cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4vg17
title: Data from: Demographic modelling reveals a history of divergence with gene flow for a glacially tied stonefly in a changing post-Pleistocene landscape

description: Aim: Climate warming is causing extensive loss of glaciers in mountainous
 regions, yet our understanding of how glacial recession influences
 evolutionary processes and genetic diversity is limited. Linking genetic
 structure with the influences shaping it can improve understanding of how
 species respond to environmental change. Here, we used genome-scale data
 and demographic modelling to resolve the evolutionary history of Lednia
 tumana, a rare, aquatic insect endemic to alpine streams. We also employed
 a range of widely used data filtering approaches to quantify how they
 influenced population structure results. Location: Alpine streams in the
 Rocky Mountains of Glacier National Park, Montana, USA. Taxon: Lednia
 tumana, a stonefly (Order Plecoptera) in the family Nemouridae. Methods:
 We generated single nucleotide polymorphism data through restriction-site
 associated DNA sequencing to assess contemporary patterns of genetic
 structure for 11 L. tumana populations. Using identified clusters, we
 assessed demographic history through model selection and parameter
 estimation in a coalescent framework. During population structure
 analyses, we filtered our data to assess the influence of singletons,
 missing data and total number of markers on results. Results: Contemporary
 patterns of population structure indicate that L. tumana exhibits a
 pattern of isolation-by-distance among populations within three genetic
 clusters that align with geography. Mean pairwise genetic differentiation
 (FST) among populations was 0.033. Coalescent-based demographic modelling
 supported divergence with gene flow among genetic clusters since the end
 of the Pleistocene (~13-17 kya), likely reflecting the south-to-north
 recession of ice sheets that accumulated during the Wisconsin glaciation.
 Main conclusions: We identified a link between glacial retreat,
 evolutionary history and patterns of genetic diversity for a
 range-restricted stonefly imperiled by climate change. This finding
 included a history of divergence with gene flow, an unexpected conclusion
 for a mountaintop species. Beyond L. tumana, this study demonstrates the
 complexity of assessing genetic structure for weakly differentiated
 species, shows the degree to which rare alleles and missing data may
 influence results, and highlights the usefulness of genome-scale data to
 extend population genetic inquiry in non-model species.
description: Dryad Accession for
 Hotaling et al. 2017, Journal of BiogeographyRelevant files for the
 associated study: input files for PLINK and Fastsimcoal2, a key of
 individuals/populations, and raw SNP catalog as output by STACKS with a
 whitelist for the loci/SNPs used in this study.Hotaling_2017_Dryad.zip
DOI: 10.15468/2g4hmz
title: Paroxythyreus stilleri, a new genus and species of South African Macrocephalini (Hemiptera: Heteroptera: Reduviidae: Phymatinae) with a note on the metathoracic glands and their evaporation areas in the Reduviidae

description: This dataset contains the digitized treatments in Plazi based on the original journal article Jacobs, Dawid H. (2025): Paroxythyreus stilleri, a new genus and species of South African Macrocephalini (Hemiptera: Heteroptera: Reduviidae: Phymatinae) with a note on the metathoracic glands and their evaporation areas in the Reduviidae. Zootaxa 5719 (1): 108-116, DOI: 10.11646/zootaxa.5719.1.5, URL: https://doi.org/10.11646/zootaxa.5719.1.5AbstractParoxythyreus gen. nov. and its type species P. stilleri sp. nov. (Hemiptera: Heteroptera: Reduviidae: Phymatinae: Macrocephalini) from South Africa are described and illustrated. The metathoracic gland system and evaporative areas in the Reduviidae and Phymatinae are briefly discussed. A unique area of modified cuticle on the metapleuron of P. stilleri is reported and its possible function discussed.
DOI: 10.5061/dryad.9cp3j
title: Data from: The chinchilla as a novel animal model of pregnancy

description: Several parameters are important when choosing the most appropriate animal
 to model human obstetrics, including gestation period, number of fetuses
 per gestation and placental structure. The domesticated long-tailed
 chinchilla (Chinchilla lanigera) is a well-suited and appropriate animal
 model of pregnancy that often will carry only one offspring and has a long
 gestation period of 105–115 days. Furthermore, the chinchilla placenta is
 of the haemomonochorial labyrinthine type and is therefore comparable to
 the human villous haemomonochorial placenta. This proof-of-concept study
 demonstrated the feasibility in laboratory settings, and demonstrated the
 potential of the pregnant chinchilla as an animal model for obstetric
 research and its potential usefulness for non-invasive measurements in the
 placenta. We demonstrate measurements of the placental and fetal
 metabolism (demonstrated in vivo by hyperpolarized MRI and in vitro by
 qPCR analyses), placental vessels (demonstrated ex vivo by
 contrast-enhanced CT angiography) and overall anatomy (demonstrated in
 vivo by whole-body CT).
description: Imaging
 dataData contains (zip
 format files): 1) reconstructed MRI data (General Electric MRI system) and
 regions-of-interests files. Excel spreadsheet is provided with signal
 intensity results. 2) CT whole-animal data (SIemens CT system). 3) CT
 angiography of placenta (Scanco CT system).supplementary
 data.zip
DOI: 10.5061/dryad.r5nf0
title: Data from: Community trees: identifying codiversification in the páramo dipteran community

description: Groups of codistributed species that responded in a concerted manner to
 environmental events are expected to share patterns of evolutionary
 diversification. However, the identification of such groups has largely
 been based on qualitative, post hoc analyses. We develop here two methods
 (PPS, K-F ANOVA) for the analysis of codistributed species that, given a
 group of species with a shared pattern of diversification, allow
 empiricists to identify those taxa that do not codiversify (i.e.,
 "outlier" species). The identification of outlier species makes
 it possible to jointly estimate the evolutionary history of
 co-diversifying taxa. To evaluate the approaches presented here, we
 collected data from Páramo dipterans, identified outlier species, and
 estimated a "community tree" from species that are identified as
 having co-diversified. Our results demonstrate that dipteran communities
 from different Páramo habitats in the same mountain range are more closely
 related than communities in other ranges. We also conduct simulation
 testing to evaluate this approach. Results suggest that our approach
 provides a useful addition to comparative phylogeographic methods, while
 identifying aspects of the analysis that require careful interpretation.
 In particular, both the PPS and K-F ANOVA perform acceptably when there
 are one or two outlier species, but less so as the number of outliers
 increase. This is likely a function of the corresponding degradation of
 the signal of community divergence; without a strong signal from a
 co-diversifying community, there is no dominant pattern from which to
 detect and outlier species. For this reason, both the magnitude of K-F
 distance distribution and outside knowledge about the phylogeographic
 history of each putative member of the community should be considered when
 interpreting results.
description: Community_Trees1. Nexus files from Paramo fly species, containing aligned COI data described in text of manuscript. 2. Results from community tree analysis of Paramo fly COI data.
DOI: 10.5061/dryad.30mv0
title: Data from: Aneuploidy causes non-genetic individuality

description: Phenotypic variability is a hallmark of diseases involving chromosome
 gains and losses, such as Down syndrome and cancer. Allelic variances have
 been thought to be the sole cause of this heterogeneity. Here, we
 systematically examine the consequences of gaining and losing single or
 multiple chromosomes to show that the aneuploid state causes non-genetic
 phenotypic variability. Yeast cell populations harboring the same defined
 aneuploidy exhibit heterogeneity in cell-cycle progression and response to
 environmental perturbations. Variability increases with degree of
 aneuploidy and is partly due to gene copy number imbalances, suggesting
 that subtle changes in gene expression impact the robustness of biological
 networks and cause alternate behaviors when they occur across many genes.
 As inbred trisomic mice also exhibit variable phenotypes, we further
 propose that non-genetic individuality is a universal characteristic of
 the aneuploid state that may contribute to variability in presentation and
 treatment responses of diseases caused by aneuploidy.
description: FC Dataset: steady-state
 GAL pathway inductionRaw FCS files and MATLAB
 analysis code. Flow cytometry analysis toolkit used in this code is
 available at https://github.com/springerlabGAL induction
 steady-state.zipFC Dataset: steady-state
 heat shock stress responseRaw FCS files and MATLAB
 analysis code. Flow cytometry analysis toolkit used in this code is
 available at https://github.com/springerlabHS stress
 steady-state.zipFC Dataset: steady-state
 DTT stress responseRaw FCS files and MATLAB
 analysis code. Flow cytometry analysis toolkit used in this code is
 available at https://github.com/springerlabDTT stress
 steady-state.zipFC Dataset: YFP/mCherry
 dual reporter noise assayRaw FCS files and MATLAB
 analysis code. Flow cytometry analysis toolkit used in this code is
 available at https://github.com/springerlabDual-reporter
 assay.zipFC Dataset: kinetic GAL
 pathway inductionRaw FCS files and MATLAB
 analysis code. Flow cytometry analysis toolkit used in this code is
 available at https://github.com/springerlabGAL induction
 kinetics.zip
DOI: 10.5061/dryad.gc72v
title: Data from: Multi-contrast submillimetric 3-Tesla hippocampal subfield segmentation protocol and dataset

description: The hippocampus is composed of distinct anatomical subregions that
 participate in multiple cognitive processes and are differentially
 affected in prevalent neurological and psychiatric conditions. Advances in
 high-field MRI allow for the non-invasive identification of hippocampal
 substructure. These approaches, however, demand time-consuming manual
 segmentation that relies heavily on anatomical expertise. Here, we share
 manual labels and associated high-resolution MRI data (MNI-HISUB25;
 submillimetric T1- and T2-weighted images, detailed sequence information,
 and stereotaxic probabilistic anatomical maps) based on 25 healthy
 subjects. Data were acquired on a widely available 3 Tesla MRI system
 using a 32 phased-array head coil. The protocol divided the hippocampal
 formation into three subregions: subicular complex, merged Cornu Ammonis
 1, 2 and 3 (CA1-3) subfields, and CA4-dentate gyrus (CA4-DG). Segmentation
 was guided by consistent intensity and morphology characteristics of the
 densely myelinated molecular layer together with few geometry-based
 boundaries flexible to overall mesiotemporal anatomy, and achieved
 excellent intra-/inter-rater reliability (Dice index ≥90/87%). The dataset
 can inform neuroimaging assessments of the mesiotemporal lobe and help to
 develop segmentation algorithms relevant for basic and clinical
 neurosciences.
description: README.txtReadme file. Naming conventions and data info.exam_card_T1w_standard.pdfParameters for the standard T1w sequence (1x1x1 mm^3); zippedexam_card_T1wHiRes.pdfParameters for the high-resolution T1w sequence (.6x.6x.6 mm^3). Two identical acquisitions of this sequence need to be made to increase SNR; zippedexam_card_T2wHiRes.pdfParameters for the high-resolution T2w sequence (.4x.4x2 mm^3); zippedTable1_demographics_participantsTable 1. Participant demographicsTable2_CNRTable 2. Contrast to noise estimates for all subjects.Table3_reliabilityTable 3. Intra- and inter-rater reliability estimates.mri_datasetHigh-resolution 3-Tesla MRI dataset including submillimetric T1-weighted images, T2-weighted images, and subregional hippocampal labels of 25 healthy subjects. Data are provided in nifti format and both native and stereotaxic space. The dataset also includes stereotaxic probabilistic anatomical maps of all subregions. Please see README.txt for further details.
DOI: 10.5061/dryad.3cb81
title: Data from: Directional selection can drive the evolution of modularity in complex traits

description: Modularity is a central concept in modern biology, providing a powerful
 framework for the study of living organisms on many organizational levels.
 Two central and related questions can be posed in regard to modularity:
 How does modularity appear in the first place, and what forces are
 responsible for keeping and/or changing modular patterns? We approached
 these questions using a quantitative genetics simulation framework,
 building on previous results obtained with bivariate systems and extending
 them to multivariate systems. We developed an individual-based model
 capable of simulating many traits controlled by many loci with variable
 pleiotropic relations between them, expressed in populations subject to
 mutation, recombination, drift, and selection. We used this model to study
 the problem of the emergence of modularity, and hereby show that drift and
 stabilizing selection are inefficient at creating modular variational
 structures. We also demonstrate that directional selection can have marked
 effects on the modular structure between traits, actively promoting a
 restructuring of genetic variation in the selected population and
 potentially facilitating the response to selection. Furthermore, we give
 examples of complex covariation created by simple regimes of combined
 directional and stabilizing selection and show that stabilizing selection
 is important in the maintenance of established covariation patterns. Our
 results are in full agreement with previous results for two-trait systems
 and further extend them to include scenarios of greater complexity.
 Finally, we discuss the evolutionary consequences of modular patterns
 being molded by directional selection.
description: C code for the
 simulationsRequires GSL to be
 instaled in the system. Makefile should work out of the box in unix
 systems.evomod_c_code.tarFirst part of the main simulation resultsmust be joined with the other parts using cat. See dryad wiki for instructions.split_resultsaaSecond part of the main simulation resultsmust be joined with the other parts using cat. See dryad wiki for instructions.split_resultsabThird part of the main simulation resultsmust bet joined with the other parts using cat. Se dryad wiki for instructions.split_resultsacFourth part of the main simulation resultsmust be joined with the other parts using cat. See dryad wiki for instructions.split_resultsadFifth part of the main simulation resultssplit_resultsaeSixt part of the main simulation resultssplit_resultsafSeventh part of the main simulation resultssplit_resultsagEigth part of the main simulation resultssplit_resultsahNinth part of the main simulation resultssplit_resultsaiTenth part of the main simulation resultssplit_resultsaj
DOI: 10.5061/dryad.5bk4c
title: Data from: Gene expression differs in codominant prairie grasses under drought

description: Grasslands of the Central US are expected to experience severe droughts
 and other climate extremes in the future, yet we know little about how
 these grasses will respond in terms of gene expression. We compared gene
 expression in Andropogon gerardii and Sorghastrum nutans, two closely
 related co-dominant C4 grasses responsible for the majority of ecosystem
 function, using RNA-seq. We compared Trinity assemblies within
 each species to determine annotated functions of transcripts responding to
 drought. Subsequently, we compared homologous annotated gene-groups across
 the two species using cross-species meta-level analysis and functional
 clustering based on key terms. The majority of variation was found between
 species, as opposed to between drought and watered treatments. However,
 there is evidence for differential responses; Andropogon allocated gene
 expression differently compared to Sorghastrum, suggesting Andropogon
 focuses on stress alleviation (such as oxygen radical scavenging) rather
 than prevention. In contrast, Sorghastrum may employ a drought
 avoidance strategy by modulating osmotic response, especially with
 hormonal regulation. We found Sorghastrum tended to be more sensitive
 within 10 key gene-groups related to stress, abscisic acid, and trichomes,
 suggesting gene expression may mechanistically parallel sensitivity at the
 physiological level. Our findings corroborate phenotypic and physiological
 differences in the field and may help explain the phenotypic mechanisms of
 these two species in the tallgrass prairie community under future drought
 scenarios.
description: raw_data Contains raw sequence
 data. 
 Trinity_andropogon_02122016.fasta Trinity assembly of the
 <em>Andropogon gerardii</em> transcriptome, assembled Feb 12,
 2016. 
 <strong>File:</strong>
 Trinity_andro_out.Trinity.02122016.fasta 
 
 Trinity_sorghastrum_04102016.fasta Trinity assembly of
 Sorghastrum nutans transcriptome, assembled Apr 10, 2016.
 
 <strong>File:</strong>
 Trinity_sorgh_out.Trinity.fasta 
 RSEM_read_counts Raw and
 TMM-normalized read counts for transcript expression prior to
 analysis. 
 edgeR_results_andropogon Counts and
 differential expression for Andropogon. 
 edgeR_results_both_species Preliminary
 count data for annotation clustered genes compared between the two
 species. This information was processed further in the pipeline to account
 for multiple copy numbers (orthologs, paralogs) 
 edgeR_results_sorghastrum Count
 and differential expression data for Sorghastrum. 
 Kristiansson_analysis_results
 Accounts for multiple different gene copy numbers in
 differential expression. 
 all_paralogs_bothspecies Counts of
 paralogs/orthologs found in each gene annotation group for each species,
 not filtered by significance. 
 <strong>File:</strong>
 all_paralogs_xspecies_2tail.csv
DOI: 10.15468/dl.x9g2hw
title: Occurrence Download

description: A dataset containing 55100 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Biodiversity4all Research-Grade Observations"
 ]
}

 The dataset includes 55100 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000320-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.p61vk
title: Data from: Recombination in the eggs and sperm in a simultaneously hermaphroditic vertebrate

description: When there is no recombination (achiasmy) in one sex, it is in the
 heterogametic one. This observation is so consistent that it constitutes
 one of the few patterns in biology that may be regarded as a ‘rule’ and
 Haldane (Haldane 1922 J. Genet. 12, 101–109. (doi:10.1007/BF02983075))
 proposed that it might be driven by selection against recombination in the
 sex chromosomes. Yet differences in recombination rates between the sexes
 (heterochiasmy) have also been reported in hermaphroditic species that
 lack sex chromosomes. In plants—the vast majority of which are
 hermaphroditic—selection at the haploid stage has been proposed to drive
 heterochiasmy. Yet few data are available for hermaphroditic animals, and
 barely any for hermaphroditic vertebrates. Here, we leverage reciprocal
 crosses between two black hamlets (Hypoplectrus nigricans, Serranidae),
 simultaneously hermaphroditic reef fishes from the wider Caribbean, to
 generate high-density egg- and sperm-specific linkage maps for each
 parent. We find globally higher recombination rates in the eggs, with
 dramatically pronounced heterochiasmy at the chromosome peripheries. We
 suggest that this pattern may be due to female meiotic drive, and that
 this process may be an important source of heterochiasmy in animals. We
 also identify a large non-recombining region that may play a role in
 speciation and local adaptation in Hypoplectrus.
description: Map for parent 1 (both
 sexes)Linkage map for parent 1
 (both sexes)Parent_1_both_sexes.xlsxMap for parent 2 (both sexes)Linkage map for parent 2 (both sexes)Parent_2_both_sexes.xlsxMap for parent 1 (eggs)Linkage map for parent 1 (eggs)Parent_1_eggs.xlsxMap for parent 1 (sperm)Linkage map for parent 1 (sperm)Parent_1_sperm.xlsxMap for parent 2 (eggs)Linkage map for parent 2 (eggs)Parent_2_eggs.xlsxMap for parent 2 (sperm)Linkage map for parent 2 (sperm)Parent_2_sperm.xlsxRAD demultiplexed filtered dataRAD data, demultiplexed and filtered (read 1)RAD_demultiplexed_filtered_data.zip
DOI: 10.5061/dryad.p8br3r4
title: Data from: Future climate change is predicted to affect the microbiome and condition of habitat-forming kelp

description: Climate change is driving global declines of marine habitat-forming
 species through physiological effects and through changes to ecological
 interactions, with projected trajectories for oceanwarming and
 acidification likely to exacerbate such impacts in coming decades.
 Interactions between habitat-formers and their microbiomes are fundamental
 for host functioning and resilience, but how such relationships will
 change in future conditions is largely unknown. We investigated
 independent and interactive effects of warming and acidification on a
 large brown seaweed, the kelp Ecklonia radiata, and its associated
 microbiome in experimental mesocosms. Microbial communities were affected
 by warming and, during the first week, by acidification. During the second
 week, kelp developed disease-like symptoms previously observed in the
 field. The tissue of some kelp blistered, bleached and eventually
 degraded, particularly under the acidification treatments, affecting
 photosynthetic efficiency. Microbial communities differed between
 blistered and healthy kelp for all treatments, except for those under
 future conditions of warming and acidification, which after two weeks
 resembled assemblages associated with healthy hosts. This indicates that
 changes in the microbiome were not easily predictable as the severity of
 future climate scenarios increased. Future ocean conditions can change
 kelp microbiomes and may lead to host disease, with potentially cascading
 impacts on associated ecosystems.
description: Amplicon sequences of
 microbial communities on the surface of ecklonia radiata under different
 environmental conditionsThis data includes
 bacterial 16S rRNA gene sequences of microbial communities on the surface
 of Ecklonia radiata under different environmental scenarios. Amplicon
 sequencing used 27F/519R primers contain V1-V3 regions.Submission_RSPB-2018-0507.tar