cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0s96k
title: Data from: Slowly switching between environments facilitates reverse evolution in small populations

description: Natural populations must constantly adapt to ever-changing environmental
 conditions. A particularly interesting question is whether such
 adaptations can be reversed by returning the population to an ancestral
 environment. Such evolutionary reversals have been observed in both
 natural and laboratory populations. However, the factors that determine
 the reversibility of evolution are still under debate. The timescales of
 environmental change vary over a wide range, but little is known about how
 the rate of environmental change influences the reversibility of
 evolution. Here we demonstrate computationally that slowly switching
 between environments increases the reversibility of evolution for small
 populations, which are subject to only modest clonal interference. For
 small populations, slow switching reduces the mean number of mutations
 acquired in a new environment and also increases the probability of
 reverse evolution at each of these “genetic distances.” As the population
 size increases, slow switching no longer reduces the genetic distance,
 thus decreasing the evolutionary reversibility. We confirm this effect
 using both a phenomenological model of clonal interference and also a
 Wright-Fisher stochastic simulation that incorporates genetic diversity.
 Our results suggest that the rate of environmental change is a key
 determinant of the reversibility of evolution, and provides testable
 hypotheses for experimental evolution.
description: Code_MatlabData1_MatlabPart 1 of sample data for the Matlab codesData2_MatlabPart 2 of sample data for the Matlab codesData3_MatlabPart 3 of sample data for the Matlab codesCode_C++Data_C++Sample data for the C++ codes
DOI: 10.5061/dryad.6tn2n
title: Data from: Trait independence primes convergent trait loss

description: The repeated, independent evolution of traits (convergent evolution) is
 often attributed to shared environmental selection pressures. However,
 developmental dependencies among traits can limit the phenotypic variation
 available to selection and bias evolutionary outcomes. Here we determine
 how changes in developmentally correlated traits may impact convergent
 loss of the tympanic middle ear, a highly labile trait within toads that
 currently lack adaptive explanation. The middle ear’s lability could
 reflect evolutionary trade-offs with other skull features under selection,
 or the middle ear may evolve independently of the rest of the skull,
 allowing it to be modified by active or passive processes without
 pleiotropic trade-offs with other skull features. We compare the skulls of
 55 species (39 eared, 16 earless) within the family Bufonidae, spanning
 six hypothesized independent middle ear transitions. We test whether
 shared or lineage-specific changes in skull shape distinguish earless
 species from eared species and whether earless skulls lack other
 late-forming skull bones. We find no evidence for pleiotropic trade-offs
 between the middle ear and other skull structures. Instead, middle ear
 loss in anurans may provide a rare example of developmental independence
 contributing to evolutionary lability of a sensory system.
description: PlyModelBufonidSkulls.ply meshes of skulls used in this studyAllSpeciesProcrustesProcrustes' fit data (landmark data) that was used in geomorph analyses. Averaged by species.SI3_MissingBonesData_FINALBone presence/absence data plus the species names and identifiers of all skull files.SI1_MuseumSpecimensMuseum specimens used in this studySI2_FieldSpecimensField-caught specimens used in this studyrawcoords_BufonidSkullsa .tps file with raw landmark coordinates for each specimen. Specimen numbers can be matched with species names using the bone analysis spreadsheet (SI_3).
DOI: 10.5061/dryad.90kt3
title: Data from: Rapid scavenging of jellyfish carcasses reveals the importance of gelatinous material to deep-sea food webs

description: Jellyfish blooms are common in many oceans, and anthropogenic changes
 appear to have increased their magnitude in some regions. Although mass
 falls of jellyfish carcasses have been observed recently at the deep
 seafloor, the dense necrophage aggregations and rapid consumption rates
 typical for vertebrate carrion have not been documented. This has led to a
 paradigm of limited energy transfer to higher trophic levels at jelly
 falls relative to vertebrate organic falls. We show from baited camera
 deployments in the Norwegian deep sea that dense aggregations of deep-sea
 scavengers (more than 1000 animals at peak densities) can rapidly form at
 jellyfish baits and consume entire jellyfish carcasses in 2.5 h. We also
 show that scavenging rates on jellyfish are not significantly different
 from fish carrion of similar mass, and reveal that scavenging communities
 typical for the NE Atlantic bathyal zone, including the Atlantic hagfish,
 galatheid crabs, decapod shrimp and lyssianasid amphipods, consume both
 types of carcasses. These rapid jellyfish carrion consumption rates
 suggest that the contribution of gelatinous material to organic fluxes may
 be seriously underestimated in some regions, because jelly falls may
 disappear much more rapidly than previously thought. Our results also
 demonstrate that the energy contained in gelatinous carrion can be
 efficiently incorporated into large numbers of deep-sea scavengers and
 food webs, lessening the expected impacts (e.g. smothering of the
 seafloor) of enhanced jellyfish production on deep-sea ecosystems and
 pelagic–benthic coupling.
description: Proc B dryad
 filesExcel, R-script and
 video files
DOI: 10.5061/dryad.gj8jv50
title: Data from: Random-sequence genetic oligomer pools display an innate potential for ligation and recombination

description: Recombination, the exchange of information between different genetic
 polymer strands, is of fundamental importance in biology for genome
 maintenance and genetic diversification mediated by dedicated recombinase
 enzymes. Here, we describe a pervasive non-enzymatic capacity for
 recombination (and ligation) in random-sequence genetic oligomer pools.
 Specifically, we examine random and semi-random eicosamer (N20) pools of
 RNA, DNA and the unnatural genetic polymers ANA (arabino-), HNA (hexitol-)
 and AtNA (altritol-nucleic acids). While DNA, ANA and HNA pools proved
 inert, RNA and AtNA pools displayed diverse modes of spontaneous
 intermolecular recombination, connecting recombination mechanistically to
 the vicinal ring cis-diol configuration shared by RNA and AtNA. Thus, the
 chemical constitution that renders both susceptible to hydrolysis emerges
 as the fundamental determinant of an innate capacity for recombination,
 which is shown to enable a concomitant increase in compositional,
 informational and structural pool complexity and hence evolutionary
 potential.
description: Sequencing files for
 Figure 1Fig1.zipSequencing files for Figure 4Fig4.zipSequencing files for Figure 5Fig5.zipSequencing files for Figure 6Fig6.zipData-sets used to identify motifs J4 and H4motif_search.zipSequencing data for starting pools used in RNA ligation / recombination experimentspre-ligation.zip
DOI: 10.5061/dryad.vq4f5
title: Data from: Breeding relationships in Macaronesian Tolpis (Asteraceae-Cichorieae): F1 hybrid pollen fertility within and among populations from the Azores, Canary Islands and Madeira

description: The pollen fertility of F1 hybrids, ranging from progeny within natural
 populations to synthetic hybrids between species of Tolpis from three
 archipelagos in Macaronesia, was determined. Pollen fertility of F1
 hybrids of inter-archipelago crosses from the Azores, Canaries, and
 Madeira were generally lower than crosses between populations or species
 in the same archipelagos. Lower pollen fertility was pronounced in hybrids
 between plants from the Canaries and the other archipelagos, which is
 concordant with a more distant phylogenetic relationship between the
 Canaries, and the Azores and Madeira. Lower average pollen fertility was
 seen between plants from different as compared to the same clades in the
 Canary Islands. However, low pollen fertilities were also detected between
 plants from some populations/species in the same archipelagos, and even
 among progeny of individual maternal plants. Some hybrids with reduced
 fertility had meiotic irregularities, suggesting chromosomal
 rearrangements; in other cases meiosis appeared normal. Results indicate
 that postzygotic isolating factors evolved subsequent to the divergence of
 Tolpis in the three archipelagos, but there are hybrid sterility factors
 among plants within each of the archipelagos, and even within some natural
 populations. Phylogenetic relationships in the Canary Islands indicate
 that divergence has occurred within the last million years. Present
 results implicate postzygotic factors as reproductive barriers
 facilitating population divergence and speciation in Macaronesian Tolpis.
description: Crawford_MSG_dataMSG data sued to estimate phylogeny for Macaronesian Tolpis.0704preproposal.phy
DOI: 10.5061/dryad.1p390
title: Data from: The York Gospels: a 1000-year biological palimpsest

description: Medieval manuscripts, carefully curated and conserved, represent not only
 an irreplaceable documentary record but also a remarkable reservoir of
 biological information. Palaeographic and codicological investigation can
 often locate and date these documents with remarkable precision. The York
 Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small
 collection of pre-conquest Gospel books to have survived the Reformation.
 By extending the non-invasive triboelectric (eraser-based) sampling
 technique eZooMS, to include the analysis of DNA, we report a
 cost-effective and simple-to-use biomolecular sampling technique for
 parchment. We apply this combined methodology to document for the first
 time a rich palimpsest of biological information contained within the York
 Gospels, which has accumulated over the 1000-year lifespan of this
 cherished object that remains an active participant in the life of York
 Minster. These biological data provide insights into the decisions made in
 the selection of materials, the construction of the codex and the use
 history of the object.
description: York_Gospels_MALDITOFMALDI-TOF data files for York Gospel samples including spreadsheet with sample information
DOI: 10.5061/dryad.bd8j403
title: Data from: Automated peak detection method for behavioral event identification: detecting Balaenoptera musculus and Grampus griseus feeding attempts

description: The desire of animal behaviorists for more flexible methods of conducting
 inter-study and inter-specific comparisons and meta-analysis of various
 animal behaviors compelled us to design an automated, animal behavior peak
 detection method that is potentially generalizable to a wide variety of
 data types, animals, and behaviors. We detected the times of feeding
 attempts by 12 Risso’s dolphins (Grampus griseus) and 36 blue whales
 (Balaenoptera musculus) using the norm-jerk (rate of change of
 acceleration) time series. The automated peak detection algorithm
 identified median true-positive rates of 0.881 for blue whale lunges and
 0.410 for Risso’s dolphin prey capture attempts, with median
 false-positive rates of 0.096 and 0.007 and median miss rates of 0.113 and
 0.314, respectively. Our study demonstrates that our peak detection method
 is efficient at automatically detecting animal behaviors from multisensor
 tag data with high accuracy for behaviors that are appropriately
 characterized by the data time series.
description: example_detectionsPDF file containing examples of how to perform detections using detect_peaks using a few different signals.testset1Dataset used in creating the example_detections PDF file.blue_whale_figuresROC and side-by-side plots similar to those seen in the manuscript for all of the blue whale data used in this study.risso_dolphin_figuresdataAll data and code used in this study.detector stats tableAll detection statistics for all individual animals used in this study.
DOI: 10.15468/dl.6ke9k9
title: Occurrence Download

description: A dataset containing 24090 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "StateProvince is one of (Cesar, La Jagua de Ibirico)",
 "Year 2020-2026",
 "Country is one of (Colombia)",
 "GadmGid is one of (COL.12.14_2)",
 "PublishingOrg is one of (1a2bfe99-b7ca-4e3c-a5a2-18c85789e7d1, 188fd36a-2d61-4f35-8b67-d5529efb0005, e2e717bf-551a-4917-bdc9-4fa0f342c530, 8ee4c3d9-b194-4f81-b41a-402e5c077e05, 28eb1a3f-1c15-4a95-931a-4af90ecb574d, 67c63221-0c74-4c18-97f9-e2b2acb739ce, 2a7e3080-28a9-11dd-97cd-b8a03c50a862, 112087f6-a6c0-4cee-8441-387f900d34f9, 69ad50d2-2560-42a4-b522-171f6eca4fa3, b8b274e0-3216-48b8-afea-5616ec326ce1)",
 "BasisOfRecord is one of (Human Observation, Material sample, Machine Observation)",
 "OccurrenceStatus is one of (Present)",
 "IucnRedListCategory is one of (CR, EN, VU, NT, LC)",
 "TaxonKey is one of (Animalia [GBIF Backbone Taxonomy])"
 ]
 }
 ]
}

 The dataset includes 24090 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000381-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2s200
title: Data from: The draft genome of Primula veris yields insights into the molecular basis of heterostyly

description: [No abstract entered]
description: Annotation files for the
 Primula veris genome assemblyThe included files were
 produced with the Maker2 annotation pipeline.Pveris_Maker2_Genome_Annotation.tgz
DOI: 10.15468/dl.yxq94q
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kraglievichia paranense"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000375-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3r8jz7
title: Occurrence Download

description: A dataset containing 5963 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Colombia",
 "GadmGid is COL",
 "OccurrenceStatus is Present",
 "TaxonKey is Chironomidae"
 ]
}

 The dataset includes 5963 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000376-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dr33pf3
title: Data from: Controls on yardang development and morphology II. Numerical modeling

description: Here I present a set of mathematical modeling results, constrained by the
 results of the companion paper, aimed at improving our understanding of
 yardang development and controls on yardang morphology. The classic model
 for yardang development posits that yardangs evolve to an aspect ratio of
 ≈ 4 in order to minimize aerodynamic drag. Computational fluid dynamics
 (CFD) model results presented here, however, demonstrate that yardangs
 with an aspect ratio of 4 do not minimize drag. As an alternative, I
 propose that yardang aspect ratios are primarily controlled by the lateral
 downwind expansion of wind and wind-blown sediments focused into the
 troughs among yardangs, which can be quantified using previous studies of
 wall-bounded turbulent jets. This approach predicts yardangs with aspect
 ratios in the range of 5 to 10, i.e., similar to those of natural
 yardangs. In addition to aerodynamics, yardang aspect ratios are
 influenced by the strikes and dips of strata, as demonstrated in the
 companion paper. To better understand the aerodynamic and bedrock
 structural controls on yardang morphology, I developed a landscape
 evolution model that combines the physics of boundary layer flow and
 abrasion by aeolian sediment transport with a model for the erosion of the
 tops and lee sides of yardangs by water-driven erosional processes.
 Yardang formation in the model is enhanced in substrates with greater
 heterogeneity (i.e., alternating strong and weak strata). Yardang
 morphology is controlled by the strikes and dips of strata as well as the
 topographic diffusivity associated with water-driven erosional processes.
description: Model files for examples
 presented in Pelletier, J.D., Controls on yardang development and
 morphology II. Numerical modelingsee readme.txt
 filemodelfiles.zip
DOI: 10.5061/dryad.23s61
title: Data from: Transcriptome-wide patterns of divergence during allopatric evolution

description: Recent studies have revealed repeated patterns of genomic divergence
 associated with species formation. Such patterns suggest that natural
 selection tends to target a set of available genes, but is also indicative
 that closely related taxa share evolutionary constraints that limit
 genetic variability. Studying patterns of genomic divergence among
 populations within the same species may shed light on the underlying
 evolutionary processes. Here, we examine transcriptome-wide divergence and
 polymorphism in the marine copepod Tigriopus californicus, a species where
 allopatric evolution has led to replicate sets of populations with varying
 degrees of divergence and hybrid incompatibility. Our analyses suggest
 that relatively small effective population sizes have resulted in an
 exponential decline of shared polymorphisms during population divergence
 and also facilitated the fixation of slightly deleterious mutations within
 allopatric populations. Five interpopulation comparisons at three
 different stages of divergence show that nonsynonymous mutations tend to
 accumulate in a specific set of proteins. These include proteins with
 central roles in cellular metabolism, such as those encoded in mtDNA, but
 also include an additional set of proteins that repeatedly show signatures
 of positive selection during allopatric divergence. Although our results
 are consistent with a contribution of nonadaptive processes, such as
 genetic drift and gene expression levels, generating repeatable patterns
 of genomic divergence in closely related taxa, they also indicate that
 adaptive evolution targeting a specific set of genes contributes to this
 pattern. Our results yield insights into the predictability of evolution
 at the gene level.
description: gene_expressioncontains all FPKM estimates plus data for correlation between expression and divergenceDoScontains complete list of polymorphisms (pN and pS) at coverage&gt;20, and calculations of DoSdN_dS_omegadN, dS, omega per gene and per population comparisonp_distancesmitochondrial and nuclear genetic distancestree_filesall tree bootstrapped ML trees and final tre filealignmentsalignments of mitochondrial and nuclear markersde_novo_assembliescomplete (all assembled genes) and partial (orthologs only) de novo assemblies per population.polymorphismspolymorphism for coverage &gt;8. Includes all bcf files and a Excel file with summaries and comparisons with polymorphisms from other species. To assess vcf files with polymorphisms with coverage &gt;20 (after reads2snp), please contact the corresponding author (ricardojn.pereira@gmail.com).cov8_samtools.zip
DOI: 10.15468/dl.fhnuck
title: Occurrence Download

description: A dataset containing 4446 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "StateProvince is one of (Washington (State), Washington, Washington (?), WASHINGTON MOUNTAIN MEADOWS (ALT: 5-6000 FEET), Washington (華盛頓州), Washington ?)",
 "TaxonKey is Apis mellifera"
 ]
}

 The dataset includes 4446 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000377-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.62fv1
title: Data from: Flow cytometry combined with viSNE for analysis of microbial biofilms and detection of microplastics

description: Biofilms serve essential ecosystem functions and are used in different
 technical applications. Studies from stream ecology and waste-water
 treatment have shown that biofilm functionality depends to a great extent
 on community structure. Here we present a fast and easy-to-use method for
 individual cell-based analysis of stream biofilms, based on stain-free
 flow cytometry and visualization of the high-dimensional data by viSNE.
 The method allows the combined assessment of community structure, decay of
 phototrophic organisms and presence of abiotic particles. In laboratory
 experiments, it allows quantification of cellular decay and detection of
 survival of larger cells after temperature stress, while in the field it
 enables detection of community structure changes that correlate with known
 environmental drivers (flow conditions, dissolved organic carbon, calcium)
 and detection of microplastic contamination. The method can potentially be
 applied to other biofilm types, for example, for inferring community
 structure for environmental and industrial research and monitoring.
description: Temperature
 ExperimentMeasurement of microbial
 biofilms single cells autofluorescence by flow cytometry, after exposure
 of the biofilm to an increase in temperature. For details, please consult
 the readme file and the associated publciation.Field
 samplesAutofluorescence based
 flow-cytometry of microbial biofilm samples, taken from six different
 sites along the stream monhaltorferAa. For details, consult the readme
 file and the associated publication.