cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n80f4
title: Data from: Simulating local adaptation to climate of forest trees with a Physio-Demo-Genetics model

description: One challenge of evolutionary ecology is to predict the rate and
 mechanisms of population adaptation to environmental variations. The
 variations in most life history traits are shaped both by individual
 genotypic and by environmental variation. Forest trees exhibit high levels
 of genetic diversity, large population sizes, and gene flow, and they also
 show a high level of plasticity for life history traits. We developed a
 new Physio-Demo-Genetics model (denoted PDG) coupling (i) a physiological
 module simulating individual tree responses to the environment; (ii) a
 demographic module simulating tree survival, reproduction, and pollen and
 seed dispersal; and (iii) a quantitative genetics module controlling the
 heritability of key life history traits. We used this model to investigate
 the plastic and genetic components of the variations in the timing of
 budburst (TBB) along an elevational gradient of Fagus sylvatica (the
 European beech). We used a repeated 5 years climatic sequence to show that
 five generations of natural selection were sufficient to develop
 nonmonotonic genetic differentiation in the TBB along the local climatic
 gradient but also that plastic variation among different elevations and
 years was higher than genetic variation. PDG complements theoretical
 models and provides testable predictions to understand the adaptive
 potential of tree populations.
description: Simulation data,
 scenario A "Neutral"Raw simulation output
 under scenario A "Neutral"dataScnA.txtSimulation data, scenario B "Evolution"Raw simulation output under scenario B "Evolution"dataScnB.txt
DOI: 10.5061/dryad.7r71q
title: Data from: Molecular dynamics investigation of gluazo, a photo-switchable ligand for the glutamate receptor GluK2

description: Photochromic ligands (PCLs), defined as photoswitchable molecules that are
 able to endow native receptors with a sensitivity towards light, have
 become a promising photopharmacological tool for various applications in
 biology. In general, PCLs consist of a ligand of the target receptor
 covalently linked to an azobenzene, which can be reversibly switched
 between two configurations upon light illumination. Gluazo, as a PCL that
 targets excitatory amino acid receptors, in its dark-adapted trans
 iso-form was characterized to be a partial agonist of the kainate
 glutamate receptor GluK2. Application of UV light leads to the formation
 of the cis form, with remarkedly reduced affinity towards GluK2. The
 mechanism of the change of ligand affinity induced by the
 photoisomerization was unresolved. The presented computational study
 explains how the isomerization of such a PCL affects the structural
 changes in the target receptor that lead to its activation.
description: GluK2-transThe subdirectory /MD includes five free MD simulation trajectories of GluK2-trans complex described in the manuscript. The subdirectory /isomerization includes five forced switching simulation trajectories from trans-gluazo to cis-gluazo. The subdirectory /umbrella-clamshell includes the files needed to reproduce the umbrella sampling simulation results of LBD clamshell motions of GluK2-trans complex. This data file could be used to reproduce all the results of GluK2-trans complex presented in the manuscript.GluK2-cisThe subdirectory /MD includes five free MD simulation trajectories of GluK2-cis complex described in the manuscript. The subdirectory /isomerization includes five forced switching simulation trajectories from cis-gluazo to trans-gluazo. The subdirectory /umbrella-clamshell includes the files needed to reproduce the umbrella sampling simulation results of LBD clamshell motions of GluK2-cis complex. This data file could be used to reproduce all the results of GluK2-cis complex presented in the manuscript.GluK2-glutamateThe subdirectory /MD includes five free MD simulation trajectories of GluK2-glutamate complex, which are used as references in the manuscript.
DOI: 10.5061/dryad.5n36j
title: Data from: The dentary of Wareolestes rex (Megazostrodontidae): a new specimen from Scotland and implications for morganucodontan tooth replacement

description: The Middle Jurassic morganucodontan, Wareolestes rex, was previously known
 from only four isolated molars from Kirtlington, England. There has been
 debate over the position of the holotype tooth as an upper or lower molar.
 We describe a new Wareolestes specimen from the Kilmaluag Formation of
 Scotland: a partial left dentary with two erupted molars, one unerupted
 molar and three unerupted premolars. Empty alveoli for a canine, p1 and p3
 are also present. Through detailed comparison of the morphology of the
 holotype and our new material, we support the original diagnosis of the
 holotype Wareolestes as a lower molar, most likely m1. The position of
 erupted and unerupted replacement teeth in the newly discovered specimen
 supports a diphyodont pattern of tooth replacement of premolariform
 dentition in Wareolestes, as suggested for other morganucodontans such as
 Morganucodon, Megazostrodon and Dinnetherium. However, damage to the
 dentary means that questions remain regarding the sequence of replacement
 in Wareolestes along the tooth row.
description: Wareolestes_NHMUKM36525_CTtifsThe .tif files of a microCT scan of Wareoeslestes rex NHMUK PV M.36525; the holotype molar.ScanTIFs_3.37microns.zipWareolestes_NHMUKM36525_3DmodelA .stl 3D model of the holotype Wareolestes rex molar, NHMUK PV M.36525W.rex_holotype.stlWareolestes_NMSG2016.34.1_3DmodelA .stl 3D model of the Wareolestes rex dentary from Skye, Scotland: NMS G.2016.34.1Wareolestes_rex_Dentary.stlWareolestes_NMSG2016.34.1_3Dmodel_teethA .stl 3D model of the Wareolestes rex dentary from Skye, Scotland: NMS G.2016.34.1 - teeth only.Wareolestes_rex_Teeth.stlWareolestes_NMSG.2016.34.1_CT.bmpThe .bmp files of a microCT scan of Wareoeslestes rex NMS G.2016.34.1; the new dentary from the Kilmaluag, Isle of Skye. Downsampled to 8bit (original 16bit).W.rex.Dentary.zip
DOI: 10.5061/dryad.49dn0
title: Data from: Does warming by open-top chambers induce change in the root-associated fungal community of the arctic dwarf shrub Cassiope tetragona (Ericaceae)?

description: Climate change may alter mycorrhizal communities, which impact ecosystem
 characteristics such as carbon sequestration processes. These impacts
 occur at a greater magnitude in Arctic ecosystems, where the climate is
 warming faster than in lower latitudes. Cassiope tetragona (L.) D. Don is
 an Arctic plant species in the Ericaceae family with a circumpolar range.
 C. tetragona has been reported to form ericoid mycorrhizal (ErM) as well
 as ectomycorrhizal (ECM) symbioses. In this study, the fungal taxa present
 within roots of C. tetragona plants collected from Svalbard were
 investigated using DNA metabarcoding. In light of ongoing climate change
 in the Arctic, the effects of artificial warming by open-top chambers
 (OTCs) on the fungal root community of C. tetragona were evaluated. We
 detected only a weak effect of warming by OTCs on the root-associated
 fungal communities that was masked by the spatial variation between
 sampling sites. The root fungal community of C. tetragona was dominated by
 fungal groups in the Basidiomycota traditionally classified as either
 saprotrophic or ECM symbionts, including the orders Sebacinales and
 Agaricales and the genera Clavaria, Cortinarius, and Mycena. Only a minor
 proportion of the operational taxonomic units (OTUs) could be annotated as
 ErM-forming fungi. This indicates that C. tetragona may be forming
 mycorrhizal symbioses with typically ECM-forming fungi, although no
 characteristic ECM root tips were observed. Previous studies have
 indicated that some saprophytic fungi may also be involved in biotrophic
 associations, but whether the saprotrophic fungi in the roots of C.
 tetragona are involved in biotrophic associations remains unclear. The
 need for more experimental and microscopy-based studies to reveal the
 nature of the fungal associations in C. tetragona roots is emphasized.
description: R
 ScriptThis is the R Script
 used running the ordinations as well as creating the figures and
 supplementary materials for this study.Cassiope_Rscript.ROTUs in BlankThis is an OTU-sample table of the OTUs found in the blank sample (negative control) and removed from further analysis. The representative sequences and the BLAST matches are included.OTU_seqs_in_Blank.xlsxMapping FileThis is the barcode and primer mapping file used in this study.Cassiope_mapfile.txtOTU TableThis is the OTU-sample table used in this study after quality filtering with raw read abundances and in presence-absence format.Cassiope_OTU_table.xlsxRaw Data (forward)Paired-end Illumina seqeuncing output fastq file with forward reads.Cassiope_raw_data01.fastq.zipRaw Data (reverse)Paired-end Illumina seqeuncing output fastq file with reverse reads.Cassiope_raw_data02.fastq.zipRepresentative SequencesThis file contains the representative sequences of the OTUs from this study in fastq format.Cassiope_rep_seqs.fasta
DOI: 10.5061/dryad.23nm1
title: Data from: The function and organization of the motor system controlling flight maneuvers in flies

description: Animals face the daunting task of controlling their limbs using a small
 set of highly constrained actuators. This problem is particularly
 demanding for insects such as Drosophila, which must adjust wing motion
 for both quick voluntary maneuvers and slow compensatory reflexes using
 only a dozen pairs of muscles. To identify strategies by which animals
 execute precise actions using sparse motor networks, we imaged the
 activity of a complete ensemble of wing control muscles in intact, flying
 flies. Our experiments uncovered a remarkably efficient logic in which
 each of the four skeletal elements at the base of the wing are equipped
 with both large phasically active muscles capable of executing large
 changes and smaller tonically active muscles specialized for continuous
 fine-scaled adjustments. Based on the responses to a broad panel of visual
 motion stimuli, we have developed a model by which the motor array
 regulates aerodynamically functional features of wing motion.
description: muscle_segmentationzip file with confocal sections of stained flight muscles.example_flyRaw data from example fly. Presented in figure 1 and 2.Trial DBDatabase of trial data for all signals collectedtrial_db.h5py
DOI: 10.5061/dryad.sn00q
title: Data from: Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet

description: Maladaptation to modern diets has been implicated in several chronic
 disorders. Given the higher prevalence of disease such as dental caries
 and chronic gum diseases in industrialized societies, we sought to
 investigate the impact of different subsistence strategies on oral health
 and physiology, as documented by the oral microbiome. To control for
 confounding variables such as environment and host genetics, we sampled
 saliva from three pairs of populations of hunter-gatherers and traditional
 farmers living in close proximity in the Philippines. Deep shotgun
 sequencing of salivary DNA generated high-coverage microbiomes along with
 human genomes. Comparing these microbiomes with publicly available data
 from individuals living on a Western diet revealed that abundance ratios
 of core species were significantly correlated with subsistence strategy,
 with hunter-gatherers and Westerners occupying either end of a gradient of
 Neisseria against Haemophilus, and traditional farmers falling in between.
 Species found preferentially in hunter-gatherers included microbes often
 considered as oral pathogens, despite their hosts' apparent good oral
 health. Discriminant analysis of gene functions revealed vitamin B5
 autotrophy and urease-mediated pH regulation as candidate adaptations of
 the microbiome to the hunter-gatherer and Western diets, respectively.
 These results suggest that major transitions in diet selected for
 different communities of commensals and likely played a role in the
 emergence of modern oral pathogens.
description: Output of Phylosift
 (placement and summary files)Phylosift (Darling et
 al., PeerJ, 2014) was run on sequencing read sets obtained using Illumina
 technology on metagenomic DNA extracted from salivary samples of 33 human
 individuals: 12 hunter-gatherers (HG) and 12 traditional farmers (TF) from
 the Philippines and 9 Western individual controls (WC). Source metagenomic
 read datasets are available at the ENA (www.ebi.ac.uk/ena): for HGs and
 TFs (original data), under BioSample accessions ERS1202862-ERS1202885; for
 WCs (previously published data): under BioSample accessions SRS013942,
 SRS014468, SRS014692, SRS015055, SRS019120, SRS104275 and SRS147126, and
 two other non-publicly available read data from BioProject
 PRJNA231652.phylosift_results_datadryad.tar.gz
DOI: 10.5061/dryad.q9h2ds8
title: Data from: Two pulses of morphological diversification in Pacific pelagic fishes following the Cretaceous–Palaeogene mass extinction

description: Molecular phylogenies suggest some major radiations of open-ocean fish
 clades occurred roughly coincident with the K/Pg boundary, however the
 timing and nature of this diversification is poorly constrained. Here we
 investigate evolutionary patterns in ray-finned fishes across the
 Cretaceous-Palaeogene (K/Pg) Mass Extinction 66 million years ago (Ma),
 using microfossils (isolated teeth) preserved in a South Pacific sediment
 core spanning 72-43 Ma. Our record does not show significant turnover of
 fish tooth morphotypes at the K/Pg boundary: only two of 48 Cretaceous
 tooth morphotypes disappear at the event in the South Pacific, a rate no
 different from background extinction. Capture-mark-recapture analysis
 finds two pulses of origination in fish tooth morphotypes following the
 mass extinction. The first pulse, at ~64 Ma, included short-lived teeth,
 as well as forms that contribute to an expansion into novel morphospace. A
 second pulse, centered at ~58 Ma, produced morphotype novelty in a
 different region of morphospace from the first pulse, and contributed
 significantly to Eocene tooth morphospace occupation. There was no
 significant increase in origination rates or expansion into novel
 morphospace during the early or middle Eocene, despite a near 10-fold
 increase in tooth abundance during that interval. Our results suggest that
 while the K/Pg event had a minor impact on fish diversity in terms of
 extinction, the removal of the few dominant Cretaceous morphotypes
 triggered a sequence of origination events allowing fishes to rapidly
 diversify morphologically, setting the stage for exceptional levels of
 ray-finned fish diversity in the Cenozoic.
description: ToothMorphToothMorph is a zipped directory which includes all code, csv files, data matrices, and analyses used in this manuscript. Details are included in a readme file within this directory. This code is also available on GitHub (see github.com/esibert/toothmorph), however this data package also includes saved RData workspace images and calculation output csv files, which are too large to include on GitHub.toothmorph.zipDSDP-596_Ichthyolith_ImagesImages of all ichthyoliths included in analysis for Two pulses of morphological diversification in Pacific pelagic fishes following the Cretaceous-Paleogene Mass Extinction, Sibert, Elizabeth, Friedman, Matthew, Hull, Pincelli, Hunt, Gene, Norris, Richard, Proceedings of the Royal Society BSibert_etal_DSDP-596_Ichthyolith_Images.zip
DOI: 10.5061/dryad.1h5183k
title: Data from: Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis

description: Necrotizing enterocolitis (NEC) remains the leading cause of
 gastrointestinal morbidity and mortality in premature infants. Human and
 animal studies suggest a role for Paneth cells in NEC pathogenesis. Paneth
 cells play critical roles in host-microbial interactions and epithelial
 homeostasis. The ramifications of eliminating Paneth cell function on the
 immature host-microbial axis remains incomplete. Paneth cell function was
 depleted in the immature murine intestine using chemical and genetic
 models, which resulted in intestinal injury consistent with NEC. Paneth
 cell depletion was confirmed using histology, electron microscopy, flow
 cytometry, and real time RT-PCR. Cecal samples were analyzed at various
 time points to determine the effects of Paneth cell depletion with and
 without Klebsiella gavage on the microbiome. Deficient Paneth cell
 function induced significant compositional changes in the cecal microbiome
 with a significant increase in Enterobacteriacae species. Further, the
 bloom of Enterobacteriaceae species that occurs is phenotypically similar
 to what is seen in human NEC. This further strengthens our understanding
 of the importance of Paneth cells to intestinal homeostasis in the
 immature intestine.
description: sequence
 dataseqs.fna.zipbarcode_01barcode_02
DOI: 10.5061/dryad.c9s61
title: Data from: A new framework for investigating biotic homogenization and exploring future trajectories: oceanic island plant and bird assemblages as a case study

description: Studies of biotic homogenization have focused primarily on characterizing
 changes that have occurred between some past baseline and the present day.
 In order to understand how homogenization may change in the future, it is
 important to contextualize the processes driving these changes. Here, we
 examine empirical patterns of change in taxonomic similarity among oceanic
 island plant and bird assemblages. We use these empirical cases to unpack
 dynamic properties of biotic homogenization, thereby elucidating two
 important factors that have received little attention: 1) initial
 similarity and 2) the influence of six classes of introduction and
 extinction events. We use Jaccard's Index to explore the interplay
 among these factors in determining the changes in similarity that have
 occurred between human settlement and the present. Specifically, we
 develop general formulas for changes in similarity resulting from each of
 the six types of introductions and extinctions, so that the effect of each
 event type is formulated in terms of initial similarity and species
 richness. We then apply these insights to project how similarity levels
 would change in the future if the present patterns of introductions and
 extinctions continue. We show that the six event types, along with initial
 similarity, can show dramatically different behavior in different systems,
 leading to widely variable influences on similarity. Plant and bird biotas
 have homogenized only slightly to date, but their trajectories of change
 are highly divergent. Although existing patterns of colonization and
 extinction might not continue unchanged, if they were to do so then plant
 assemblages would show little additional change, whereas bird assemblages
 would become much more strongly homogenized. Our results suggest that
 moderate changes in similarity observed to date mask the potential for
 more dramatic changes in the future, and that the interaction among
 initial similarity and differential introduction and extinction regimes
 drives these dynamics.
description: Initial and current
 species lists by islandRows represent species
 or, in a few cases, other taxonomic entities. Within a given row, any cell
 containing a 1 indicates that the given species is or was present on the
 island indicated by the corresponding column heading at the time indicated
 by the column heading.Appendix A3--Initial and
 current species lists.xlsx
DOI: 10.5061/dryad.kh6j6
title: Data from: Does primary productivity modulate the indirect effects of large herbivores? A global meta-analysis

description: 1. Indirect effects of large mammalian herbivores (LMH), while much less
 studied than those of apex predators, are increasingly recognized to exert
 powerful influences on communities and ecosystems. The strength of these
 effects is spatiotemporally variable, and several sets of authors have
 suggested that they are governed in part by primary productivity. However,
 prior theoretical and field studies have generated conflicting results and
 predictions, underscoring the need for a synthetic global analysis. 2. We
 conducted a meta-analysis of the direction and magnitude of large
 mammalian herbivore-initiated indirect interactions using 67 published
 studies comprising 456 individual responses. We georeferenced 41 of these
 studies (comprising 253 responses from 33 locations on 5 continents) to a
 satellite-derived map of primary productivity. Because predator
 assemblages might also influence the impact of large herbivores, we
 conducted a similar analysis using a global map of large-carnivore species
 richness. 3. In general, LMH reduced the abundance of other consumer
 species and also tended to reduce consumer richness, although the latter
 effect was only marginally significant. 4. There was a pronounced
 reduction in the strength of negative (i.e., suppressive, due e.g. to
 competition) indirect effects of LMH on consumer abundance in more
 productive ecosystems. In contrast, positive (facilitative) indirect
 effects were not significantly correlated with productivity, likely
 because these comprised a more heterogeneous array of mechanisms. We found
 no effect of carnivore species richness on herbivore-initiated indirect
 effect strength. 5. Our findings help to resolve the fundamental problem
 of ecological contingency as it pertains to the strength of an
 under-studied class of multi-trophic interactions. Moreover, these results
 will aid in predicting the indirect effects of anthropogenic wildlife
 declines and irruptions, and how these effects might be mediated by
 climatically driven shifts in resource availability. To the extent that
 intact ungulate guilds help to suppress populations of small animals that
 act as agricultural pests and disease reservoirs, the negative impacts of
 large-mammal declines on human well-being may be relatively stronger in
 low-productivity areas.
description: DaskinRawData_160225Raw data extracted from each reviewed publication. See Readme file for complete documentation.SpatialWeightsMatrix_151224Spatial weight matrix for the spatial auto-correlation corrections used in meta-regressions. Row and column headers correspond to "Productivity.Location" in DaskinRawData_160225.csv and indicate the location of reviewed studies.