cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ks01r
title: Data from: Ancestral population reconstitution from isofemale lines as a tool for experimental evolution

description: Experimental evolution is a powerful tool to study adaptation under
 controlled conditions. Laboratory natural selection experiments mimic
 adaptation in the wild with better-adapted genotypes having more
 offspring. Because the selected traits are frequently not known,
 adaptation is typically measured as fitness increase by comparing evolved
 populations against an unselected reference population maintained in a
 laboratory environment. With adaptation to the laboratory conditions and
 genetic drift, however, it is not clear to what extent such comparisons
 provide unbiased estimates of adaptation. Alternatively, ancestral
 variation could be preserved in isofemale lines that can be combined to
 reconstitute the ancestral population. Here, we assess the impact of
 selection on alleles segregating in newly established Drosophila isofemale
 lines. We reconstituted two populations from isofemale lines and compared
 them to two original ancestral populations (AP) founded from the same
 lines shortly after collection. No significant allele frequency changes
 could be detected between both AP and simulations showed that drift had a
 low impact compared to Pool-Seq-associated sampling effects. We conclude
 that laboratory selection on segregating variation in isofemale lines is
 too weak to have detectable effects, which validates ancestral population
 reconstitution from isofemale lines as an unbiased approach for measuring
 adaptation in evolved populations.
description: Dmel_AP1-AP2-RAP1-RAP2_bwa.syncDrosophila melanogaster SNP data. Reads were mapped using bwa. Populations were sequenced as a single sample (e.g Pool-Seq). Their order in the sync file is as follows: AP1-AP2-RAP1-RAP2. The sync file only contains high-quality SNPs with downsampled allele counts (see main publication for additional information).Dmel_AP1-AP2-RAP1-RAP2_novoalign.syncDrosophila melanogaster SNP data. Reads were mapped using novoalign. Populations were sequenced as a single sample (e.g Pool-Seq). Their order in the sync file is as follows: AP1-AP2-RAP1-RAP2. The sync file only contains high-quality SNPs with downsampled allele counts (see main publication for additional information).Dsim_AP1-AP2-RAP1-RAP2_bwa.syncDrosophila simulans SNP data. Reads were mapped using bwa. Populations were sequenced as a single sample (e.g Pool-Seq). Their order in the sync file is as follows: AP1-AP2-RAP1-RAP2. The sync file only contains high-quality SNPs with downsampled allele counts (see main publication for additional information).Dsim_AP1-AP2-RAP1-RAP2_novoalign.syncDrosophila simulans SNP data. Reads were mapped using novoalign. Populations were sequenced as a single sample (e.g Pool-Seq). Their order in the sync file is as follows: AP1-AP2-RAP1-RAP2. The sync file only contains high-quality SNPs with downsampled allele counts (see main publication for additional information).drift_expectations_pool-sampling_mated_females.RR script simulating genetic drift in isofemale lines.
DOI: 10.5061/dryad.q2k15
title: Data from: A FISH-based chromosome map for the European corn borer yields insights into ancient chromosomal fusions in the silkworm

description: A significant feature of the genomes of Lepidoptera, butterflies and
 moths, is the high conservation of chromosome organization. Recent
 remarkable progress in genome sequencing of Lepidoptera has revealed that
 syntenic gene order is extensively conserved across phylogenetically
 distant species. The ancestral karyotype of Lepidoptera is thought to be n
 = 31; however, that of the most well studied moth, Bombyx mori, is n = 28,
 and diverse studies suggest that three chromosomal fusion events occurred
 in this lineage. To identify the boundaries between predicted ancient
 fusions involving B. mori chromosomes 11, 23 and 24, we constructed
 FISH-based chromosome maps of the European corn borer, Ostrinia nubilalis
 (n = 31). We first determined 511 Mb genomic sequence of the Asian corn
 borer, Ostrinia furnacalis, a congener of O. nubilalis, and isolated BAC
 and fosmid clones that were expected to localize in candidate regions for
 the boundaries using these sequences. Combined with FISH and genetic
 analysis, we narrowed down the candidate regions to 40 kb-1.5 Mb, in
 strong agreement with a previous estimate based on the genome of a
 butterfly, Melitaea cinxia. The significant difference in the lengths of
 the candidate regions where no functional genes were observed may reflect
 the evolutionary time after fusion events.
description: O. furnacalis
 scaffold
DOI: 10.5061/dryad.jr421
title: Data from: Differential effects of landscape-level environmental features on genetic structure in three co-distributed tree species in Central America

description: Landscape genetic studies use spatially explicit population genetic
 information to determine the physical and environmental causes of
 population genetic structure on regional scales. Comparative studies that
 identify common barriers to gene flow across multiple species within a
 community are important to both understand the evolutionary trajectories
 of populations and to prioritize habitat conservation. Here, we use a
 comparative landscape genetic approach to ask whether gradients in
 temperature or precipitation seasonality structure genetic variation
 across three co-distributed tree species in Central America, or if a
 simpler (geographic distance) or more complex, species-specific
 environmental niche model is necessary to individually explain population
 genetic structure. Using descriptive statistics and causal modeling, we
 find that different environmental factors best explain genetic distance in
 each of the three species: environmental niche distance in Bursera
 simaruba, geographic distance in Ficus insipida, while either historical
 contingency or cryptic reproductive barriers influence predictions for
 Brosimum alicastrum. This study confirms suggestions from previous studies
 of Central American tree species that imply that population genetic
 structure of trees in this region is determined by complex interactions of
 both historical and current barriers to gene flow.
description: Circuitscape
 inputThe files in this folder
 were used as input for Circuitscape.circuitscape_files.tar.gzstructure_files.tarThis folder contains all input and output from the Structure analysis, as well as downstream analyses (Structure harvester, Clumpp, and Distruct).Mantel_tests.tarThis folder contains all distance matrices used for Mantel tests, as well as R code used to run the Mantel tests.f.insipida.tarThis folder contains raw AFLP chromatograms for F. insipida. AFLP profiles are split between two files: Files containing the word "all" contain the first three selective primer pairs. Fam profiles correspond to primer 2c in "aflp_profiles_by_species_genalex.xlsx"; Hex profiles correspond to primer 2b; and Ned profiles correspond to primer 1a. Files containing the digits "1-4" contain the last two selective primer pairs, 1-ned and 4-fam.b.alicastrum.tarThis folder contains raw chromatograms of AFLP profiles of B. alicastrum. AFLP profiles are split between two files: Files containing the word "all" contain the first two selective primer pairs, and files containing "all2" contain the second 2.b.simaruba.tarThis folder contains raw chromatograms of AFLP profiles of B. simaruba. AFLP profiles from all three selective primers are in one .fsa file.aflp_profiles_by_species_genalexThis file contains scored AFLP profiles used in all downstream analyses in GenAlEx format.
DOI: 10.5061/dryad.c32jg
title: Data from: Midbrain adaptation may set the stage for the perception of musical beat

description: The ability to spontaneously feel a beat in music is a phenomenon widely
 believed to be unique to humans. Though beat perception involves the
 coordinated engagement of sensory, motor, and cognitive processes in
 humans, the contribution of low-level auditory processing to the
 activation of these networks in a beat-specific manner is poorly
 understood. Here, we present evidence from a rodent model that midbrain
 pre-processing of sounds may already be shaping where the beat is
 ultimately felt. For the tested set of musical rhythms, on-beat sounds on
 average evoked higher firing rates than off-beat sounds, and this
 difference was a defining feature of the set of beat interpretations most
 commonly perceived by human listeners over others. Basic firing rate
 adaptation provided a sufficient explanation for these results. Our
 findings suggest that midbrain adaptation, by encoding the temporal
 context of sounds, creates points of neural emphasis that may influence
 the perceptual emergence of a beat.
description: Stimuli + gerbil
 electrophysiology and human tapping dataThis .zip file contains
 spike PSTH and LFP data from the gerbil IC and human tapping data in
 Matlab format. Audio files of the stimuli are also included. See README
 for full details.Stimuli_and_Data.zip
DOI: 10.5061/dryad.c2b53
title: Data from: How random is social behaviour? Disentangling social complexity through the study of a wild house mouse population

description: Out of all the complex phenomena displayed in the behaviour of animal
 groups, many are thought to be emergent properties of rather simple
 decisions at the individual level. Some of these phenomena may also be
 explained by random processes only. Here we investigate to what extent the
 interaction dynamics of a population of wild house mice (Mus domesticus)
 in their natural environment can be explained by a simple stochastic
 model. We first introduce the notion of perceptual landscape, a novel tool
 used here to describe the utilisation of space by the mouse colony based
 on the sampling of individuals in discrete locations. We then implement
 the behavioural assumptions of the perceptual landscape in a multi-agent
 simulation to verify their accuracy in the reproduction of observed social
 patterns. We find that many high-level features -- with the exception of
 territoriality -- of our behavioural dataset can be accounted for at the
 population level through the use of this simplified representation. Our
 findings underline the potential importance of random factors in the
 apparent complexity of the mice's social structure. These results
 resonate in the general context of adaptive behaviour versus elementary
 environmental interactions.
description: Behavioural dataset
 (RFID recordings) with full descriptionFull experimental
 dataset. The structure of the data is described in detail in the ReadMe
 file (also included in the archive as "Data set
 description.pdf")Antenna_data_2008-2009.tar.gz
DOI: 10.5061/dryad.d03qr
title: Data from: X-Ray computed tomography of two mammoth calf mummies

description: Two female woolly mammoth neonates from permafrost in the Siberian Arctic
 are the most complete mammoth specimens known. Lyuba, found on the Yamal
 Peninsula, and Khroma, from northernmost Yakutia, died at ages of
 approximately one and two months, respectively. Both specimens were
 CT-scanned, yielding detailed information on the stage of development of
 their dentition and skeleton and insight into conditions associated with
 death. Both mammoths died after aspirating mud. Khroma's body was
 frozen soon after death, leaving her tissues in excellent condition,
 whereas Lyuba's body underwent postmortem changes that resulted in
 authigenic formation of nodules of the mineral vivianite associated with
 her cranium and within diaphyses of long bones. CT data provide the only
 comprehensive approach to mapping vivianite distribution.
 Three-dimensional modeling and measurement of segmented long bones permits
 comparison between these individuals and with previously recovered
 specimens. CT scans of long bones and foot bones show developmental
 features such as density gradients that reveal ossification centers. The
 braincase of Khroma was segmented to show the approximate morphology of
 the brain; its volume is slightly less (∼2,300 cm3) than that of neonate
 elephants (∼2,500 cm3). Lyuba's premaxillae are more gracile than
 those of Khroma, possibly a result of temporal and/or geographic variation
 but probably also reflective of their age difference. Segmentation of CT
 data and 3-D modeling software were used to produce models of teeth that
 were too complex for traditional molding and casting techniques.
description: Supplemental Data
 1Animation based on
 segmented or thresholded features from a full-body CT-scan of Lyuba, a
 woolly mammoth neonate from the Yamal Peninsula,
 Siberia
DOI: 10.5061/dryad.t12v8
title: Data from: Partitioning of genetic variation across the genome using multimarker methods in a wild bird population

description: The underlying basis of genetic variation in quantitative traits, in terms
 of the number of causal variants and the size of their effects, is largely
 unknown in natural populations. The expectation is that complex
 quantitative trait variation is attributable to many, possibly
 interacting, causal variants, whose effects may depend upon the sex, age
 and the environment in which they are expressed. A recently developed
 methodology in animal breeding derives a value of relatedness among
 individuals from high-density genomic marker data, to estimate additive
 genetic variance within livestock populations. Here, we adapt and test the
 effectiveness of these methods to partition genetic variation for complex
 traits across genomic regions within ecological study populations where
 individuals have varying degrees of relatedness. We then apply this
 approach for the first time to a natural population and demonstrate that
 genetic variation in wing length in the great tit (Parus major) reflects
 contributions from multiple genomic regions. We show that a polygenic
 additive mode of gene action best describes the patterns observed, and we
 find no evidence of dosage compensation for the sex chromosome. Our
 results suggest that most of the genomic regions that influence wing
 length have the same effects in both sexes. We found a limited amount of
 genetic variance in males that is attributed to regions that have no
 effects in females, which could facilitate the sexual dimorphism observed
 for this trait. Although this exploratory work focuses on one complex
 trait, the methodology is generally applicable to any trait for any
 laboratory or wild population, paving the way for investigating sex-, age-
 and environment-specific genetic effects and thus the underlying genetic
 architecture of phenotype in biological study systems.
description: 2497_indiv_5591_markersThe 2497_indiv_5591_markers.map file is a file of marker names and positions, slightly amended from the plink format with column headings: chromosome, marker_name, marker_order, genetic_distance_(cM). For more information see the ReadMe.txt file.2497_indiv_5591_markersThe .ped file is a file of genotypes in plink style (see http://pngu.mgh.harvard.edu/~purcell/plink/). The column headings are: Family ID, Individual ID, Paternal ID, Maternal ID, Sex (1=male; 2=female; other=unknown), Phenotype (followed by the genotypes). For more information see the ReadMe.txt file2497_indiv_phenotype2497_indiv_phenotype.txt file. This file contains the phenotypes used in the analysis. Note that phenotypes are not available for all genotyped individuals. For more information please see the ReadMe.txt fileSimulated_dataSimulated data created using the QMSim software. Three genetic architecture types were simulated each with ten replicates (see manuscript), giving ten of each file type within each of the three folders. Folders contain phenotypic, genotypic, QTL, marker and linkage data.
DOI: 10.5061/dryad.68m52
title: Data from: Stepping inside the niche: microclimate data are critical for accurate assessment of species’ vulnerability to climate change

description: To assess a species' vulnerability to climate change, we commonly use
 mapped environmental data that are coarsely resolved in time and space.
 Coarsely resolved temperature data are typically inaccurate at predicting
 temperatures in microhabitats used by an organism and may also exhibit
 spatial bias in topographically complex areas. One consequence of these
 inaccuracies is that coarsely resolved layers may predict thermal regimes
 at a site that exceed species' known thermal limits. In this study,
 we use statistical downscaling to account for environmental factors and
 develop high-resolution estimates of daily maximum temperatures for a 36
 000 km2 study area over a 38-year period. We then demonstrate that this
 statistical downscaling provides temperature estimates that consistently
 place focal species within their fundamental thermal niche, whereas
 coarsely resolved layers do not. Our results highlight the need for
 incorporation of fine-scale weather data into species' vulnerability
 analyses and demonstrate that a statistical downscaling approach can yield
 biologically relevant estimates of thermal regimes.
description: CTMax
 DataEstimates of Critical
 Thermal Maxima for seven species of Microhylid frogs. Includes number of
 animals measured, mean CTmax, and SD of CTmaxCTMax.csvEmpirical_Microclimate_DataPaired empirical measurements of open-air and under-log temperature daily maxima and minima. These data were used to create the linear microclimate model.Daily max temperature data for all known occurrence locations for seven species of microhylid frog.Daily max temperature data for all known occurrence locations of seven species of microhylid frog. Max temperatures only are given for AWAP. Max and min temperatures are provided for downscaled air temperatures (DS1), both of which are necessary to calculate under-log daily max temperature (DS2). Each point of occurrence has 4 temperature records (AWAP, DS1 Tmax, DS1 Tmin, and DS2) for every day of the year between 1st January 1971 and 31st December 2008.Summary.zip
DOI: 10.5061/dryad.7kq17
title: Data from: No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon

description: Genes of the major histocompatibility complex (MHC) are a likely target of
 mate choice because of their role in inbreeding avoidance and potential
 benefits for offspring immunocompetence. Evidence for female choice for
 complementary MHC alleles among competing males exists both for the pre-
 and the postmating stages. However, it remains unclear whether the latter
 may involve non-random fusion of gametes depending on gametic haplotypes
 resulting in transmission ratio distortion or non-random sequence
 divergence among fused gametes. We tested whether non-random gametic
 fusion of MHC-II haplotypes occurs in Atlantic salmon Salmo salar. We
 performed in vitro fertilizations that excluded interindividual sperm
 competition using a split family design with large clutch sample sizes to
 test for a possible role of the gametic haplotype in mate choice. We
 sequenced two MHC-II loci in 50 embryos per clutch to assess allelic
 frequencies and sequence divergence. We found no evidence for transmission
 ratio distortion at two linked MHC-II loci, nor for non-random gamete
 fusion with respect to MHC-II alleles. Our findings suggest that the
 gametic MHC-II haplotypes play no role in gamete association in Atlantic
 salmon and that earlier findings of MHC-based mate choice most likely
 reflect choice among diploid genotypes. We discuss possible explanations
 for these findings and how they differ from findings in mammals.
description: Raw read for No evidence
 for MHC class II-based non-random mating at the gametic haplotype in
 Atlantic salmonMiSeq platform
 (Illumina) raw reads as described in Promerová et al (2016). "No
 evidence for MHC class II-based non-random mating at the gametic haplotype
 in Atlantic salmon". The data file consists on a compressed file
 divided in 6 folders. Each folder (named e.g. lib1) contains reads from
 one sequencing lain. Inside there are individual fasta files with reads
 from one individual. Each individuals is coded (file name) with three
 codes separated by underscore: "sample code" + "family
 code" + "offspring code". Codes are listed in supplementary
 information in files "README.csv" including also used barre code
 for sample identification inside within libraries.raw_reads.tar.gz
DOI: 10.5061/dryad.1b776v2
title: Data from: Despite high levels of expression in thymic epithelial cells, miR-181a1 and miR-181b1 are not required for thymic development

description: MicroRNAs (miRNAs) have been shown to be key modulators of
 post-transcriptional gene silencing in many cellular processes. In
 previous studies designed to understand the role of miRNAs in thymic
 development, we globally deleted miRNA exclusively in thymic epithelial
 cells (TECs), which are critical in thymic selection. This resulted in the
 loss of stromal cells that instruct T cell lineage commitment and affect
 thymocyte positive selection, required for mature T cell development.
 Since murine miR-181 is expressed in the thymus and miR-181 deficiency
 disrupts thymocyte development, we first quantified and thereby
 demonstrated that miR181a1 and miR181b1 are expressed in purified TECs. By
 generating mice with TEC targeted loss of miR-181a1 and miR-181b1
 expression, we observed that neither TEC cellularity nor thymocyte number
 nor differentiation was adversely affected. Thus, disrupted thymopoiesis
 in miR-181 deficient mice was not due to miR-181 loss of expression in
 TECs. Importantly, in mice with restricted TEC deficiency of miR-181a1 and
 miR-181b1, there were similar numbers of mature T cells in the periphery
 in regards to frequencies, differentiation, and function as compared to
 controls. Moreover miR-181a1 and miR-181b1 were not required for
 maintenance of thymus integrity over time, as thymic involution was not
 accelerated in gene-targeted mice. Taken together our data indicate that
 miR-181a1 and miR-181b1 are dispensable for TEC differentiation, their
 control of thymocyte development and mature T cell export to and
 homeostasis within the periphery.
description: Figure1Bmir181Figure1Bmir181Figure4Bmir181Figure4Bmir181Figure4Cmir181Figure4Cmir181Figure5A1mir181Figure5A1mir181Figure5Bmir181Figure5Bmir181FIgure5DMir181FIgure5DMir181Figure5Cmir181Figure2Band3mir181Figure2Band3mir181Figure 2a cre- mouseFigure 2a example FCS fileThy-A_Cre-neg #2_002.fcsFigure 2a cre positiveFigure 2a, exampleThy-A_Cre-pos #5_005.fcsTEC sort cre negative Figure 1aFigure 1aSpecimen_001-cre neg_10062016165112.pdfTEC sort Figure1a cre positiveFigure 1a cre+Specimen_001-cre pos_10062016165157.pdf
DOI: 10.60520/ieda/114202
title: SEM-EDS settings for volcanic glass analysis UoC v1

description: SEM-EDS instrument settings applied to analyze volcanic glass fragments of tephra layers.
DOI: 10.5061/dryad.p212867
title: Data from: Microbeam two-dimensional small-angle X-ray scattering investigating the effects of reduced graphene oxide on local microstructures of high-density polyethylene/reduced graphene oxide nanocomposite bars

description: It has reported that the introduction of reduced graphene oxide (RGO) can
 enhance the crystallization and orientation of high density polyethylene
 (HDPE) matrix and thus improve the mechanical properties of HDPE/RGO
 nanocomposites. Herein, the local microstructures and orientations in
 different regions of HDPE/RGO bars with varied RGO contents were further
 explored by two dimensional small angle X-ray scattering (2D SAXS) using a
 microbeam technique. It is unveiled that the orientation orderings of
 every positions are all intensified with increasing RGO amount, and of
 particular interest is the observation of the quite slight change of the
 ordering degrees in diverse zones of HDPE/RGO nanocomposite bars,
 implicating that RGO imposes a uniform enhancing effect upon HDPE matrix
 within different areas and consequently reflects an effective increase of
 mechanical properties of HDPE/RGO nanocomposites.
description: Microbeam
 SAXSThe original data of
 microbeam SAXS and linear data from fit2d.microbeam
 SAXS.zip