cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cc2sk
title: Data from: Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

description: The metaphor of “genomic islands of speciation” was first used to describe
 heterogeneous differentiation among loci between the genomes of closely
 related species. The biological model proposed to explain these
 differences was that the regions showing high levels of differentiation
 were resistant to gene flow between species, while the remainder of the
 genome was being homogenized by gene flow and consequently showed lower
 levels of differentiation. However, the conditions under which such
 differentiation can occur at multiple unlinked loci are restrictive;
 additionally, essentially all previous analyses have been carried out
 using relative measures of divergence, which can be misleading when
 regions with different levels of recombination are compared. Here we test
 the model of differential gene flow by asking whether absolute divergence
 is also higher in the previously identified “islands.” Using five
 species-pairs for which full sequence data is available, we find that
 absolute measures of divergence are not higher in genomic islands.
 Instead, in all cases examined we find reduced diversity in these regions,
 a consequence of which is that relative measures of divergence are
 abnormally high. These data therefore do not support a model of
 differential gene flow among loci, though islands of relative divergence
 may represent loci involved in local adaptation. Simulations using the
 program IMa2 further suggest that inferences of any gene flow may be
 incorrect in many comparisons. We instead present an alternative
 explanation for heterogeneous patterns of differentiation, one in which
 post-speciation selection generates patterns consistent with multiple
 aspects of the data.
description: Alignments and
 Supplement.tar
DOI: 10.5061/dryad.v7g26
title: Data from: Predatory fish sounds can alter crab foraging behavior and influence bivalve abundance

description: The risk of predation can have large effects on ecological communities via
 changes in prey behaviour, morphology and reproduction. Although prey can
 use a variety of sensory signals to detect predation risk, relatively
 little is known regarding the effects of predator acoustic cues on prey
 foraging behaviour. Here we show that an ecologically important marine
 crab species can detect sound across a range of frequencies, probably in
 response to particle acceleration. Further, crabs suppress their resource
 consumption in the presence of experimental acoustic stimuli from multiple
 predatory fish species, and the sign and strength of this response is
 similar to that elicited by water-borne chemical cues. When acoustic and
 chemical cues were combined, consumption differed from expectations based
 on independent cue effects, suggesting redundancies among cue types. These
 results highlight that predator acoustic cues may influence prey behaviour
 across a range of vertebrate and invertebrate taxa, with the potential for
 cascading effects on resource abundance.
description: AEP files from Biosig
 softwareAEP waveform data
 collected from 8 crabs in response to sound stimuliBiosig_AEP_files.zipPredator acoustic cue experimentData on crab consumption of bivalve prey in response to predator and non-predator acoustic treatments.acoustic_cue.csvPredator acoustic cue experiment - day 1 onlyData from day 1 of an experiment on crab consumption of bivalve prey in response to predator and non-predator acoustic cues.acoustic_cue_day1only.csvPredator acoustic cue vs. chemical cue experimentData from an experiment testing the independent and interactive effects of predator (catfish) acoustic and chemical cues on crab consumption of bivalve resources.acoustic_chemical.csv
DOI: 10.15468/dl.ftf3gc
title: Occurrence Download

description: A dataset containing 16367 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Spodoptera frugiperda"
 ]
}

 The dataset includes 16367 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001619-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ds6c4
title: Data from: Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

description: Mounting evidence of climatic effects on riverine environments, and
 adaptive responses of fishes has elicited growing conservation concerns.
 Measures to rectify population declines include assessment of local
 extinction risk, population ecology, viability, and genetic
 differentiation. While conservation planning has been largely informed by
 neutral genetic structure, there has been a dearth of critical information
 regarding the role of non-neutral or functional genetic variation. We
 evaluated genetic variation among steelhead trout of the Columbia River
 Basin, which supports diverse populations distributed among dynamic
 landscapes. We categorized 188 SNP loci as either putatively neutral or
 candidates for divergent selection (non-neutral) using a multi-test
 association approach. Neutral variation distinguished lineages and defined
 broad-scale population structure consistent with previous studies, but
 fine-scale resolution was also detected at levels not previously observed.
 Within distinct coastal and inland lineages, we identified 9 and 22
 candidate loci (respectively) commonly associated with precipitation or
 temperature variables, and putatively under divergent selection. Observed
 patterns of non-neutral variation suggest overall climate is likely to
 shape local adaptation (e.g., potential rapid evolution) of steelhead
 trout in the Columbia River region. Broad geographic patterns of neutral
 and non-neutral variation demonstrated here can be used to accommodate
 priorities for regional management and inform long-term conservation of
 this species.
description: Columbia River steelhead
 trout SNP dataThese data are genotypes
 for biallelic SNPs (two alleles). Data is formatted for the program
 GENALEX: (Peakall, R., and P. E. Smouse. 2006. GENALEX 6: genetic analysis
 in Excel. Population genetic software for teaching and research. Molecular
 Ecology Notes 6, 288-295. Program note available from:
 http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-8286.2005.01155.x). The first row in the file contains: #loci, total#samples, #populations, and #samples/population. Row two has the data set title in column A, followed by two empty cells, then the name or designation of each population beginning in column D. In row three, column A is the header “sample ID” followed by “popID” in column B, and then a list of locus names. Between each locus name is an empty cell (every other column). Raw genotypic data begins on row four, column C. Individuals are sequential in column A, and genotypes for 180 SNP are in columns C-MX. Each three digit allele appears in its own column. Populations designations, POP1-POP145 correspond with population reference numbers in the manuscript supplemental 1.Matala et al.xlsx
DOI: 10.5061/dryad.pk75d
title: Data from: Tipping elements in the human intestinal ecosystem

description: The microbial communities living in the human intestine can have profound
 impact on our well-being and health. However, we have limited
 understanding of the mechanisms that control this complex ecosystem. Here,
 based on a deep phylogenetic analysis of the intestinal microbiota in a
 thousand western adults, we identify groups of bacteria that exhibit
 robust bistable abundance distributions. These bacteria are either
 abundant or nearly absent in most individuals, and exhibit decreased
 temporal stability at the intermediate abundance range. The abundances of
 these bimodally distributed bacteria vary independently, and their
 abundance distributions are not affected by short-term dietary
 interventions. However, their contrasting alternative states are
 associated with host factors such as ageing and overweight. We propose
 that the bistable groups reflect tipping elements of the intestinal
 microbiota, whose critical transitions may have profound health
 implications and diagnostic potential.
description: HITChip phylogenetic
 microarray data matrixProfiling of 130
 genus-like taxa across 1006 western subjects based on the Human Intestinal
 Tract (HIT)Chip phylogenetic microarray.HITChip.tabMetadataMetadata for the 1172 samples in the HITChip data matrix including age, sex, geographic region, DNA extraction information, projectID, probe-level Shannon diversity, BMI group,subjectID and time point. For units and other details, see the README file.
DOI: 10.5067/tsis/sim/data305
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V03
DOI: 10.5061/dryad.f6c34
title: Data from: Ancient hybridizations among the ancestral genomes of bread wheat

description: The allohexaploid bread wheat genome consists of three closely related
 subgenomes (A, B, and D), but a clear understanding of their phylogenetic
 history has been lacking. We used genome assemblies of bread wheat and
 five diploid relatives to analyze genome-wide samples of gene trees, as
 well as to estimate evolutionary relatedness and divergence times. We show
 that the A and B genomes diverged from a common ancestor ~7 million years
 ago and that these genomes gave rise to the D genome through homoploid
 hybrid speciation 1 to 2 million years later. Our findings imply that the
 present-day bread wheat genome is a product of multiple rounds of hybrid
 speciation (homoploid and polyploid) and lay the foundation for a new
 framework for understanding the wheat genome as a multilevel phylogenetic
 mosaic.
description: Marcussen_et_al_alignments_gene_trees_and_coalescent_modelThis .zip file contains multiple sequence alignments in fasta format, gene trees in newick format, and a WINBUGS model for coalescent estimates of genome divergence times
DOI: 10.5067/tsis/sim/data301
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V01
DOI: 10.5067/tsis/sim/data303
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V02
DOI: 10.5061/dryad.1485f
title: Data from: Community psychological and behavioral responses through the first wave of the 2009 influenza A(H1N1) pandemic in Hong Kong

description: Background. Little is known about the community psychological and
 behavioral responses to influenza pandemics. Methods. Using random digit
 dialing, we sampled 12,965 Hong Kong residents in 13 cross-sectional
 telephone surveys between April and November 2009, covering the entire
 first wave of the 2009 influenza A(H1N1) pandemic. We examined trends in
 anxiety, risk perception, knowledge on modes of transmission, and
 preventive behaviors. Results. Respondents reported low anxiety levels
 throughout the epidemic. Perceived susceptibility to infection and
 perceived severity of H1N1 were initially high but declined early in the
 epidemic and remained stable thereafter. As the epidemic grew, knowledge
 on modes of transmission did not improve, the adoption of hygiene measures
 and use of face masks did not change, and social distancing declined.
 Greater anxiety was associated with lower reported use of hygiene measures
 but greater social distancing. Knowledge that H1N1 could be spread by
 indirect contact was associated with greater use of hygiene measures and
 social distancing. Conclusions. The lack of substantial change in
 preventive measures or knowledge about the modes of H1N1 transmission in
 the general population suggests that community mitigation measures played
 little role in mitigating the impact of the first wave of 2009 influenza
 A(H1N1) pandemic in Hong Kong.
description: Daily H1N1pdm09
 casesThis data file contains
 daily information on laboratory-confirmed cases in the first wave of the
 2009 influenza A(H1N1) pandemic in Hong Kong.H1N1_cum_cases.csvH1N1 survey resultsThis data file contains information collected from the 13 waves of surveys conducted in Hong Kong.H1N1_surveys.csvRead me (data file explanations)Scripts to reformat the raw datadataframe.rFigure 2 scriptsFigure_2.rTable 3 scriptsTable_3.rTable 4 scriptsTable_4.rTable 5 scriptsTable_5.r
DOI: 10.5067/tsis/sim/data307
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V04
DOI: 10.5061/dryad.47r16
title: Data from: An unexpected clade of South American ground beetles (Coleoptera: Carabidae: Bembidion)

description: Phylogenetic relationships of the Antiperyphanes Complex of the genus
 Bembidion are inferred using DNA sequences from seven genes (two nuclear
 ribosomal, four nuclear protein coding, and one mitochondrial protein
 coding). Redefined subgenera within the complex are each well-supported as
 monophyletic. Most striking was the discovery that a small set of
 morphologically and ecologically heterogeneous species formed a clade,
 here called subgenus Nothonepha. This unexpected result was corroborated
 by the discovery of deep pits in the lateral body wall (in the
 mesepisternum) of all Nothonepha, a trait unique within Bembidion. These
 pits are filled with a waxy substance in ethanol-preserved specimens. In
 one newly discovered species (Bembidion tetrapholeon sp. n., described
 here), these pits are so deep that their projections into the body cavity
 from the two sides touch each other internally. These structures in
 Bembidion (Nothonepha) are compared to very similar mesepisternal pits
 which have convergently evolved in two other groups of carabid beetles.
 The function of these thoracic pits is unknown. Most members of subgenus
 Nothonepha have in addition similar but smaller pits in the abdomen. A
 revised classification is proposed for the Antiperyphanes Complex.
description: DNA matrices and maximum
 likelihood treesThis is a NEXUS file
 containing the aligned DNA matrices, the optimal likelihood trees, and all
 of the original boostrap trees. If opened in Mesquite (version 2.75 or
 later), you will be able to see the majority consensus trees of the
 bootstrap runs and other details.PittedClade.MatricesAndTrees.nexBembidion tetrapholeon DNA variationThis is a NEXUS file containing the aligned data matrices for all the sequences gathered for specimens of Bembidion tetrapholeonBembidion tetrapholeon variation.nexMaximum Likelihood TreesThis file shows images of the maximum likelihood trees for the concatenated, 7-gene matrices as well as each individual gene. Each figure is labeled to indicate the nature of that data analyzed for that tree.MLTrees.pdfMaximum Likelihood Bootstrap treesThis file shows images of the majority rule consensus trees from maximum likelihood bootstrap analyses for the concatenated, 7-gene matrices as well as each individual gene. Each figure is labeled to indicate the nature of that data analyzed for that tree. Numbers on each branch are the frequencies of that clade in the bootstrap replicates, expressed as a percentage.MLBootstrapTrees.pdf
DOI: 10.5067/tsis/sim/data309
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V05
DOI: 10.5067/tsis/sim/data311
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V06
DOI: 10.5061/dryad.80822
title: Data from: Insight into genomic changes accompanying divergence: genetic linkage maps and synteny of Lucania goodei and L. parva reveal a Robertsonian fusion

description: Linkage maps are important tools in evolutionary genetics and in studies
 of speciation. We performed a karyotyping study and constructed
 high-density linkage maps for two closely related killifish species,
 Lucania parva and Lucania goodei, that differ in salinity tolerance and
 still hybridize in their contact zone in Florida. Using SNPs from
 orthologous EST contigs, we compared synteny between the two species to
 determine how genomic architecture has shifted with divergence.
 Karyotyping revealed that L. goodei possesses 24 acrocentric chromosomes
 (1N) while L. parva possesses 23 chromosomes (1N), one of which is a large
 metacentric chromosome. Likewise, high-density SNP-based linkage maps
 indicated 24 linkage groups for L. goodei and 23 linkage groups for L.
 parva. Synteny mapping revealed two linkage groups in L. goodei that were
 highly syntenic with the largest linkage group in L. parva. Together, this
 evidence points to the largest linkage group in L. parva being the result
 of a chromosomal fusion. We further compared synteny between Lucania with
 the genome of a more distant teleost relative medaka (Oryzias latipes) and
 found good conservation of synteny at the chromosomal level. Each Lucania
 linkage group had a single best match with each medaka chromosome. These
 results provide the groundwork for future studies on the genetic
 architecture of reproductive isolation and salinity tolerance in Lucania
 and other Fundulidae.
description: L.goodei_contigsThis file contains 454 EST sequences that were used as a reference for assembling our new Illumina reads. These EST sequences were created using pooled DNA from several populations. See the ReadMe file for further details. Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM (2009) Shedding light on an extremophile lifestyle through transcriptomics. New Phytologist 183, 764-775.454large300Contigs.fnaL. goodei joinmap file for all familiesThis excel file contains the joinmap data for all of the families used to resolve the L. goodei linkage map. Each family is listed on a separate excel sheet. The joinmap code for each individual at each SNP marker is listed. The individuals are the progeny of an F2 cross between two L. goodei populations (Upper Bridge River of the Wakulla River and Everglades populations). Also, the segregation type and the phase of each marker is listed. These are joinmap codes.L.goodei-all-famillies-joinmapfile.xlsxL.parva joinmap file for all familiesThis excel file contains the joinmap data for all of the families used to resolve the L. parva linkage map. Each F2 family is listed on a separate excel sheet. The joinmap code for each individual at each SNP marker is listed. The individuals are the progeny of an F2 cross between two L. parva populations (Indian River Lagoon, FL and Pecos River, TX populations). Also, the segregation type and the phase of each marker is listed. These are joinmap codes.L.parva-all-families-joinmapfile.xlsx
DOI: 10.5067/tsis/sim/data313
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V07
DOI: 10.5067/tsis/sim/data315
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V08
DOI: 10.5061/dryad.281f2
title: Data from: Adaptive admixture in the West African bovine hybrid zone: insight from the Borgou population

description: Understanding the adaptive response to environmental fluctuations
 represents a central issue in evolutionary biology. Population admixture
 between divergent ancestries has often been considered as an efficient
 short-term adaptation strategy. Cattle populations from the West African
 Bos taurus x Bos indicus hybrid zone represent a valuable resource to
 characterize the effect of such adaptive admixture at the genome level. We
 here provide a detailed assessment of the global and local genome
 ancestries of the Borgou breed, one of the most representative cattle of
 this hybrid zone. We analyzed a large data set consisting of 38,100 SNPs
 genotyped on 203 Borgou and 591 individuals representative of all the
 different cattle ancestries. At the global genomic level, we show that
 Borgou is a stabilized admixed breed whose origin (130 years ago) traces
 back to the great African rinderpest pandemic, several centuries after the
 last admixture events, the West-African zebus originate from (512 years
 ago). To identify footprints of adaptive admixture, we combined the
 identification of signatures of selection and the functional annotation of
 the underlying genes using systems biology tools. The detection of the
 SILV coat coloration gene likely under artificial selection may be viewed
 as a validation of our approach. Overall our results suggest that the
 long-term presence of pathogens and the intermediate environmental
 conditions are the main acting selective pressures. Our analytical
 framework can be extended to other model or non-model species to
 understand the process that shapes the patterns of genetic variability in
 hybrid zones.
description: data_dryad.tar
DOI: 10.5067/tsis/sim/data317
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V09
DOI: 10.5067/tsis/sim/data319
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V10
DOI: 10.5061/dryad.bk537
title: Data from: An immunological marker of tolerance to infection in wild rodents

description: Hosts are likely to respond to parasitic infections by a combination of
 resistance (expulsion of pathogens) and tolerance (active mitigation of
 pathology). Of these strategies, the basis of tolerance in animal hosts is
 relatively poorly understood, with especially little known about how
 tolerance is manifested in natural populations. We monitored a natural
 population of field voles using longitudinal and cross-sectional sampling
 modes and taking measurements on body condition, infection, immune gene
 expression, and survival. Using analyses stratified by life history stage,
 we demonstrate a pattern of tolerance to macroparasites in mature compared
 to immature males. In comparison to immature males, mature males resisted
 infection less and instead increased investment in body condition in
 response to accumulating burdens, but at the expense of reduced
 reproductive effort. We identified expression of the transcription factor
 Gata3 (a mediator of Th2 immunity) as an immunological biomarker of this
 tolerance response. Time series data for individual animals suggested that
 macroparasite infections gave rise to increased expression of Gata3, which
 gave rise to improved body condition and enhanced survival as hosts aged.
 These findings provide a clear and unexpected insight into tolerance
 responses (and their life history sequelae) in a natural vertebrate
 population. The demonstration that such responses (potentially promoting
 parasite transmission) can move from resistance to tolerance through the
 course of an individual's lifetime emphasises the need to incorporate
 them into our understanding of the dynamics and risk of infection in the
 natural environment. Moreover, the identification of Gata3 as a marker of
 tolerance to macroparasites raises important new questions regarding the
 role of Th2 immunity and the mechanistic nature of the tolerance response
 itself. A more manipulative, experimental approach is likely to be
 valuable in elaborating this further.
description: Cross-sectional
 databaseData for cross-sectional
 element of studyLongitudinal
 database
DOI: 10.5067/tsis/sim/data321
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V11
DOI: 10.5067/tsis/sim/data323
title: TSIS SIM Level 3 Solar Spectral Irradiance 12-Hour Means V12