cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gb135
title: Data from: Complete dosage compensation and sex-biased gene expression in the moth Manduca sexta

description: Sex chromosome dosage compensation balances homogametic sex chromosome
 expression with autosomal expression in the heterogametic sex, leading to
 sex chromosome expression parity between the sexes. If compensation is
 incomplete this can lead to expression imbalance and sex-biased gene
 expression. Recent work has uncovered an intriguing and variable pattern
 of dosage compensation across species that includes a lack of complete
 dosage compensation in ZW species compared to XY species. This has led to
 the hypothesis that ZW species do not require complete compensation or
 that complete compensation would negatively affect their fitness. To date
 only one study, a study of the moth Bombyx mori, has discovered evidence
 for complete dosage compensation in a ZW species. We examined another moth
 species, Manduca sexta, using high-throughput sequencing to survey gene
 expression in the head tissue of males and females. We found dosage
 compensation to be complete in M. sexta with average expression between
 the Z chromosome in males and females being equal. When genes expressed at
 very low levels are removed by filtering, we found that average autosome
 expression was highly similar to average Z expression, suggesting that the
 majority of genes in M. sexta are completely dosage compensated. Further,
 this compensation was accompanied by sex-specific gene expression
 associated with important sexually dimorphic traits. We suggest that
 complete dosage compensation in ZW species might be more common than
 previously appreciated and linked to additional selective processes, such
 as sexual selection. More ZW and lepidopteran species should now be
 examined in a phylogenetic framework, in order to understand the evolution
 of dosage compensation.
description: FASTA sequence file of
 de novo Trinity assembly of mRNA transcripts from Manduca sexta head
 tissuesThis file contains de
 novo assembled contigs constructed from Illumina short read sequencing of
 mRNA from the head tissues of the moth Manduca sexta. De novo assembly was
 carried out in the program Trinity. Assembled contigs represent genes and
 gene transcripts expressed in the head tissues of both male and female
 individuals.Msexta_Trinity.fasta
DOI: 10.5061/dryad.2gj3n
title: Data from: Basal dinosauriform and theropod dinosaurs from the middle-late Norian (Late Triassic) of Poland: implications for Triassic dinosaur evolution and distribution

description: The rise of dinosaurs during the Triassic is a widely studied evolutionary
 radiation, but there are still many unanswered questions about early
 dinosaur evolution and biogeography that are hampered by an unevenly
 sampled Late Triassic fossil record. Although very common in western North
 America and parts of South America, dinosaur (and more basal
 dinosauriform) remains are relatively rare in the Upper Triassic deposits
 of Europe, making any new discoveries critically important. One of the
 most diverse dinosauriform assemblages from Europe comes from the Poręba
 site in Poland, a recently described locality with exposures of the
 Zbąszynek Beds, which have a palynomorph assemblage characteristic for the
 mid–late Norian in the biostratigraphic schemes of the Germanic Basin.
 Using a synapomorphy-based approach, we evaluate several isolated
 dinosauriform specimens from Poręba. This assemblage includes a
 silesaurid, a herrerasaurid and remains of another type of theropod
 (potentially a neotheropod). The Poręba herrerasaurid is the first record
 of this rare group of primitive dinosaurs from Europe and one of the
 youngest records worldwide, whereas the silesaurid is the youngest record
 of a silesaurid from Europe. These findings indicate that silesaurids
 persisted alongside true dinosaurs into the mid–late Norian of Europe and
 that silesaurid–herrerasaurid–neotheropod assemblages (which are also
 known from the Norian of North America, at low latitudes) were more
 widespread geographically and latitudinally than previously thought.
 Silesaurid–herrerasaurid–neotheropod assemblages may have been a common
 ecological structuring of dinosaurs during their early evolution, and
 their widespread distribution may indicate weak palaeolatitudinal controls
 on early dinosaur biogeography during the latest Triassic.
description: SUPPLEMENTARY Figure
 1-7Phylogenetic
 analysisappendix
 1
DOI: 10.5061/dryad.m4cc1
title: Data from: Mapping and expression of candidate genes for development rate in rainbow trout (Oncorhynchus mykiss)

description: Development rate has important implications for individual fitness and
 physiology. In salmonid fishes, development rate correlates with many
 traits later in life, including life history diversity, growth, and age
 and size at sexual maturation. In rainbow trout (Oncorhynchus mykiss), a
 Quantitative Trait Locus (QTL) for embryonic development rate has been
 detected on chromosome 5 across populations. However, few candidate genes
 have been identified within this region. In this study, we use gene
 mapping, gene expression, and quantitative genetic methods to further
 identify the genetic basis of embryonic developmental rate in O. mykiss.
 Among the genes located in the region of the major development rate QTL
 (GHR1, Clock1a, Myd118-1, and their paralogs), all were expressed early in
 embryonic development (fertilization through hatch), but none were
 differentially expressed between individuals with the fast- or
 slow-developing alleles for a major embryonic development rate QTL. In a
 follow up study of migratory and resident rainbow trout from natural
 populations in Alaska, we found significant additive variation in
 development rate, and moreover found associations between development rate
 and allelic variation in all three candidate genes within the QTL for
 embryonic development. The mapping of these genes to this region and
 associations in multiple populations provide positional candidates for
 further study of their roles in growth, development, and life history
 diversity in this model salmonid.
description: raw mapping
 dataGenotypes used to
 construct linkage maps used in paper. First sheet contains the data from
 the smolt dataset. Second sheet contains the data from the meristics
 dataset.Sashin_supplementalfile_h2linecrossExcel file with ATU data used for quantitative genetics. Sheet one contains the heritability, live cross, and ATU data. Sheet 2 family means for the number of ATUs. Sheet 3 sample, cross, ATUs, and genotypes for three candidate genes; clock1a, GHR1 and Myd118-1
DOI: 10.5061/dryad.jp43c
title: Data from: Pharmacological inhibition of cystine-glutamate exchange induces endoplasmic reticulum stress and ferroptosis

description: Exchange of extracellular cystine for intracellular glutamate by the
 antiporter system xc− is implicated in numerous pathologies.
 Pharmacological agents that inhibit system xc− activity with high potency
 have long been sought, but have remained elusive. In this study, we report
 that the small molecule erastin is a potent, selective inhibitor of system
 xc−. RNA sequencing revealed that inhibition of cystine–glutamate exchange
 leads to activation of an ER stress response and upregulation of CHAC1,
 providing a pharmacodynamic marker for system xc− inhibition. We also
 found that the clinically approved anti-cancer drug sorafenib, but not
 other kinase inhibitors, inhibits system xc− function and can trigger ER
 stress and ferroptosis. In an analysis of hospital records and adverse
 event reports, we found that patients treated with sorafenib exhibited
 unique metabolic and phenotypic alterations compared to patients treated
 with other kinase-inhibiting drugs. Finally, using a genetic approach, we
 identified new genes dramatically upregulated in cells resistant to
 ferroptosis.
description: Data Package
 1FPKM
 expression values from RNA-seq using HT-1080 fibrosarcoma cells under four
 different conditions, with samples submitted in two biological replicates.
 The column titles map to these four conditions: 1) DMSO (no treatment), 2)
 B-ME (ferroptosis inhibitor), 3) Erastin (ferroptosis inducer), and 4)
 Erastin + B-ME. Fold changes were calculated for Erastin/DMSO and
 Erastin+B-ME/DMSO. For these experiments, only genes with FPKM not equal
 to zero in any condition and FPKM≥1 for both replicates in the DMSO
 condition were considered in the analysis. To further restrict the
 analysis to high quality data, we only examined those genes where the
 difference between replicate values in the two DMSO and the two
 erastin-treated samples was &lt;2.5x.DataPackage1.xlsxData Package 2FPKM expression values from RNA-seq using parental DU-145 prostate cancer cells and clonal cell lines derived from the parental line with resistance to erastin-induced ferroptosis. Sample nomenclature is as follows: "2.5E-2" means this resistant line was produced using a selective pressure of 2.5uM Erastin, and was the second clone evaluated at that concentration. The column titles map to one parental and five resistant clonal lines tested: DU-145 (parental, sensitive), 2.5E-1, 2.5E-2, 2.5E-3, 2.5E-5, and 2.6E-23 (all resistant). Fold changes were calculated using the ratio of each resistant line/parental (column directly to the right of each resistant line). Average fold changes (resistant/parental, column M) and average ΔFPKM (resistant - parental, column N) for each gene across all resistant lines were calculated. For these experiments, only genes with FPKM &gt; 0.1 in the DU-145 condition and FPKM ≥ 1 for all other conditions were evaluated.DataPackage2.xlsxExtended Materials & Methods
DOI: 10.7927/5s2t-2j81
title: IPCC AR6 Synthesis Report LR Figure 4.3 (b): Increased frequency of extreme sea level events by 2040

description: Every region faces more severe or frequent compound and/or cascading climate risks in the near term. Changes in risk result from changes in the degree of the hazard, the population exposed, and the degree of vulnerability of people, assets, or ecosystems. This panel shows the projected median probability in the year 2040 for extreme water levels resulting from a combination of mean sea level rise, tides and storm surges, which have a historical 1% average annual probability. A peak-over-threshold (99.7%) method was applied to the historical tide gauge observations. This panel uses relative sea level projections under SSP2-4.5 for the year 2040. The absence of a circle indicates an inability to perform an assessment due to a lack of data, but does not indicate absence of increasing frequencies.
DOI: 10.5061/dryad.8167k
title: Data from: Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates

description: High-throughput sequencing platforms are generating massive amounts of
 genomic data from nonmodel species, and these data sets are valuable
 resources that can be mined to advance a number of research areas. An
 example is the growing amount of transcriptome data that allow for
 examination of gene expression in nonmodel species. Here, we show how
 publicly available transcriptome data from nonmodel primates can be used
 to design novel research focused on immunogenomics. We mined transcriptome
 data from the world's most endangered group of primates, the lemurs
 of Madagascar, for sequences corresponding to immunoglobulins. Our results
 confirmed homology between strepsirrhine and haplorrhine primate
 immunoglobulins and allowed for high-throughput sequencing of expressed
 antibodies (Ig-seq) in Coquerel's sifaka (Propithecus coquereli).
 Using both Pacific Biosciences RS and Ion Torrent PGM sequencing, we
 performed Ig-seq on two individuals of Coquerel's sifaka. We
 generated over 150 000 sequences of expressed antibodies, allowing for
 molecular characterization of the antigen-binding region. Our analyses
 suggest that similar VDJ expression patterns exist across all primates,
 with sequences closely related to the human VH3 immunoglobulin family
 being heavily represented in sifaka antibodies. Moreover, the
 antigen-binding region of sifaka antibodies exhibited similar amino acid
 variation with respect to haplorrhine primates. Our study represents the
 first attempt to characterize sequence diversity of the expressed antibody
 repertoire in a species of lemur. We anticipate that methods similar to
 ours will provide the framework for investigating the adaptive immune
 response in wild populations of other nonmodel organisms and can be used
 to advance the burgeoning field of eco-immunology.
description: Larsen_etal_PacBioCCS_filtered_DLC6884_Sifaka1_IgG.fastqQuality filtered PacBio SMRT CCS Ig-seq data from Sifaka 1 (DLC6884).Larsen_etal_IonTorrent_filtered_DLC6583_Sifaka2_IgH.fastqQuality filtered Ion Torrent Ig-seq sequence data from Sifaka 2 (DLC6583).
DOI: 10.5061/dryad.qd3pd
title: Data from: Reconciling hierarchical taxonomy with molecular phylogenies

description: Taxonomy has a history dating back to Aristotle (350BC) and has
 facilitated a wide range of developments in the biological sciences.
 Linnaeus’ Systema Naturae assumed that organisms were static creations of
 God and formulated the hierarchical framework of classification that we
 currently use. Today we know that organisms continuously evolve and it is
 generally accepted that these hierarchies are arbitrary constructs (Coyne
 and Orr 2004). The arbitrary nature of these higher taxonomic ranks does
 not prevent their practical use with regards to cataloguing, and
 communicating about, biological diversity, provided such arbitrary
 decisions are made on a consistent basis. However, current taxonomic
 hierarchies are suggested to be inconsistent, both between and within
 major clades (Avise and Liu 2011), reflecting the work of systematists
 with diverging views regarding the constitution of higher taxonomic ranks.
 In this study, we present a comprehensive analysis of the overall levels
 of consistency within current higher taxonomic ranks using dated
 phylogenies for all bird and mammal species. Building on work by Hennig
 (1966), and proposed by Avise and Johns (1999), “temporal banding”
 provides an opportunity to assess the consistency of ancestral
 relationships within and among higher taxonomic ranks, as well as a
 practical solution to these temporal inconsistencies. Temporal banding
 standardises taxonomic ranks by “cutting” dated phylogenies at specified
 points in time and applying this concept requires comprehensive dated
 phylogenies, which has so far limited the application of the approach.
 Here we apply temporal banding to two vertebrate classes (birds and
 mammals) and produce standardised error metrics to compare the consistency
 of existing taxonomic ranks within and between the two classes. We discuss
 the implications of error within the phylogenies used, as well as the
 practicalities of the temporal banding approach.
description: SM1 - Temporal banding
 taxonomic classifications for birds and mammalsTaxonomic hierarchies
 for birds and mammals, produced by temporal banding of dated phylogenies
 with corresponding traditional taxonomies.SM2 - Taxonomic error
 for bird and mammal cladesTaxonomic error scores
 for traditional bird and mammal taxonomic order, families and
 genera.SM3 - Results for
 alternative bird analysisSummary results for
 alternative versions of bird temporal banding classification
 analysis.SM4 R code and example
 dataExample code and data
 for applying temporal banding to a phylogeny and calculating standardised
 error scores. See manuscript for references to original data
 sources.
DOI: 10.25574/28122
title: Chandra X-ray Observatory ObsId 28122

description: PHANGS-Chandra: A Legacy Survey for Detailing the First Billion Years of X-ray Evolution in Galaxies
DOI: 10.5061/dryad.7n696
title: Data from: Flies on the move: an inherited virus mirrors Drosophila melanogaster’s elusive ecology and demography

description: Vertically transmitted parasites rely on their host's reproduction
 for their transmission, leading to the evolutionary histories of both
 parties being intimately entwined. Parasites can thus serve as a
 population genetic magnifying glass for their host's demographic
 history. Here, we study the fruitfly Drosophila melanogaster's
 vertically transmitted sigma virus DMelSV. The virus has a high mutation
 rate and low effective population size, allowing us to reconstruct at a
 fine scale how the combined forces of the movement of flies and selection
 on the virus have shaped its migration patterns. We found that the virus
 is likely to have spread to Europe from Africa, mirroring the colonization
 route of Drosophila. The North American DMelSV population appears to be
 the result of a recent single immigration from Europe, invading together
 with its host in the late 19th century. Across Europe, DMelSV migration
 rates are low and populations are highly genetically structured, likely
 reflecting limited fly movement. Despite being intolerant of extreme cold,
 viral diversity suggests that fly populations can persist in harsh
 continental climates and that recolonisation from the warmer south plays a
 minor role. In conclusion, studying DMelSV can provide insights into the
 poorly understood ecology of D. melanogaster, one of the best-studied
 organisms in biology.
description: alignment_longFasta alignment of the 'long' data setalignment_shortFasta alignment for the 'short' data setbeast_fig1XML file for beast analysis visualised in figure 1beast_fig2&3XML file for beast analysis depicted in figures 2 and 3MCC_fig1Nexus file of MCC tree in figure 1MCC_fig3Nexus file for MCC tree in figure 3
DOI: 10.5061/dryad.ps0f0
title: Data from: Highly resolved early Eocene food webs show development of modern trophic structure after the end-Cretaceous extinction

description: Generalities of food web structure have been identified for extant
 ecosystems. However, the trophic organization of ancient ecosystems is
 unresolved, as prior studies of fossil webs have been limited by
 low-resolution, high-uncertainty data. We compiled highly resolved,
 well-documented feeding interaction data for 700 taxa from the 48
 million-year-old latest early Eocene Messel Shale, which contains a
 species assemblage that developed after an interval of protracted
 environmental and biotal change during and following the end-Cretaceous
 extinction. We compared the network structure of Messel lake and forest
 food webs to extant webs using analyses that account for scale dependence
 of structure with diversity and complexity. The Messel lake web, with 94
 taxa, displays unambiguous similarities in structure to extant webs. While
 the Messel forest web, with 630 taxa, displays differences compared to
 extant webs, they appear to result from high diversity and resolution of
 insect–plant interactions, rather than substantive differences in
 structure. The evidence presented here suggests that modern trophic
 organization developed along with the modern Messel biota during an 18 Myr
 interval of dramatic post-extinction change. Our study also has
 methodological implications, as the Messel forest web analysis highlights
 limitations of current food web data and models.
description: Food web data for the
 uppermost early Eocene Messel ShaleLabanderiaDunne2014DryadData.xls
DOI: 10.5061/dryad.94jt2
title: Data from: Occam's Razor in sensorimotor learning

description: A large number of recent studies suggest that the sensorimotor system
 employs probabilistic models to predict its environment and makes
 inferences about unobserved variables in line with Bayesian statistics.
 One of the important features of Bayesian statistics is Occam's Razor
 - an inbuilt preference for simpler models when comparing competing models
 that explain some observed data equally well. Here we test directly for
 Occam's Razor in sensorimotor control. We designed a sensorimotor
 task, where participants had to draw lines through clouds of noisy samples
 of an unobserved curve generated by one of two possible probabilistic
 models - a simple model with a large length scale, leading to smooth
 curves and a complex model with a short length scale, leading to more
 wiggly curves. In training trials participants were informed about the
 model that generated the stimulus so that they could learn the statistics
 of each model. In probe trials participants were then exposed to ambiguous
 stimuli. In probe trials where the ambiguous stimulus could be fit equally
 well by both models, we found that participants showed a clear preference
 for the simpler model. Moreover, we found that participants' choice
 behavior was quantitatively consistent with Bayesian Occam's Razor.
 We could also show that participants' drawn trajectories were similar
 to samples from the Bayesian predictive distribution over trajectories and
 significantly different from two non-probabilistic heuristics. In two
 control experiments, we show that the preference of the simpler model
 cannot be simply explained by a difference in physical effort or by a
 preference for curve smoothness. Our results suggest that Occam's
 Razor is a general behavioral principle already present during
 sensorimotor processing.
description: Occam's Razor in
 sensorimotor learning - human trajectory dataThe data-file contains
 recordings of human motion data that was acquired in a virtual reality
 setup. Participants of the experiment were controlling a virtual cursor
 using a 3D manipulandum in order to draw regression trajectories through
 clouds of noisy observations that were presented to them through a head
 mounted display. See corresponding publication and included Readme-file
 for details.Data.zip
DOI: 10.5061/dryad.120p0
title: Data from: The role of climatic tolerances and seed traits in reduced extinction rates of temperate Polygonaceae

description: The latitudinal diversity gradient (LDG) is one of the most striking and
 consistent biodiversity patterns across taxonomic groups. We investigate
 the species richness gradient in the buckwheat family, Polygonaceae, which
 exhibits a reverse LDG and is, thus, decoupled from dominant gradients of
 energy and environmental stability that increase towards the tropics and
 confound mechanistic interpretations. We test competing age and
 evolutionary diversification hypotheses, which may explain the
 diversification of this plant family over the past 70 million years. Our
 analyses show that the age hypothesis, which posits that clade richness is
 positively correlated with the ecological and evolutionary time since
 clade origin, fails to explain the richness gradient observed in
 Polygonaceae. However, an evolutionary diversification hypothesis is
 highly supported, with diversification rates being 3.5 times higher in
 temperate clades compared to tropical clades. We demonstrate that
 differences in rates of speciation, migration, and molecular evolution
 insufficiently explain the observed patterns of differential
 diversification rates. We suggest that reduced extinction rates in
 temperate clades may be associated with adaptive responses to selection,
 through which seed morphology and climatic tolerances potentially act to
 minimize risk in temporally variable environments. Further study is needed
 to understand causal pathways among these traits and factors correlated
 with latitude.
description: KostikovaetalExtinction_SIThe Supplementary information file