cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cc2tc
title: Data from: The K=2 conundrum

description: Assessments of population genetic structure have become an increasing
 focus as they can provide valuable insight into patterns of migration and
 gene flow. STRUCTURE, the most highly cited of several clustering-based
 methods, was developed to provide robust estimates without the need for
 populations to be determined a priori. STRUCTURE introduces the problem of
 selecting the optimal number of clusters and as a result the ΔK method was
 proposed to assist in the identification of the ‘true’ number of clusters.
 In our review of 1,264 studies using STRUCTURE to explore population
 subdivision, studies that used ΔK were more likely to identify K=2 (54%,
 443/822) than studies that did not use ΔK (21%, 82/386). A troubling
 finding was that very few studies performed the hierarchical analysis
 recommended by the authors of both ΔK and STRUCTURE to fully explore
 population subdivision. Furthermore, extensions of earlier simulations
 indicate that, with a representative number of markers, ΔK frequently
 identifies K=2 as the top level of hierarchical structure, even when more
 subpopulations are present. This review suggests that many studies may
 have been over- or underestimating population genetic structure; both
 scenarios have serious consequences, particularly with respect to
 conservation and management. We recommend publication standards for
 population structure results so that readers can assess the implications
 of the results given their own understanding of the species biology.
description: Janes et al. (2017). The
 K=2 conundrum. Review data and simulations.The zip file contains
 the raw meta-analysis/review data and all data associated with the
 simulations and STRUCTURE runs.Janes_K2_data.zip
DOI: 10.5061/dryad.f5q10
title: Data from: A bird-like skull in a Triassic diapsid reptile increases heterogeneity of the morphological and phylogenetic radiation of Diapsida

description: The Triassic Period saw the first appearance of numerous amniote lineages
 (e.g. Lepidosauria, Archosauria, Mammalia) that defined Mesozoic
 ecosystems following the end Permian Mass Extinction, as well as the first
 major morphological diversification of crown-group reptiles.
 Unfortunately, much of our understanding of this event comes from the
 record of large-bodied reptiles (total body length &gt; 1 m). Here we
 present a new species of drepanosaurid (small-bodied, chameleon-like
 diapsids) from the Upper Triassic Chinle Formation of New Mexico. Using
 reconstructions of micro-computed tomography data, we reveal the
 three-dimensional skull osteology of this clade for the first time. The
 skull presents many archaic anatomical traits unknown in Triassic
 crown-group reptiles (e.g. absence of bony support for the external ear),
 whereas other traits (e.g. toothless rostrum, anteriorly directed orbits,
 inflated endocranium) resemble derived avian theropods. A phylogenetic
 analysis of Permo-Triassic diapsids supports the hypothesis that
 drepanosaurs are an archaic lineage that originated in the Permian, far
 removed from crown-group Reptilia. The phylogenetic position of
 drepanosaurids indicates the presence of archaic Permian clades among
 Triassic small reptile assemblages and that morphological convergence
 produced a remarkably bird-like skull nearly 100 Myr before one is known
 to have emerged in Theropoda.
description: Zip file containing CQ
 Drepanosaur CT scan dataDICOM slices of the
 Coelophysis Quarry drepanosaur (Avicranium renestoi) CT
 datasetCropped.zipPhylogenetic data matrix in Nexus formPhylogenetic data matrix from the primary phylogenetic analysis of this paper. Parameters for analysis are noted in Appendix C.CQDrepanosaurMatrix.nex
DOI: 10.5061/dryad.ch352
title: Data from: An integrated approach reveals regulatory controls on bacterial translation elongation

description: Ribosomes elongate at a nonuniform rate during translation. Theoretical
 models and experiments disagree on the in vivo determinants of elongation
 rate and the mechanism by which elongation rate affects protein levels. To
 resolve this conflict, we measured transcriptome-wide ribosome occupancy
 under multiple conditions and used it to formulate a whole-cell model of
 translation in E. coli. Our model predicts that elongation rates at most
 codons during nutrient-rich growth are not limited by the intracellular
 concentrations of aminoacyl-tRNAs. However, elongation pausing during
 starvation for single amino acids is highly sensitive to the kinetics of
 tRNA aminoacylation. We further show that translation abortion upon
 pausing accounts for the observed ribosome occupancy along mRNAs during
 starvation. Abortion reduces global protein synthesis, but it enhances the
 translation of a subset of mRNAs. These results suggest a regulatory role
 for aminoacylation and abortion during stress, and our study provides an
 experimentally constrained framework for modeling translation.
description: Code tarball for
 simulation, data analysis and reproduction of figuresThis tarball contains 4
 IPython Notebook files and a static html version of each Notebook. The
 IPython Notebooks provide the code for running the simulation (E. coli and
 yeast separate), the sequencing and simulation data analysis, and
 reproduction of most figures from the paper. Use tar -xvzf filename to
 expand.notebooks_html_files.tar.gzSimulation results tarballThis tarball contains the raw output results of running all the simulations (present as 10 subfolders). Expand output_files.tar.gz within the notebook_html_files folder.output_files.tar.gz
DOI: 10.5061/dryad.6983c
title: Data from: Incorporating explicit geospatial data shows more species at risk of extinction than the current Red List

description: The IUCN (International Union for Conservation of Nature) Red List
 classifies species according to their risk of extinction, informing global
 to local conservation decisions. Unfortunately, important geospatial data
 do not explicitly or efficiently enter this process. Rapid growth in the
 availability of remotely sensed observations provides fine-scale data on
 elevation and increasingly sophisticated characterizations of land cover
 and its changes. These data readily show that species are likely not
 present within many areas within the overall envelopes of their
 distributions. Additionally, global databases on protected areas inform
 how extensively ranges are protected. We selected 586 endemic and
 threatened forest bird species from six of the world’s most biodiverse and
 threatened places (Atlantic Forest of Brazil, Central America, Western
 Andes of Colombia, Madagascar, Sumatra, and Southeast Asia). The Red List
 deems 18% of these species to be threatened (15 critically endangered, 29
 endangered, and 64 vulnerable). Inevitably, after refining ranges by
 elevation and forest cover, ranges shrink. Do they do so consistently? For
 example, refined ranges of critically endangered species might reduce by
 (say) 50% but so might the ranges of endangered, vulnerable, and
 nonthreatened species. Critically, this is not the case. We find that 43%
 of species fall below the range threshold where comparable species are
 deemed threatened. Some 210 bird species belong in a higher-threat
 category than the current Red List placement, including 189 species that
 are currently deemed nonthreatened. Incorporating readily available
 spatial data substantially increases the numbers of species that should be
 considered at risk and alters priority areas for conservation.
description: Data from: Incorporating
 explicit geospatial data shows more species at risk of extinction than the
 current Red ListThere are six folders in
 the zip file, one for each region we covered. Inside each region's
 folder there are two .tiff files: the first one is a composite of ranges
 of endemic and threatened birds using their original range map from
 BirdLifer and Natureserve; the second file is a composite of the same
 species but after their ranges were refined by elevation and habitat using
 the methods described in the publication.Supp.
 Data.zip
DOI: 10.5061/dryad.f0h49
title: Data from: The biogeography of the atlantic salmon (Salmo salar) gut microbiome

description: Although understood in many vertebrate systems, the natural diversity of
 host-associated microbiota has been little studied in teleosts. For
 migratory fishes, successful exploitation of multiple habitats may affect
 and be affected by the composition of the intestinal microbiome. We
 collected 96 Salmo salar from across the Atlantic encompassing both
 freshwater and marine phases. Dramatic differences between environmental
 and gut bacterial communities were observed. Furthermore, community
 composition was not significantly impacted by geography. Instead
 life-cycle stage strongly defined both the diversity and identity of
 microbial assemblages in the gut, with evidence for community
 destabilisation in migratory phases. Mycoplasmataceae phylotypes were
 abundantly recovered in all life-cycle stages. Patterns of
 Mycoplasmataceae phylotype recruitment to the intestinal microbial
 community among sites and life-cycle stages support a dual role for
 deterministic and stochastic processes in defining the composition of the
 S. salar gut microbiome.
description: raw_data_salmon_microbiomeSalmon salar gut microbiome sequences. Samples are identified by their "FLD0001.****_R1.fastq" code in the samples' name.raw_data.zip
DOI: 10.5061/dryad.kk1qj10
title: Data from: Eco-evolutionary dynamics in metacommunities: ecological inheritance, helping within species, and harming between species

description: Understanding selection on intra- and inter-specific interactions that
 take place in dispersal-limited communities is a challenge for ecology and
 evolutionary biology. The problem is that local demographic stochasticity
 generates eco-evolutionary dynamics that are generally too complicated to
 make tractable analytical investigations. Here, we circumvent this problem
 by approximating the selection gradient on a quantitative trait that
 influences local community dynamics, assuming that such dynamics are
 deterministic with a stable fixed point. We nonetheless incorporate
 unavoidable kin selection effects arising from demographic stochasticity.
 Our approximation reveals that selection depends on how an individual
 expressing a trait-change influences: (1) its own fitness and the fitness
 of its current relatives; and (2) the fitness of its downstream relatives
 through modifications of local ecological conditions (i.e., through
 ecological inheritance). Mathematically, the effects of ecological
 inheritance on selection are captured by dispersal-limited versions of
 press-perturbations of community ecology. We use our approximation to
 investigate the evolution of helping within- and harming between-species
 when these behaviours influence demography. We find that altruistic
 helping evolves more readily when intra-specific competition is for
 material resources rather than for space because in this case, the costs
 of kin competition tend to paid by downstream relatives. Similarly,
 altruistic harming between species evolves when it alleviates downstream
 relatives from inter-specific competition. Beyond these examples, our
 approximation can help better understand the influence of ecological
 inheritance on a variety of eco-evolutionary dynamics in metacommunities,
 from consumer-resource and predator-prey coevolution to selection on
 mating systems with demographic feedbacks.
description: M-files and simulated
 dataThis contains the
 simulation source codes (for Mathematica), as well as the simulated data,
 used to produce Figures 1, 2, 5, 6, and 7 of Eco-evolutionary dynamics in
 metacommunities: ecological inheritance, helping within- and harming
 between-species, by Charles Mullon and Laurent Lehmann.Simulated data for
 figures.zip
DOI: 10.5061/dryad.qf1dp
title: Data from: Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

description: As a direct result of intense heat and aridity, deserts are thought to be
 among the most harsh of environments, particularly for their mammalian
 inhabitants. Given that osmoregulation can be challenging for these
 animals, with failure resulting in death, strong selection should be
 observed on genes related to the maintenance of water and solute balance.
 One such animal, Peromyscus eremicus, is native to the desert regions of
 the southwest United States and may live its entire life without oral
 fluid intake. As a first step toward understanding the genetics that
 underlie this phenotype, we present a characterization of the P. eremicus
 transcriptome. We assay four tissues (kidney, liver, brain, testes) from a
 single individual and supplement this with population level renal
 transcriptome sequencing from 15 additional animals. We identified a set
 of transcripts undergoing both purifying and balancing selection based on
 estimates of Tajima’s D. In addition, we used the branch-site test to
 identify a transcript—Slc2a9, likely related to desert
 osmoregulation—undergoing enhanced selection in P. eremicus relative to a
 set of related non-desert rodents.
description: Brain derived
 contigsThese are the contigs
 derived from the RNA collected from brain tissue.brain.final.fastaKidney derived contigsPutative transcripts from renal tissue.kidney.final.fastaLiver derived transcriptsPutative transcripts from liver tissue.liver.final.fastaTestes derived transcriptsPutative transcripts from testes tissue.testes.final.fastaPfam resultsThese are the results from the Pfam search against Pero.BLTK.fastapero.pfam4Tissue.transcriptsThis file contains the putative transcripts from all tissues, and serves as the basis for most of the downstream analyses.Pero.BLTK.fastaTranscript expressionThis file contains the expression data for all transcripts in the Pero.BLTK.fasta file.Pero.tissue.xprsCoding sequencesThis file contains the predicted coding sequencesPero.BLTK.cdsAnalysis codeThis file contains code used in the bioinformatic analyses.analyses.md
DOI: 10.5061/dryad.n82g9
title: Data from: Abrupt changes in the composition and function of fungal communities along an environmental gradient in the High Arctic

description: Fungi play a key role in soil-plant interactions, nutrient cycling, and
 carbon flow and are essential for the functioning of arctic terrestrial
 ecosystems. Some studies have shown that the composition of fungal
 communities is highly sensitive to variations in environmental conditions,
 but little is known about how the conditions control the role of fungal
 communities (i.e. their ecosystem function). We used DNA metabarcoding to
 compare taxonomic and functional composition of fungal communities along a
 gradient of environmental severity in Northeast Greenland. We analysed
 soil samples from fell fields, heaths, and snowbeds, three habitats with
 very contrasting abiotic conditions. We also assessed within-habitat
 differences by comparing three widespread microhabitats (patches with high
 cover of Dryas, Salix, or bare soil). The data suggest that, along the
 sampled mesotopographic gradient, the greatest differences in both fungal
 richness and community composition are observed among habitats, while the
 effect of microhabitat is weaker, although still significant. Furthermore,
 we found that richness and community composition of fungi are shaped
 primarily by abiotic factors and to a lesser, though still significant
 extent, by floristic composition. Along this mesotopographic gradient,
 environmental severity is strongly correlated with richness in all fungal
 functional groups: positively in saprotrophic, pathogenic, and lichenised
 fungi, and negatively in ectomycorrhizal and root-endophytic fungi. Our
 results suggest complex interactions amongst functional groups, possibly
 due to nutrient limitation or competitive exclusion, with potential
 implications on soil carbon stocks. These findings are important in light
 of the environmental changes predicted for the Arctic.
description: Z1 (Fell field-Bare
 ground-Plot 1)Z1.fastqZ2 (Fell field-Salix-Plot 1)Z2.fastqZ3 (Fell field-Dryas-Plot 1)Z3.fastqZ4 (Fell field-Bare ground-Plot 2)Z4.fastqZ5 (Fell field-Salix-Plot 2)Z5.fastqZ6 (Fell field-Dryas-Plot 2)Z6.fastqZ7 (Fell-field-Bare ground-Plot 3)Z7.fastqZ8 (Fell field-Dryas-Plot 3)Z8.fastqZ9 (Fell field-Salix-Plot 3)Z9.fastqZ10 (Heath-Bare ground-Plot 2)Z10.fastqZ11 (Snowbed-Bare ground-Plot 1)Z11.fastqZ12 (Snowbed-Salix-Plot 1)Z12.fastqZ13 (Snowbed-Bare ground-Plot 3)Z13.fastqZ14 (Snowbed-Salix-Plot 3)Z14.fastqZ15 (Snowbed-Dryas-Plot 3)Z15.fastqZ16 (Snowbed-Bare ground-Plot 2)Z16.fastqZ17 (Snowbed-Salix-Plot 2)Z17.fastqZ18 (Snowbed-Dryas-Plot 2)Z18.fastqZ19 (Snowbed-Dryas-Plot 1)Z19.fastqZ20 (Heath-Dryas-Plot 2)Z20.fastqZ21 (Heath-Salix-Plot 2)Z21.fastqZ22 (Heath-Bare ground-Plot 1)Z22.fastqZ23 (Heath-Dryas-Plot 1)Z23.fastqZ24 (Heath-Salix-Plot 1)Z24.fastqZ25 (Heath-Bare ground-Plot 3)Z25.fastqZ26 (Heath-Salix-Plot 3)Z26.fastqZ27 (Heath-Dryas-Plot 3)Z27.fastq
DOI: 10.5061/dryad.fr1r2
title: Data from: Na+/K+ pump interacts with the h-current to control bursting activity in central pattern generator neurons of leeches

description: The dynamics of different ionic currents shape the bursting activity of
 neurons and networks that control motor output. Despite being ubiquitous
 in all animal cells, the contribution of the Na+/K+ pump current to such
 bursting activity has not been well studied. We used monensin, a Na+/H+
 antiporter, to examine the role of the pump on the bursting activity of
 oscillator heart interneurons in leeches. When we stimulated the pump with
 monensin, the period of these neurons decreased significantly, an effect
 that was prevented or reversed when the h-current was blocked by Cs+. The
 decreased period could also occur if the pump was inhibited with
 strophanthidin or K+-free saline. Our monensin results were reproduced in
 model, which explains the pump’s contributions to bursting activity based
 on Na+ dynamics. Our results indicate that a dynamically oscillating pump
 current that interacts with the h-current can regulate the bursting
 activity of neurons and networks.
description: Figure
 7This
 archive contains the source for figure 7 A1 A2 A3 B2 B3. In the directory
 B2_B3, the matlab script fixedIPump_withNa_JustHCO.m produces an eps file
 containing the figures found in 7B2 and 7B3. In the directory A1_A2_A3,
 the matlab scrip trjHCO.m produces an eps file which contains the figures
 found in 7A1, 7A2, and 7A3.fig7.zip
DOI: 10.5061/dryad.k1v01
title: Data from: Changes in activity of the same thalamic neurons to repeated nociception in behaving mice

description: The sensory thalamus has been reported to play a key role in central pain
 sensory modulation and processing, but its response to repeated
 nociception at thalamic level is not well known. Current study
 investigated thalamic response to repeated nociception by recording and
 comparing the activity of the same thalamic neuron during the 1st and 2nd
 formalin injection induced nociception, with a week interval between
 injections, in awake and behaving mice. Behaviorally, the 2nd injection
 induced greater nociceptive responses than the 1st. Thalamic activity
 mirrored these behavioral changes with greater firing rate during the 2nd
 injection. Analysis of tonic and burst firing, characteristic firing
 pattern of thalamic neurons, revealed that tonic firing activity was
 potentiated while burst firing activity was not significantly changed by
 the 2nd injection relative to the 1st. Likewise, burst firing property
 changes, which has been consistently associated with different phases of
 nociception, were not induced by the 2nd injection. Overall, data suggest
 that repeated nociception potentiated responsiveness of thalamic neurons
 and confirmed that tonic firing transmits nociceptive signals.
description: Behavior and
 thalamocortical activity to repeated nociceptionBehavior_TC_neuronal_activity.zip
DOI: 10.5061/dryad.dk51c
title: Data from: Pupil dilation as an index of preferred mutual gaze duration

description: Most animals look at each other to signal threat or interest. In humans,
 this social interaction is usually punctuated with brief periods of mutual
 eye contact. Deviations from this pattern of gazing behaviour generally
 make us feel uncomfortable and are a defining characteristic of clinical
 conditions such as autism or schizophrenia, yet it is unclear what
 constitutes normal eye contact. Here, we measured, across a wide range of
 ages, cultures and personality types, the period of direct gaze that feels
 comfortable and examined whether autonomic factors linked to arousal were
 indicative of people's preferred amount of eye contact. Surprisingly,
 we find that preferred period of gaze duration is not dependent on
 fundamental characteristics such as gender, personality traits or
 attractiveness. However, we do find that subtle pupillary changes,
 indicative of physiological arousal, correlate with the amount of eye
 contact people find comfortable. Specifically, people preferring longer
 durations of eye contact display faster increases in pupil size when
 viewing another person than those preferring shorter durations. These
 results reveal that a person's preferred duration of eye contact is
 signalled by physiological indices (pupil dilation) beyond volitional
 control that may play a modulatory role in gaze behaviour.
description: raw behavioural and eye
 tracking datadata.zip
DOI: 10.5061/dryad.5rp65
title: Data from: Novel, continuous monitoring of fine-scale movement using fixed-position radiotelemetry arrays and random forest location fingerprinting

description: 1. Radio-tag signals from fixed-position antennas are most often used to
 indicate presence/absence of individuals, or to estimate individual
 activity levels from signal strength variation within an antenna’s
 detection zone. The potential of such systems to provide more precise
 information on tag location and movement has not been explored in great
 detail in an ecological setting. 2. By reversing the roles that
 transmitters and receivers play in localization methods common to the
 telecommunications industry, we present a new telemetric tool for
 accurately estimating the location of tagged individuals from received
 signal strength values. The methods used to characterize the study area in
 terms of received signal strength are described, as is the random forest
 model used for localization. The resulting method is then validated using
 test data before being applied to true data collected from tagged
 individuals in the study site. 3. Application of the localization method
 to test data withheld from the learning dataset indicated a low average
 error over the entire study area (&lt; 1m) while application of the
 localization method to real data produced highly probable results
 consistent with field observations. 4. This telemetric approach provided
 detailed movement data for tagged fish along a single axis (a migratory
 path) and is particularly useful for monitoring passage along migratory
 routes. The new methods applied in this study can also be expanded to
 include multiple axes (x, y, z) and multiple environments (aquatic and
 terrestrial) for remotely monitoring wildlife movement.
description: BoquetData_River_Radio_MapThis radio map of the Willsboro rapids was used as learning data in a random forest location fingerprinting exercise to identify the progress of migrating Atlantic salmon in the Boquet River.BoquetData_River_Telemetry_DataThis radio telemetry data was collected from 24 tagged Atlantic salmon as they migrated up the Boquet River through the Willsboro rapids. Sites correspond to separate antenna & receivers throughout the study reach, while the Code corresponds to separate fish.