cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s5v7b
title: Data from: A new method to scan genomes for introgression in a secondary contact model

description: Secondary contact between divergent populations or incipient species may
 result in the exchange and introgression of genomic material. We develop a
 simple DNA sequence measure, called Gmin, which is designed to identify
 genomic regions experiencing introgression in a secondary contact model.
 Gmin is defined as the ratio of the minimum between-population number of
 nucleotide differences in a genomic window to the average number of
 between-population differences. Although it is conceptually simple, one
 advantage of Gmin is that it is computationally inexpensive relative to
 model-based methods for detecting gene flow and it scales easily to the
 level of whole-genome analysis. We compare the sensitivity and specificity
 of Gmin to those of the widely used index of population differentiation,
 FST, and suggest a simple statistical test for identifying genomic
 outliers. Extensive computer simulations demonstrate that Gmin has both
 greater sensitivity and specificity for detecting recent introgression
 than does FST. Furthermore, we find that the sensitivity of Gmin is robust
 with respect to both the population mutation and recombination rates.
 Finally, a scan of Gmin across the X chromosome of Drosophila melanogaster
 identifies candidate regions of introgression between sub-Saharan African
 and cosmopolitan populations that were previously missed by other methods.
 These results show that Gmin is a biologically straightforward, yet
 powerful, alternative to FST, as well as to more computationally intensive
 model-based methods for detecting gene flow.
description: Summary of results from
 coalescent simulations under isolation and secondary contact
 modelsThis Rdata file contains
 two objects, "isolation" containing the parameters and summary
 output of coalescent simulations under an isolation model, and
 "secondary contact" containing the parameters and summary output
 of coalescent simulations under a secondary contact model. These data are
 also available as tab delimited files in this repository. See README for
 definitions of each column name. All simulations were performed using
 MSMOVE (https://github.com/geneva/msmove).coalescent_simulation_summary.RDataSummary of results from coalescent simulations under and isolation modelThis tab delimited file contains the parameters and summary output of coalescent simulations under an isolation model. All simulations were performed using MSMOVE (https://github.com/geneva/msmove).isolation.tsvSummary of results from coalescent simulations under a secondary contact modelThis tab delimited file contains the parameters and summary output of coalescent simulations under a secondary contact model. See README for definitions of each column name. All simulations were performed using MSMOVE (https://github.com/geneva/msmove).secondary_contact.tsv
DOI: 10.25500/edata.bham.00001517
title: The feature-extraction and sequence-construction code.

description: File 1: Bots_with_sub_sequences.csv
Description: the feature-extraction and sequence-construction code

File 2: All_string.xlsx
Description:  the behavioural block vocabulary and per-account sequences in encoded form

File 3:  bot_similarity_matrix.csv
Description: similarity matrices between behavioural sequences of bots 

File 4: Clustered_string.csv
Description: Clustering assignments of bots based on a similarity matrix

File 5: Mutation_frequency.csv
Description: Aggregate mutation statistics

File 6 and File 7: Christmas.csv and Halloween.csv
Description:  Trigger-event summaries
DOI: 10.5061/dryad.rd28k4r
title: Data from: Natural selection interacts with recombination to shape the evolution of hybrid genomes

description: To investigate the consequences of hybridization between species, we
 studied three replicate hybrid populations that formed naturally between
 two swordtail fish species, estimating their fine-scale genetic map and
 inferring ancestry along the genomes of 690 individuals. In all three
 populations, ancestry from the “minor” parental species is more common in
 regions of high recombination and where there is linkage to fewer putative
 targets of selection. The same patterns are apparent in a reanalysis of
 human and archaic admixture. These results support models in which
 ancestry from the minor parental species is more likely to persist when
 rapidly uncoupled from alleles that are deleterious in hybrids. Our
 analyses further indicate that selection on swordtail hybrids stems
 predominantly from deleterious combinations of epistatically-interacting
 alleles.
description: admixem_example_files.tarAdmix'em configuration files and examplesancestral_SNP_probabilities.tarancestral SNP probability files for LDhelmet analysisped_and_map_files.tarped and map files for LDhelmet analysisphased_haplotypes.tarPhased haplotypes for LDhelmetLDhelmet_results.tarLDhelmet results files in LDhelmet .post format. These files can be converted to text format using LDhelmet's post_to_text program. LDhelmet programs can be found at https://sourceforge.net/projects/ldhelmet/Skov_et_al_Neanderthal_Denisovan_data.tarNeanderthal and Denisovan data analyzed in this paper from Skov L, Hui R, Hobolth A, Scally A, Schierup M, Durbin R. Detecting archaic introgression without archaic reference genomes. bioRxiv doi: https://doi.org/10.1101/283606.additional_scripts.taradditional scripts used in data processing and analysisMSG_ancestry_files_scripts.tarMSG ancestry files and scripts
DOI: 10.5061/dryad.v6q20
title: Data from: Cross-modal influence of mechanosensory input on gaze responses to visual motion in Drosophila

description: Animals typically combine inertial and visual information to stabilize
 their gaze against confounding self-generated visual motion, and to
 maintain a level gaze when the body is perturbed by external forces. In
 vertebrates, an inner ear vestibular system provides information about
 body rotations and accelerations, but gaze stabilization is less
 understood in insects, which lack a vestibular organ. In flies, the
 halteres, reduced hindwings imbued with hundreds of mechanosensory cells,
 sense inertial forces and provide input to neck motoneurons that control
 gaze. These neck motoneurons also receive input from the visual system.
 Head movement responses to visual motion and physical rotations of the
 body have been measured independently, but how inertial information might
 influence gaze responses to visual motion has not been fully explored. We
 measured the head movement responses to visual motion in intact and
 haltere-ablated tethered flies to explore the role of the halteres in
 modulating visually guided head movements in the absence of rotation. We
 note that visually guided head movements occur only during flight.
 Although halteres are not necessary for head movements, the amplitude of
 the response is smaller in haltereless flies at higher speeds of visual
 motion. This modulation occurred in the absence of rotational body
 movements, demonstrating that the inertial forces associated with straight
 tethered flight are important for gaze-control behavior. The cross-modal
 influence of halteres on the fly's responses to fast visual motion
 indicates that the haltere's role in gaze stabilization extends
 beyond its canonical function as a sensor of angular rotations of the
 thorax.
description: alldatajess's data reanalysis
DOI: 10.5061/dryad.83q32
title: Data from: Four decades of cultural evolution in House Finch songs

description: Bird song is the primary animal model system for cultural evolution.
 Longitudinal studies of bird song across many generations can provide
 insights into patterns and mechanisms of change in socially transmitted
 traits. In this study, we conducted a comparative analysis of songs of the
 House Finch (Haemorhous mexicanus) across an interval of 37 years (in 1975
 and in 2012). Recordings from both years were collected in western Long
 Island, New York, which is thought to be the initial site of introduction
 of the House Finch around 1940 from the West Coast. Song types experienced
 a complete turnover during this period, although half of the syllable
 types were represented in both samples. Song length, frequency bandwidth
 and several other spectrographic features were the same in both years, and
 no structural features predicted recurrence of individual syllables.
 Consistent with the fact that our study population expanded substantially
 following a cultural founder effect, song and syllable sharing and
 similarity between individuals were lower in 2012 than in 1975, reflecting
 an increase in song diversity at the population level. However, in the
 more recent sample individual songs had fewer syllables, and were sung
 with less sequence stereotypy across renditions than in the earlier
 sample. Syllable prevalence in 2012 was associated both with complexity
 (as gauged by frequency excursion) and increased minimum frequency. Thus,
 over nearly 4 decades, Eastern House Finch songs remained structurally
 similar at the whole-song level, diversified between individuals, but
 became simpler and less consistent within an individual.
description: 2012_song1975_song
DOI: 10.5061/dryad.s56rq
title: Data from: Joint histology in Alligator mississippiensis challenges the identification of synovial joints in fossil archosaurs and inferences of cranial kinesis

description: Archosaurs, like all vertebrates, have different types of joints that
 allow or restrict cranial kinesis, such as synovial joints and fibrous
 joints. In general, synovial joints are more kinetic than fibrous joints,
 because the former possess a fluid-filled cavity and articular cartilage
 that facilitate movement. Even though there is a considerable lack of data
 on the microstructure and the structure–function relationships in the
 joints of extant archosaurs, many functional inferences of cranial kinesis
 in fossil archosaurs have hinged on the assumption that elongated condylar
 joints are (i) synovial and/or (ii) kinetic. Cranial joint microstructure
 was investigated in an ontogenetic series of American alligators,
 Alligator mississippiensis. All the presumably synovial, condylar joints
 found within the head of the American alligator (the jaw joint, otic joint
 and laterosphenoid–postorbital (LS–PO) joint) were studied by means of
 paraffin histology and undecalcified histology paired with micro-computed
 tomography data to better visualize three-dimensional morphology. Results
 show that among the three condylar joints of A. mississippiensis, the jaw
 joint was synovial as expected, but the otherwise immobile otic and LS–PO
 joints lacked a synovial cavity. Therefore, condylar morphology does not
 always imply the presence of a synovial articulation nor mobility. These
 findings reveal an undocumented diversity in the joint structure of
 alligators and show that crocodylians and birds build novel, kinetic
 cranial joints differently. This complicates accurate identification of
 synovial joints and functional inferences of cranial kinesis in fossil
 archosaurs and tetrapods in general.
description: MUVC AL_721
 DICOMMedical CT data of adult
 Alligator mississippiensis scanned at 600µm slice
 thickness.MUVC AL_623
 DICOMmicroCT data of a
 juvenile American alligator (Alligator mississippiensis) scanned on a
 Siemens Inveon MicroCT at 21µm.
DOI: 10.5061/dryad.74631
title: Data from: Range expansion compromises adaptive evolution in an outcrossing plant

description: Neutral genetic diversity gradients have long been used to infer the
 colonization history of species, but range expansion may also influence
 the efficacy of natural selection and patterns of non-synonymous
 polymorphism in different parts of a species’ range. Recent theory
 predicts both an accumulation of deleterious mutations and a reduction in
 the efficacy of positive selection as a result of range expansion. These
 signatures have been sought in a number of studies of the human range
 expansion out of Africa, but with contradictory results. We analyzed the
 polymorphism patterns of 578,125 SNPs (17,648 genes) in the European
 diploid plant Mercurialis annua, which expanded its range from an eastern
 Mediterranean refugium into western habitats with contrasted climates. Our
 results confirmed strong signatures of bottlenecks and revealed the
 accumulation of mildly to strongly deleterious mutations in range-front
 populations. A significantly higher number of these mutations were
 homozygous in individuals in range-front populations, pointing to
 increased genetic load and reduced fitness under a model of recessive
 deleterious effects. We also inferred a reduction in the number of
 selective sweeps in range-front versus core populations. These signatures
 have persisted even in a dioecious herb subject to substantial
 interpopulation gene flow. Our results extend support from humans to
 plants for theory on the dynamics of mutations under selection during
 range expansion, showing that colonization bottlenecks can compromise
 adaptive potential.
description: Mercurialis annua SNP
 fileThis VCF file includes
 the filtered SNP dataset for 40 Mercurialis annua samples (578,125 SNPs).
 Information on gene capture probe, ancestral state (by comparison with M.
 huetti outgroup), and SnpEff annotation is provided in the VCF INFO
 field.annua.vcf
DOI: 10.5061/dryad.q1n97
title: Data from: From inside to outside and back again: changing waste dump formation, defecation and worker localization in a clonal ant

description: Reproductive division of labor is a defining feature of all eusocial
 organisms. In the eusocial insects, non-reproductive labor is often also
 divided into safe tasks within the nest, such as nursing, and risky
 extranidal tasks, such as scouting and foraging. Within-nest (intranidal)
 tasks are usually performed by younger workers while older workers forage
 outside. This temporal specialization can be delayed, accelerated or even
 reversed if the need arises. Here, we studied reversion in the clonal ant
 Platythyrea punctata. Rather than focusing on traditional markers of
 temporal polyethism, such as nursing vs. foraging, we examined neglected
 behaviors, such as waste management and defecation, as well as the
 proportion of ants outside the nest and the onset of egg laying. We formed
 single-age groups of young intranidal, old intranidal and forager workers,
 and found strong differences in behavior between these groups. Intranidal
 workers rapidly created well-formed waste dumps (middens) and defecated
 within the nest, initiated egg laying sooner, and remained mostly inside
 the nest. Forager workers showed the reverse pattern. However, the
 behavior of the groups gradually converged, and after 8 weeks midden
 formation was similar and the proportion of ants outside the nest was
 identical across all groups. This study demonstrates reversible temporal
 polyethism in defecation and waste management, which correlates well with
 more traditionally studied age-related traits. Different traits seem to
 revert at different rates. Waste management behavior may provide an easy
 and low-impact way of examining behavioral reversions and allows insights
 into aspects of colony life not usually examined.
description: Photographs of all the
 nests used in experiment 1Photographs of all the
 nests used in experiment 1, compressed as a .zip file. Folder numbers
 refer to the date of the experiment. Labels within each photograph provide
 more information.Experiment 1
 photos.zipPhotographs of all the
 nests used in experiment 2Photographs of all nests
 evaluated in experiment 2. File names are dates. More information about
 each photograph is provided in a label within the
 photograph.Experiment 2
 photos.zip
DOI: 10.5061/dryad.4p080
title: Data from: Diffantom: whole-brain diffusion MRI phantoms derived from real datasets of the Human Connectome Project

description: Diffantom is a whole-brain diffusion MRI (dMRI) phantom publicly available
 through the Dryad Digital Repository (doi:10.5061/dryad.4p080). The
 dataset contains two single-shell dMRI images, along with the
 corresponding gradient information, packed following the BIDS standard
 (Brain Imaging Data Structure, Gorgolewski et al., 2015). The released
 dataset is designed for the evaluation of the impact of susceptibility
 distortions and benchmarking existing correction methods. In this Data
 Report we also release the software instruments involved in generating
 diffantoms, so that researchers are able to generate new phantoms derived
 from different subjects, and apply these data in other applications like
 investigating diffusion sampling schemes, the assessment of dMRI
 processing methods, the simulation of pathologies and imaging artifacts,
 etc. In summary, Diffantom is intended for unit testing of novel methods,
 cross-comparison of established methods, and integration testing of
 partial or complete processing flows to extract connectivity networks from
 dMRI.
description: Diffantom - pkg 1 of
 2diffantom-bids.zipDiffantom - pkg 2 of 2diffantom-bids.z01
DOI: 10.5061/dryad.6d02s
title: Data from: Dietary overlap and seasonality in three species of mormoopid bats from a tropical dry forest

description: Competing hypotheses explaining species’ use of resources have been
 advanced. Resource limitations in habitat and/or food are factors that
 affect assemblages of species. These limitations could drive the evolution
 of morphological and/or behavioural specialization, permitting the
 coexistence of closely related species through resource partitioning and
 niche differentiation. Alternatively, when resources are unlimited,
 fluctuations in resources availability will cause concomitant shifts in
 resource use regardless of species identity. Here, we used next-generation
 sequencing to test these hypotheses and characterize the diversity,
 overlap and seasonal variation in the diet of three species of
 insectivorous bats of the genus Pteronotus. We identified 465 prey (MOTUs)
 in the guano of 192 individuals. Lepidoptera and Diptera represented the
 most consumed insect orders. Diet of bats exhibited a moderate level of
 overlap, with the highest value between Pteronotus parnellii and
 Pteronotus personatus in the wet season. We found higher dietary overlap
 between species during the same seasons than within any single species
 across seasons. This suggests that diets of the three species are driven
 more by prey availability than by any particular predator-specific
 characteristic. P. davyi and P. personatus increased their dietary breadth
 during the dry season, whereas P. parnellii diet was broader and had the
 highest effective number of prey species in all seasons. This supports the
 existence of dietary flexibility in generalist bats and dietary niche
 overlapping among groups of closely related species in highly seasonal
 ecosystems. Moreover, the abundance and availability of insect prey may
 drive the diet of insectivores.
description: Morphological
 DataMorphological
 DataPlate
 1First plate of samples
 with MID identification coordinates.Plate
 2Second plate of samples
 with Mid identifications.ForwardMIDsForward MIDsReverseMIDsReverse MIDsMatrix of MOTUs and assigned sequencesMatrix showing which sequences were assigned to each MOTUrep_seq_92_AllRepresentative sequences for each MOTURaw_Sequence_DataRaw Sequence Data in fastq format
DOI: 10.5061/dryad.fq1sj
title: Data from: Defector clustering is linked to cooperation in a pathogenic bacterium

description: Spatial clustering is thought to favour the evolution of cooperation
 because it puts cooperators in a position to help each other. However,
 clustering also increases competition. The fate of cooperation may depend
 on how much cooperators cluster relative to defectors, but these
 clustering differences have not been the focus of previous models and
 experiments. By competing siderophore-producing cooperator and defector
 strains of the opportunistic pathogen Pseudomonas aeruginosa in
 experimental microhabitats, we found that at the spatial scale of
 individual interactions, cooperator clustering lowers cooperation, but
 defector clustering favours cooperation. A theoretical model and
 individual-based simulations show these counterintuitive effects can arise
 when competition and cooperation occur at a single resource-determined
 scale, with population dynamics crucially allowing cooperators and
 defectors to cluster differently. The results suggest that cooperation
 relies on the regulation of sufficient defector clustering relative to
 cooperator clustering, which may be important in bacteria, social amoeba,
 and cancer inhibition.
description: ImarisData_calibrationMatlab code and data for calibrating microhabitat bacteria locations, which are acquired using ImarisImarisData_experimentMatlab code and data for microhabitat experiment, with bacteria locations acquired using Imaris fluorescent analysesImarisImages_experimentExperimental flourescent images (downsized), acquired using Zeiss confocal microscope, and cell positions and counts processed using ImarisImarisImages_calibrationCalibration flourescent images (downsized), acquired using Zeiss confocal microscope, and cell positions and counts processed using ImarisTekwa et al 2017 PRSB readmeFile description and instruction for running experimental and simulation codesSimulationMatlab code and data for simulations of cooperators versus defectors