cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kn568
title: Data from: A test of genomic modularity among life-history adaptations promoting speciation with gene flow

description: Speciation with gene flow may require adaptive divergence of multiple
 traits to generate strong ecologically based reproductive isolation.
 Extensive negative pleiotropy or physical linkage of genes in the wrong
 phase affecting these diverging traits may therefore hinder speciation,
 while genetic independence or “modularity” among phenotypic traits may
 reduce constraints and facilitate divergence. Here, we test whether the
 genetics underlying two components of diapause life history, initial
 diapause intensity and diapause termination timing, constrain
 differentiation between sympatric hawthorn and apple-infesting host races
 of the fly Rhagoletis pomonella through analysis of 10,256 SNPs measured
 via genotyping-by-sequencing (GBS). Loci genetically associated with
 diapause termination timing were mainly observed for SNPs mapping to
 chromosomes 1–3 in the genome, most notably for SNPs displaying higher
 levels of linkage disequilibrium (LD), likely due to inversions. In
 contrast, selection on initial diapause intensity affected loci on all
 five major chromosomes of the genome, specifically those showing low
 levels of LD. This lack of overlap in genetically associated loci suggests
 that the two diapause phenotypes are largely modular. On chromosome 2,
 however, intermediate level LD loci and a subgroup of high LD loci
 displayed significant negative relationships between initial diapause
 intensity and diapause termination time. These gene regions on chromosome
 2 therefore affected both traits, while most regions were largely
 independent. Moreover, loci associated with both measured traits also
 tended to exhibit highly divergent allele frequencies between the host
 races. Thus, the presence of nonoverlapping genetic modules likely
 facilitates simultaneous, adaptive divergence for the measured
 life-history components.
description: Filtered vcf file with
 genotype probabilitiesThis is a vcf file
 generated using the GATK unified genotyper, then filtered as describe in
 the paper. The PL field provides the phred-scaled and normalized genotype
 probabilities produced using the GATK model.PJM123.UG.GATK.all.filtered.HWE.vcfFile mapping barcodes and ids to population/phenotypecolumn 1 = inline barcode (5' end of the forward read), column 2 = sample id (sample id in the vcf file), column 3 = population_phenotype: Haw_L = Hawthorn late, Haw_E = Hawthorn early, Apple_L = Apple late, Apple_E = Apple earlyPJM_12_barcode_map.txt140109_I1135_FCC2U5MACXX_L6_PJM_1_1.fq.gzIllumina forward reads, lane 1140109_I1135_FCC2U5MACXX_L6_PJM_1_2.fq.gzIllumina reverse reads, lane 1140114_I456_FCC3JBKACXX_L1_PJM_2_F_1.fq.gzllumina forward reads, lane 2140114_I456_FCC3JBKACXX_L1_PJM_2_F_2.fq.gzIllumina reverse reads, lane 2
DOI: 10.5061/dryad.b15bh
title: Data from: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

description: Background: Microbial diversity and community structures in acidic hot
 springs have been characterized by 16S rRNA gene-based diversity surveys.
 However, our understanding regarding the interactions among microbes, or
 between microbes and environmental factors, remains limited. Results: In
 the present study, a metagenomic approach, followed by bioinformatics
 analyses, were used to predict interactions within the microbial ecosystem
 in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan.
 Characterizing environmental parameters and potential metabolic pathways
 highlighted the importance of carbon assimilatory pathways. Four distinct
 carbon assimilatory pathways were identified in five dominant genera of
 bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria
 outcompeted other carbon assimilators and dominated the SHP, presumably
 due to their ability to metabolize hydrogen and to withstand an anaerobic
 environment with fluctuating temperatures. Furthermore, most dominant
 microbes were capable of metabolizing inorganic sulfur-related compounds
 (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only
 species among key rare microbes with the capability to fix nitrogen,
 suggesting a key role in nitrogen cycling. In addition to potential
 metabolic interactions, based on the 16S rRNAs gene sequence of
 Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as
 well as sequences of viruses and CRISPR arrays, we inferred that there
 were complex microbe-microbe interactions. Conclusions: Our study provided
 evidence that there were numerous microbe-microbe and microbe-environment
 interactions within the microbial community in an acidic hot spring. We
 proposed that Hydrogenobaculum bacteria were the dominant microbial genus,
 as they were able to metabolize hydrogen, assimilate carbon and live in an
 anaerobic environment with fluctuating temperatures.
description: 16S_GraPhlAn_20RACode for constructing phylogenetic tree in GraPhlAn16S_abundance_95-15Summary of 16S rRNA based abundance calculation resultBlastn resultsApplying blastn to obtain the taxonomic information of each direct shotgun sequencing read that contain 16S rRNA gene sequenceDSS_bln_refgenomic_besthit_taxonomy.csvReadme
DOI: 10.5061/dryad.7k3h4
title: Data from: Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms

description: The Cyclophyllidea is the most diverse order of tapeworms, encompassing
 species that infect all classes of terrestrial tetrapods including humans
 and domesticated animals. Available phylogenetic reconstructions based
 either on morphology or molecular data lack the resolution to allow
 scientists to either propose a solid taxonomy or infer evolutionary
 associations. Molecular markers available for the Cyclophyllidea mostly
 include ribosomal DNA and mitochondrial loci. In this study, we identified
 3,641 single-copy nuclear coding loci by comparing the genomes of
 Hymenolepis microstoma, Echinococcus granulosus, and Taenia solium. We
 designed RNA baits based on the sequence of H. microstoma, and applied
 target enrichment and Illumina sequencing to test the utility of those
 baits to recover loci useful for phylogenetic analyses. We captured DNA
 from five species of tapeworms representing two families of
 cyclophyllideans. We obtained an average of 3,284 (90%) of the targets
 from the test samples and then used captured sequences (2,181,361 bp in
 total; fragment size ranging from 301 bp to 6,969 bp) to reconstruct a
 phylogeny for the five test species plus the three species for which
 genomic data are available. The results were consistent with the current
 consensus regarding cyclophyllidean relationships. To assess the potential
 for our method to yield informative genetic variation at intraspecific
 scales, we extracted 14,074 single nucleotide polymorphisms (SNPs) from
 alignments of four Arostrilepis macrocirrosa and two A. cooki and
 successfully inferred their relationships. The results showed that our
 target gene tools yield datasets that provide robust inferences at a range
 of taxonomic scales in the Cyclophyllidea.
description: Data for intraspecific
 and interspecific analysisThe zip file includes 1
 nexus file for building ML tree, 1 vcf files(snp analysis results) and 1
 nexus for SNAPP tree, 1 vcf file and structure file for STRUCTURE
 analysisdata.zip
DOI: 10.5061/dryad.t3r02
title: Data from: Evolutionary novelty in a butterfly wing pattern through enhancer shuffling

description: An important goal in evolutionary biology is to understand the genetic
 changes underlying novel morphological structures. We investigated the
 origins of a complex wing pattern found among Amazonian Heliconius
 butterflies. Genome sequence data from 142 individuals across 17 species
 identified narrow regions associated with two distinct red colour pattern
 elements, dennis and ray. We hypothesise that these modules in non-coding
 sequence represent distinct cis-regulatory loci that control expression of
 the transcription factor optix, which in turn controls red pattern
 variation across Heliconius. Phylogenetic analysis of the two elements
 demonstrated that they have distinct evolutionary histories and that novel
 adaptive morphological variation was created by shuffling these
 cis-regulatory modules through recombination between divergent lineages.
 In addition, recombination of modules into different combinations within
 species further contributes to diversity. Analysis of the timing of
 diversification in these two regions supports the hypothesis of
 introgression moving regulatory modules between species, rather than
 shared ancestral variation. The dennis phenotype introgressed into
 Heliconius melpomene at about the same time that ray originated in this
 group, while ray introgressed back into H. elevatus much more recently. We
 show that shuffling of existing enhancer elements both within and between
 species provides a mechanism for rapid diversification and generation of
 novel morphological combinations during adaptive radiation.
description: ML_tree_DennisMaximum likelihood tree generated from the dennis region multiple alignmentML_tree_RayMaximum likelihood tree generated from the ray region multiple alignmentPlot data and codeData, code and readme for producing association plots and sliding window analysis in figs 2B, 2C, and S1A-CFig2B_2C_FigS1A-C_data_and_code.zipDennis BEAST dated FigTree fileCompiled Tree Annotator file for Dennis with dated node numerical values. Opens with FigTree program.Dennis_BEAST_TreeAnnotateRay BEAST dated TreeFig fileCompiled Tree Annotator file for Ray with dated node numerical values. Opens with FigTree program.Rays_BEAST_TreeAnnotateDennis and Ray AlignmentsMultiple alignment fasta files for dennis and ray regions composed of full versions (including flanking regions and alleles with very poor coverage) and 'tree' versions (poor coverage rogue alleles removed) used to generate ML and BEAST trees.Alignments.zipDennis_BEASTBEAST input file for generating dennis region dated treeRay_BEASTBEAST input file for generating ray region dated tree
DOI: 10.15468/n765pf
title: Checklist of Vascular Plant Species in Communities Hosting the Narrow-Range Kazakh Endemic Tanacetum ulutavicum Tzvelev

description: This dataset documents the species richness and floristic composition of plant
communities associated with the narrow-range Kazakh endemic Tanacetum
ulutavicum Tzvelev in the Ulytau low-mountain massif (Ulytau Region,
Central Kazakhstan). The core of the dataset is linked to the Important Plant
Area (IPA) “Ulytau petrophytic steppes with Tanacetum ulutavicum”,
proposed on the basis of field surveys conducted in 2025.Most vegetation descriptions are located within the boundaries of the IPA “Ulytau
petrophytic steppes with T. ulutavicum”, while a smaller portion
originates from nearby localities in the Ulytau massif that fall outside the
proposed IPA polygons but represent the same ecological context of petrophytic
steppe mosaics.The target species forms local population patches of up to approximately 1,200 m²,
with densities ranging from 0.06 to 3 individuals per m², typically occurring
on rocky substrates and petrophytic microhabitats.The associated communities exhibit relatively high floristic richness (82 vascular
plant species) and include nationally protected and regionally significant taxa
(e.g., national Red Book’ Tulipa patens, T. suaveolens, and
subendemic species such as Artemisia semiarida and Atraphaxis
decipiens).The dataset is intended to support site-based
conservation planning and management, including IPA/KBT documentation,
biodiversity monitoring, and future Red List and habitat assessments in the
petrophytic steppe landscapes of Central Kazakhstan.<b>Note on checklist reliability</b>Species names and authorships were harmonised
and updated using modern nomenclatural resources (POWO/WCVP/IPNI) and regional
floras and identification guides. Records with uncertain identification or
unclear locality attribution should be treated as provisional and may be
corrected as new vouchers, expert revisions, or additional surveys become
available.
DOI: 10.5061/dryad.9133p
title: Data from: Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown rats Rattus norvegicus on South Georgia

description: The control and eradication of invasive species is a common management
 strategy to protect or restore native biodiversity. On South Georgia in
 the Southern Ocean, the brown rat Rattus norvegicus was brought onto the
 island with the onset of whaling and sealing activity in the 1800s and has
 had a significant detrimental impact on key bird species of conservation
 concern. Efforts to eradicate rats from South Georgia using poisoned bait
 are ongoing. Despite the South Georgia rat eradication programme being the
 geographically largest and most ambitious eradication initiative to date,
 its success is facilitated by the potential that rat populations are
 effectively isolated by glacial barriers. This allows for localized
 eradication effort at manageable scales, leading to sequential eradication
 of individual populations with minimal risk of incursion from neighbouring
 areas. Here, we use the levels of population genetic divergence estimated
 from 299 single nucleotide polymorphism (SNP) loci and DNA sequence
 variation across 993 base pairs of the mitochondrial DNA cytochrome B
 locus to examine whether rat populations from nine glacially isolated
 areas on South Georgia are genetically distinct and so can be treated as
 independent eradication units. Bayesian clustering of individuals based on
 SNP similarity identified seven different genetic groups, which were
 confirmed using analyses based on pairwise genetic distance estimates and
 ordination of individuals using principal coordinate analysis. From a
 management perspective, these seven groups represent individual targets in
 baiting operations. Two mtDNA haplotypes were resolved across South
 Georgia, with a distinct geographical separation between the north-western
 and south-eastern populations. Approximate Bayesian computation (ABC) was
 used to identify that this divergence was a consequence of two separate
 historical colonization events. Synthesis and applications. We illustrate
 that molecular markers are a valuable tool in species management and pest
 eradication given that the spatial distribution of genetic diversity can:
 (i) identify demographically and genetically independent populations on
 which local eradication effort can be focussed, (ii) distinguish between
 incomplete eradication and immigration in situations where individuals
 remain after eradication has been attempted and (iii) identify the source
 of migrants when dispersal occurs over large spatial scales.
description: SNP
 genotypesSNP genotypes for all
 rats.
DOI: 10.5061/dryad.1n6s9
title: Data from: Evolution of the assassin’s arms: insights from a phylogeny of combined transcriptomic and ribosomal DNA data (Heteroptera: Reduvioidea)

description: Assassin bugs (Reduvioidea) are one of the most diverse (&gt;7,000
 spp.) lineages of predatory animals and have evolved an astounding
 diversity of raptorial leg modifications for handling prey. The evolution
 of these modifications is not well understood due to the lack of a robust
 phylogeny, especially at deeper nodes. We here utilize refined data from
 transcriptomes (370 loci) to stabilize the backbone phylogeny of
 Reduvioidea, revealing the position of major clades (e.g., the Chagas
 disease vectors Triatominae). Analyses combining transcriptomic and
 Sanger-sequencing datasets result in the first well-resolved phylogeny of
 Reduvioidea. Despite amounts of missing data, the transcriptomic loci
 resolve deeper nodes while the targeted ribosomal genes anchor taxa at
 shallower nodes, both with high support. This phylogeny reveals patterns
 of raptorial leg evolution across major leg types. Hairy attachment
 structures (fossula spongiosa), present in the ancestor of Reduvioidea,
 were lost multiple times within the clade. In contrast to prior
 hypotheses, this loss is not directly correlated with the evolution of
 alternative raptorial leg types. Our results suggest that prey type,
 predatory behavior, salivary toxicity, and morphological adaptations pose
 intricate and interrelated factors influencing the evolution of this
 diverse group of predators.
description: Taxon
 NamesFull descriptions of
 taxon names matched to abbreviations used in figuresZhang et
 al.TaxonNames.txtPartitioning scheme
 (transcriptomes; 23 taxa)Partitioning scheme for
 370genes and 23 taxa datasetZhang et
 al.370genes_23taxa_partition.txtAlignment file
 (transcriptomes; 23 taxa)Phylip alignment file
 for transcriptome dataset of 370 genes and 23 taxa.Zhang et
 al.370genes_23taxa.phyPartitioning scheme
 (ribosomal; 52 taxa)Partitioning scheme for
 3 gene ribosomal dataset of 52 taxa.Zhang et
 al.Ribosomal_52taxa_partition.txtAlignment file (ribosomal; 52 taxa)Phylip alignment file of 3 gene ribosomal dataset for 52 taxaZhang et al.Ribosomal_52taxa.phyPartitioning scheme (combined; 52 taxa)Partitioning scheme for combined datasetZhang et al.TranscriptomeAndRibosomal_52taxa_partition.txtAlignment file (combined; 52 taxa)Phylip alignment file for combined dataset of 52 taxaZhang et al.TranscriptomeAndRibosomal_52taxa.phyBootstrap Trees for each gene for STARZip file of 370 rooted bootstrap gene trees. Each file contains 100 bootstrap replicates of each gene. Gene ID's in file names correspond to those listed Gene regions file which correspond to positions in the Phylip file.Zhang et al.370genes_BootstrapTreesForSTAR_rooted.zipGeneID and partition in alignmentThe make up of the concatenated alignment file by Gene ID (as in STAR gene trees).Zhang et al.GeneRegions.txt
DOI: 10.5061/dryad.4f3c5
title: Data from: A rotational cylindrical fMRI phantom for image quality control

description: Purpose: A novel phantom for image quality testing for functional magnetic
 resonance imaging (fMRI) scans is described. Methods: The cylindrical,
 rotatable, ~4.5L phantom, with eight wedge-shaped compartments, is used to
 simulate rest and activated states. The compartments contain NiCl2 doped
 agar gel with alternating concentrations of agar (1.4%, 1.6%) to produce
 T1 and T2 values approximating brain grey matter. The Jacard index was
 used to compare the image distortions for echo planar imaging (EPI) and
 gradient recalled echo (GRE) scans. Contrast to noise ratio (CNR) was
 compared across the imaging volume for GRE and EPI. Results: The mean T2
 for the two agar concentrations were found to be 106.5±4.8, 94.5±4.7 ms,
 and T1 of 1500±40 and 1485±30 ms, respectively. The Jacard index for GRE
 was generally found to be higher than for EPI (0.95 versus 0.8). The CNR
 varied from 20 to 50 across the slices and echo times used for EPI scans,
 and from 20 to 40 across the slices for the GRE scans. The phantom
 provided a reproducible CNR over 25 days. Conclusions: The phantom
 provides a quantifiable signal change over a head-size imaging volume with
 EPI and GRE sequences, which was used for image quality assessment.
description: EPI image data
 simulating BOLD fMRI runThis zip archive
 contains phantom images (nifti format), using a EPI pulse sequence,
 corresponding to 60 repetitions (sets). Each set consists of 30 slices
 across the entire phantom. The phantom is rotated after every 15 sets to
 simulate a BOLD-EPI fMRI scan.5_040_ep2d_bold_axi_V60_S30_TE30_20130517.zipGradient Echo scan of the phantom 1 st setThis zip archive contains phantom images (nifti format), using a Gradient Echo pulse sequence, corresponding to the 1st of 4 repetitions (sets). Each set consists of 30 slices across the entire phantom. The phantom is rotated once after the 2nd set to simulate a BOLD-GRE fMRI scan.5_047_gre_bold_tra_S30_V4_20130517.zipGradient echo scan of phantom 2nd setThis zip archive contains phantom images (nifti format), using a Gradient Echo pulse sequence, corresponding to the 2nd of 4 repetitions (sets). Each set consists of 30 slices across the entire phantom. The phantom is rotated once after the 2nd set to simulate a BOLD-GRE fMRI scan.5_048_gre_bold_tra_S30_V4_20130517.zipGradient echo scan of phantom 3rd setThis zip archive contains phantom images (nifti format), using a Gradient Echo pulse sequence, corresponding to the 3rd of 4 repetitions (sets). Each set consists of 30 slices across the entire phantom. The phantom is rotated once after the 2nd set to simulate a BOLD-GRE fMRI scan.5_049_gre_bold_tra_S30_V4_20130517.zipGradient Echo Scan of phantom 4th setThis zip archive contains phantom images (nifti format), using a Gradient Echo pulse sequence, corresponding to the 4th of 4 repetitions (sets). Each set consists of 30 slices across the entire phantom. The phantom is rotated once after the 2nd set to simulate a BOLD-GRE fMRI scan.5_050_gre_bold_tra_S30_V4_20130517.zip
DOI: 10.5061/dryad.59gg3
title: Data from: The Odocoileus virginianus femur: mechanical behavior and morphology

description: Biomechanical research relies heavily on laboratory evaluation and testing
 with osseous animal structures. While many femora models are currently in
 use, including those of the European red deer (Cervus elaphus), the
 Odocoileus virginianus femur remains undocumented, despite its regional
 abundance in North America. The objective of this study was to compare
 biomechanical and morphological properties of the Odocoileus virginianus
 femur with those of the human and commonly used animal models. Sixteen
 pairs of fresh-frozen cervine femora (10 male, 6 female, aged 2.1 ± 0.9
 years) were used for this study. Axial and torsional stiffnesses (whole
 bone) were calculated following compression and torsion to failure tests
 (at rates of 0.1 mm/sec and 0.2°/sec). Lengths, angles, femoral head
 diameter and position, periosteal and endosteal diaphyseal dimensions, and
 condylar dimensions were measured. The results show that the cervine femur
 is closer in length, axial and torsional stiffness, torsional strength,
 and overall morphology to the human femur than many other commonly used
 animal femora models; additional morphological measurements are comparable
 to many other species’ femora. The distal bicondylar width of 59.3mm
 suggests that cervine femora may be excellent models for use in total knee
 replacement simulations. Furthermore, the cervine femoral head is more
 ovoid than other commonly-used models for hip research, making it a more
 suitable model for studies of hip implants. Thus, with further, more
 application-specific investigations, the cervine femur could be a suitable
 model for biomechanical research, including the study of ballistic
 injuries and orthopaedic device development.
description: Specimen Data
 Spreadsheet for PLos OneThis Excel spreadsheet
 gives the raw data for the morphology measurements and mechanical testing
 measurement.