintained higher expression levels of
 these genes bleached severely. Return to normal levels of gene expression
 after stress has been termed transcriptome resilience, and in the case of
 some specific genes may signal the physiological health and response
 ability of individuals to environmental stress.
description: Raw_counts_dataRead counts for all 152 samples and 33,496 contigs.Supp_mat_Spreadsheet1_Raw_counts_data.xlsxFull experimental designExperimental design for DESeq analysis.fullRTEdesign.csvDESeq Analysis 5hR commands for DESeq analysis on 5 hr data.DESeqAnalysis5h_nov2013.RDESeq Analysis 20hR commands for DESeq analysis on 20 hr data.DESeqAnalysis20h_nov2013.R33,496 Acropora hyacinthus contigsFasta file of the 33,496 assembled contiguous sequences from Acropora hyacinthus type E from Ofu Island, American Samoa.33496_Ahyacinthus_CoralContigs.fasta33496 Acropora hyacinthus Contigs AnnotationAnnotations for the 33,496 contigs from Acropora hyacinthus.33496_Ahyacinthus_Contigs_Annotation.xlsxRead counts for 5 hr samplesInput file for DESeq analysis on 5 hr samples.CombinedCounts_5h.txtRead counts for 20 hr samplesInput file for DESeq analysis on 20 hr samples.CombinedCounts_20h.txt
DOI: 10.5061/dryad.1fq675j
title: Data from: Phenotypic evolution shaped by current enzyme function in the bioluminescent courtship signals of sea fireflies

description: Mating behaviours are diverse and noteworthy, especially within species
 radiations where they may contribute to speciation. Studying how
 differences in mating behaviours arise between species can help us
 understand how diversity is generated at multiple biological levels. The
 bioluminescent courtship displays of cypridinid ostracods (or sea
 fireflies) are an excellent system for this since amazing variety evolves
 while using a conserved biochemical mechanism. We find that the evolution
 of one aspect in this behavioural phenotype - the duration of
 bioluminescent courtship pulses - is shaped by biochemical function.
 First, by measuring light production from induced bioluminescence in 38
 species, we discovered differences between species in their biochemical
 reactions. Then, for 16 species of which biochemical, phylogenetic, and
 behavioral data are all available, we used phylogenetic comparative models
 to show that differences in biochemical reaction are nonlinearly
 correlated with the duration of courtship pulses. This relationship
 indicates that changes to both enzyme (c-luciferase) function and usage
 have shaped the evolution of courtship displays, but that they
 differentially contribute to these phenotypic changes. This nonlinear
 dynamic may have consequences for the disparity of signaling phenotypes
 observed across species, and demonstrates how unappreciated diversity at
 the biochemical level can lead to inferences about behavioural evolution.
description: RSPB_Hensley_etal_2018_ESMZIP file containing the following subfolders and files: (1) Phylogeny generated and used in the comparative analyses, (2) Hypothetical dataset used to plot Figure 1B, (3) Table S2 with all comparative models, (4) Table S3 of the morphological measures from the species used in this paper, (5) a Codes folder to run the analyses in the paper, (6) three folders of model fits and visual plots depicting the different biochemical models fit to the stimulated bioluminescence data, (7) two folders of raw time series traces from stimulated bioluminescence, and (8) raw behavioral data of pulse durations from species in this paper
DOI: 10.5061/dryad.56bq0m1
title: Data from: Effect of arsenate substitution on phosphate repository of cell: a computational study

description: The structural analogy with phosphate derives arsenate into various
 metabolic processes associated with phosphate inside the organisms. But it
 is difficult to evaluate the effect of arsenate substitution on the
 stability of individual biological phosphate species, which span from a
 simpler monoester form like pyrophosphate to a more complex phosphodiester
 variant like DNA. In this study, we have classified the physiological
 phosphate esters into three different classes on the basis of their
 structural differences.This classification has helped us to present a
 concise theoretical study on the kinetic stability of phosphate analogue
 species of arsenate against hydrolysis. All the calculations have been
 carried out using QM/MM methods of our Own N-layer Integrated molecular
 Orbital molecular Mechanics. For quantum mechanical region we have used
 M06-2X density functional with 6-31+G(2d,2p) basis set and for molecular
 mechanics region AMBER force field. The calculated rate constants for
 hydrolysis show that none of the phosphate analogue species of arsenate
 has a reasonable stability against hydrolysis.
description: Supplementary
 GeometriesOptimized Geometries of
 all reactants and TS structures.suppl_geometry.pdfirc_moviesMovie files showing IRC calculations for all the computed compounds.
DOI: 10.6084/m9.figshare.31151530.v1
title: Avocado Spectral Dataset

description: This dataset contains the reflectance values of avocado leaves at five dehydration stages for the article Integrative Nutritional Assessment of avocado leaves using entropy-weighted spectral indices and fusion learning.
DOI: 10.6084/m9.figshare.31151530
title: Avocado Spectral Dataset

description: This dataset contains the reflectance values of avocado leaves at five dehydration stages for the article Integrative Nutritional Assessment of avocado leaves using entropy-weighted spectral indices and fusion learning.
DOI: 10.5061/dryad.7tv59
title: Data from: Vestigial singing behaviour persists after the evolutionary loss of song in crickets

description: The evolutionary loss of sexual traits is widely predicted. Because sexual
 signals can arise from the coupling of specialised motor activity with
 morphological structures, disruption to a single component could lead to
 overall loss of function. Opportunities to observe this process and
 characterise any remaining signal components are rare, but could provide
 insight into the mechanisms, indirect costs, and evolutionary consequences
 of signal loss. We investigated the recent evolutionary loss of a
 long-range acoustic sexual signal in the Hawaiian field cricket
 Teleogryllus oceanicus. Flatwing males carry mutations that remove
 sound-producing wing structures, eliminating all acoustic signalling and
 affording protection against an acoustically-orientating parasitoid fly.
 We show that flatwing males produce wing movement patterns
 indistinguishable from those that generate sonorous calling song in
 normal-wing males. Evolutionary song loss caused by the disappearance of
 structural components of the sound-producing apparatus has left behind the
 energetically-costly motor behaviour underlying normal singing. These
 results provide a rare example of a vestigial behaviour and raise the
 possibility that such traits could be co-opted for novel functions.
description: Schneider et al.
 DataSchneider et al.
 Flatwing 1 (Supplement)Schneider et al.
 Flatwing 2 (Supplement)Schneider et al.
 Flatwing 3 (Supplement)Schneider et al.
 Flatwing 4 (Supplement)Schneider et al.
 Normal-Wing (Supplement)
DOI: 10.5061/dryad.2tk0q
title: Data from: Assessing the trophic ecology of top predators across a recolonisation frontier using DNA metabarcoding of diets

description: Top predator populations, once intensively hunted, are rebounding in size
 and geographic distribution. The cessation of sealing along coastal
 Australia and subsequent recovery of Australian Arctocephalus pusillus
 doriferus and long-nosed A. forsteri fur seals represents a unique
 opportunity to investigate trophic linkages at a frontier of predator
 recolonisation. We characterised the diets of both species across 2
 locations of recolonisation, one site an established breeding colony, and
 the other, a new but permanent haul-out site. Using DNA metabarcoding,
 high taxonomic resolution data on diets was used to inform ecological
 trait-based analyses across time and location. Australian and long-nosed
 fur seals consumed 76 and 73 prey taxa, respectively, a prey diversity
 greater than previously reported. We found unexpected overlap of prey
 functional traits in the diets of both seal species at the haul-out site,
 where we observed strong trophic linkages with coastal ecosystems due to
 the prevalence of benthic, demersal and reef-associated prey. The diets of
 both seal species at the breeding colony were consistent with foraging
 patterns observed in the centre of their geographic range regarding diet
 partitioning between predator species and seasonal trends typically
 observed. The unexpected differences between sites in this region and the
 convergence of both predators’ effective ecological roles at the
 range-edge haul-out site correlate with known differences in seal
 population densities and demographics at these and other newly recolonised
 locations. This study provides a baseline for the diets and trophic
 interactions for recovering fur seal populations and from which to
 understand the evolving ecology of predator recolonisation.
description: Hardy-etal_2017_MEPS_M12165We include three sets of data. (1) Raw FASTQ files with all primers and adaptors trimmed using the software GENEIOUS 8.1.5; (2) FASTA files of filtered Illumina NGS reads, the "FabunX" in the file title refers to the number corresponding to 1% of total unique sequences and thus the percentage of sequences that were filtered out if they clustered at lower than this density in order to be conservative in avoiding sources of sequencing error. See methods in the manuscript for further details. (3) Details of prey identified in each sample, including GenBank accession numbers, bit scores and the percentage match over the length of the sequence.
DOI: 10.5061/dryad.5vb840f
title: Data from: Virtual endocasts of fossil Sciuroidea: brain size reduction in the evolution of fossoriality

description: Aplodontia rufa (Mountain Beaver) is the only extant member of
 Aplodontidae. The fossil record indicates that this family displayed
 greater taxonomic and ecological diversity in the past, and that the
 burrowing adaptations of Aplodontia might be derived. We describe the
 first virtual endocasts of A. rufa and of three fossil aplodontids:
 Prosciurus relictus and Pros. aff. saskatchewaensis (Early Oligocene), and
 Mesogaulus paniensis (late Miocene). Our results show that the endocasts
 of early aplodontid rodents are more similar to those of early arboreal
 squirrels than to the later occurring aplodontids in terms of both
 relative size and morphology. The endocranial features observed in
 sciurids and early aplodontids, missing in later aplodontids, have been
 associated with better vision and the development of arboreality in
 squirrels. Basal Aplodontidae known from postcrania have been described as
 generalists with some features for arboreality, which may provide a basis
 for these similarities. In contrast, the relatively small endocasts of the
 later occurring aplodontids, which lack traits related to visual
 specialization, may reflect their burrowing adaptations, as they would be
 less reliant on visual cues. When integrated with data from the most
 primitive fossil rodents, the Ischyromyidae, these new data suggest early
 squirrels and aplodontids diverged from more terrestrial ischyromyids to
 become more arboreal, with relatively larger brains showing traits for
 improved vision. Recent Aplodontidae with fossorial adaptations returned
 to a more ischyromyid-like condition in their endocranial features. These
 results are consistent with previous observations that changes in
 locomotion are reflected in the endocranial anatomy of rodents.
description: SUPPORTING
 FIGURES-AplodontidaeSuplementary figures for
 article entitled: "First virtual endocasts of fossil Aplodontidae:
 brain size reduction in the evolution of
 fossoriality"SUPPLEMENTARY_TABLES_Sciuridae_AplodontidaeSuplementary tables for article entitled: "First virtual endocasts of fossil Aplodontidae: brain size reduction in the evolution of fossoriality"