cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.708k0
title: Data from: Rapid phenotypic change in a native bird population following conversion of the Colorado Desert to agriculture

description: Humans are modifying our planet’s ecosystems with increasing frequency and
 intensity. Exploring population responses to anthropogenic modifications
 of natural habitat provides insights into how species persist in the
 Anthropocene. Here, we leverage natural history collections to document
 rapid phenotypic change within a native bird population following 80 years
 of agriculture in the Colorado Desert of southeastern California. By
 comparing spectrophotometric measurements of Horned Lark (Eremophila
 alpestris) specimens collected in the Imperial Valley from 1918 to 1934 to
 those collected from 1984 to 2014, we found that more recent birds have
 darker backs, napes, and crowns. This dorsal darkening may have resulted
 from a shift in selective pressures for camouflage induced by land use:
 previously, the lark population nested on light-colored desert flats,
 whereas contemporary larks occupy darker soil associated with agricultural
 fields. Adaptation and/or introgression may have contributed to this
 instance of rapid phenotypic change following the rise of agriculture in
 the Imperial Valley.
description: Voucher
 TableLocality and date of
 collection data for vouchered specimens used in this
 study.VoucherTable_v6.xlsxSpectrophotometryData_DryadZip file containing raw output of OceanOptics spectrophotometer for all individuals included in this study.SpecProcessing_v2R script showing line-by-line code used to analyze data included in this study.
DOI: 10.5061/dryad.t8ph5
title: Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias

description: There has been remarkably little attention to using the high resolution
 provided by genotyping-by-sequencing (i.e. RADseq and similar methods)
 datasets for assessing relatedness in wildlife populations. A major hurdle
 is the genotyping error, especially allelic dropout, often found in this
 type of dataset that could lead to downward-biased, yet precise, estimates
 of relatedness. Here we assess the applicability of
 genotyping-by-sequencing datasets for relatedness inferences given their
 relatively high genotyping error rates. Individuals of known relatedness
 were simulated under genotyping error, allelic dropout, and missing data
 scenarios based on an empirical ddRAD dataset, and their true relatedness
 was compared to that estimated by seven relatedness estimators. We found
 that an estimator chosen through such analyses can circumvent the
 influence of genotyping error, with the estimator of Ritland (1996) shown
 to be unaffected by allelic dropout and to be the most accurate when there
 is genotyping error. We also found that the choice of estimator should not
 rely solely on the strength of correlation between estimated and true
 relatedness as a strong correlation does not necessarily mean estimates
 are close to true relatedness. We also demonstrated how even a large SNP
 dataset with genotyping error (allelic dropout or otherwise) or missing
 data still performs better than a perfectly genotyped microsatellite
 dataset of tens of markers. The simulation-based approach used here can be
 easily implemented by others on their own genotyping-by-sequencing
 datasets to confirm the most appropriate and powerful estimator for their
 dataset.
description: SNP
 genotypesGenotype data in
 COANCESTRY format for 8,294 SNPsCOANCESTRY_input.txtMicrosatellite genotypeGenotype data for one individual at 20 microsatellites. The microsatellite genotypes for the remaining individuals are available in a previous Dryad entry, doi:10.5061/dryad.8m0t6 . The format of the data in the current Dryad entry is the same as the previous entry, except in the current entry there is no sex data column.Microsatellite_genotype.txt
DOI: 10.5061/dryad.1tq09
title: Data from: Ancient chromosomal rearrangement associated with local adaptation of a post-glacially colonized population of Atlantic Cod in the northwest Atlantic

description: Intraspecific diversity is central to the management and conservation of
 exploited species, yet knowledge of how this diversity is distributed and
 maintained in the genome of many marine species is lacking. Recent
 advances in genomic analyses allow for genome-wide surveys of
 intraspecific diversity and offer new opportunities for exploring genomic
 patterns of divergence. Here, we analyzed genome-wide polymorphisms to
 measure genetic differentiation between an offshore migratory and a
 non-migratory population and to define conservation units of Atlantic Cod
 (Gadus morhua) in coastal Labrador. A total of 141 individuals, collected
 from offshore sites and from a coastal site within Gilbert Bay, Labrador,
 were genotyped using an ~11k single nucleotide polymorphism array.
 Analyses of population structure revealed strong genetic differentiation
 between migratory offshore cod and non-migratory Gilbert Bay cod. Genetic
 differentiation was elevated for loci within a chromosomal rearrangement
 found on linkage group 1 (LG1) that coincides with a previously found
 double inversion associated with migratory and non-migratory ecotype
 divergence of cod in the northeast Atlantic. This inverted region includes
 several genes potentially associated with adaptation to differences in
 salinity and temperature, as well as influencing migratory behaviour. Our
 work provides evidence that a chromosomal rearrangement on LG1 is
 associated with parallel patterns of divergence between migratory and
 non-migratory ecotypes on both sides of the Atlantic Ocean.
description: Sinclair-Waters_et_al_MEC_2017_8581_SNPsGenepop file containing SNP array data for 141 Atlantic Cod (Gadus morhua) genotyped at 8,581 loci. All SNPs are referred to by their database of Single Nucleotide Polymorphisms (dbSNP) accession numbers (http://www.ncbi.nlm.nih.gov/SNP). Geographic coordinates of sample collection sites can be found in Table 1 of the associated publication.
DOI: 10.5061/dryad.641hb
title: Data from: A novel approach to improve immune effector responses post transplant by restoration of CCL21 expression

description: Chemotherapy or chemoradiotherapy conditioning regimens required for bone
 marrow transplantation (BMT) cause significant morbidity and mortality as
 a result of insufficient immune surveillance mechanisms leading to
 increased risks of infection and tumor recurrence. Such conditioning
 causes host stromal cell injury, impairing restoration of the central
 (thymus) and peripheral (spleen and lymph node) T cell compartments and
 slow immune reconstitution. The chemokine, CCL21, produced by host stromal
 cells, recruits T- and B-cells that provide lymphotoxin mediated
 instructive signals to stromal cells for lymphoid organogenesis. Moreover,
 T- and B-cell recruitment into these sites is required for optimal
 adaptive immune responses to pathogens and tumor antigens. Previously, we
 reported that CCL21 was markedly reduced in secondary lymphoid organs of
 transplanted animals. Here, we utilized adenoviral CCL21 gene transduced
 dendritic cells (DC/CCL21) given by footpad injections as a novel approach
 to restore CCL21 expression in secondary lymphoid organs post-transplant.
 CCL21 expression in secondary lymphoid organs reached levels of naïve
 controls and resulted in increased T cell trafficking to draining lymph
 nodes (LNs). An increase in both lymphoid tissue inducer cells and the B
 cell chemokine CXCL13 known to be important in LN formation was observed.
 Strikingly, only mice vaccinated with DC/CCL21 loaded with bacterial,
 viral or tumor antigens and not recipients of DC/control adenovirus loaded
 cells or no DCs had a marked increase in the systemic clearance of
 pathogens (bacteria; virus) and leukemia cells. Because DC/CCL21 vaccines
 have been tested in clinical trials for patients with lung cancer and
 melanoma, our studies provide the foundation for future trials of DC/CCL21
 vaccination in patients receiving pre-transplant conditioning regimens.
description: FIgure
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DOI: 10.5061/dryad.5164v
title: Data from: Decreases in beetle body size linked to climate change and warming temperatures

description: 1. Body size is a fundamental ecological trait and is correlated with
 population dynamics, community structure and function, and ecosystem
 fluxes. Laboratory data from broad taxonomic groups suggest that a
 widespread response to a warming world may be an overall decrease in
 organism body size. However, given the myriad of biotic and abiotic
 factors that can also influence organism body size in the wild, it is
 unclear whether results from these laboratory assays hold in nature. 2.
 Here we use data sets spanning 30 to 100 years to examine whether the body
 size of wild-caught beetles has changed over time, whether body size
 changes are correlated with increased temperatures, and we frame these
 results using predictions derived from a quantitative review of laboratory
 responses of 22 beetle species to temperature. 3. We found that 95% of
 lab-reared beetles decreased in size with increased rearing temperature,
 with larger-bodied species shrinking disproportionately more than
 smaller-bodied beetles. In addition, the museum data sets revealed that
 larger-bodied beetle species have decreased in size over time, that mean
 beetle body size explains much of the interspecific variation in beetle
 responses to temperature, and that long-term beetle size changes are
 explained by increases in autumn temperature and decreases in spring
 temperature in this region. 4. Our data demonstrate that the relationship
 between body size and temperature of wild-caught beetles matches
 relatively well with results from laboratory studies, and that variation
 in this relationship is largely explained by interspecific variation in
 mean beetle body size. 5. This long-term beetle dataset is one of the most
 comprehensive arthropod body size datasets compiled to date, it improves
 predictions regarding the shrinking of organisms with global climate
 change, and together with the meta-analysis data, call for new hypotheses
 to explain why larger-bodied organisms may be more sensitive to
 temperature.
description: Tseng-et-al-JAE-Museum-Data-dryadThis file contains the data used to generate the main results for the museum beetles portion of the paper. The data for the meta-analysis portion of the paper is available as supplementary materials on the Journal of Animal Ecology website.
DOI: 10.5061/dryad.n70q6
title: Data from: Widespread introgression of mountain hare genes into Fennoscandian brown hare populations

description: In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus
 europaeus) hybridize and produce fertile offspring, resulting in gene flow
 across the species barrier. Analyses of maternally inherited mitochondrial
 DNA (mtDNA) show that introgression occur frequently, but unavailability
 of appropriate nuclear DNA markers has made it difficult to evaluate the
 scale- and significance for the species. The extent of introgression has
 become important as the brown hare is continuously expanding its range
 northward, at the apparent expense of the mountain hare, raising concerns
 about possible competition. We report here, based on analysis of 6833 SNP
 markers, that the introgression is highly asymmetrical in the direction of
 gene flow from mountain hare to brown hare, and that the levels of nuclear
 gene introgression are independent of mtDNA introgression. While it is
 possible that brown hares obtain locally adapted alleles from the resident
 mountain hares, the lower levels of mountain hare alleles among allopatric
 brown hares suggest that hybridization is driven by stochastic processes.
 Interspecific geneflow with the brown hare is unlikely to have major
 impacts on mountain hare in Fennoscandia, but direct competition may.
description: SNP genotypes for 6833
 loci from 21 mountain hares (Lepus timidus) and 27 brown hares (Lepus
 europaeus)SNP genotypes for 6833
 loci from 21 mountain hares (Lepus timidus) and 27 brown hares (Lepus
 europaeus) from Sweden and Finland. Data sheet includes sample number,
 sampling location coordinates, mtDNA haplotype and notes for species
 co-existence at the sampling location
 (sympatry/allopatry).SNPdataset_Levanen_Final.xlsx
DOI: 10.5281/zenodo.18334926
title: Replication materials for: The Polarised Electorate: Affective Polarisation and Electoral Loyalty in Turkey's 2023 Critical Election

description: Replication materials for: Aytaç, S. E., Irmak, S., & Söylemez-Karakoç, B. (2025). The polarised electorate: affective polarisation and electoral loyalty in Turkey’s 2023 critical election. South European Society and Politics, 1–27. https://doi.org/10.1080/13608746.2025.2597287.
DOI: 10.5281/zenodo.18334927
title: Replication materials for: The Polarised Electorate: Affective Polarisation and Electoral Loyalty in Turkey's 2023 Critical Election

description: Replication materials for: Aytaç, S. E., Irmak, S., & Söylemez-Karakoç, B. (2025). The polarised electorate: affective polarisation and electoral loyalty in Turkey’s 2023 critical election. South European Society and Politics, 1–27. https://doi.org/10.1080/13608746.2025.2597287.
DOI: 10.5061/dryad.n976p
title: Data from: Total duplication of the small single copy region in the angiosperm plastome: rearrangement and inverted repeat instability in Asarum

description: Premise of the Study: As more plastomes are assembled, it is evident that
 rearrangements, losses, intergenic spacer expansion and contraction, and
 syntenic breaks within otherwise functioning plastids are more common than
 was thought previously, and such changes have developed independently in
 disparate lineages. However, to date, the magnoliids remain characterized
 by their highly conserved plastid genomes (plastomes). Methods: Illumina
 HiSeq and MiSeq platforms were used to sequence the plastomes of Saruma
 henryi and those of representative species from each of the six taxonomic
 sections of Asarum. Sequenced plastomes were compared in a phylogenetic
 context provided by maximum likelihood and parsimony inferences made using
 an additional 18 publicly available plastomes from early‐diverging
 angiosperm lineages. Key Results: In contrast to previously published
 magnoliid plastomes and the newly sequenced Saruma henryi plastome
 published here, Asarum plastomes have undergone extensive disruption and
 contain extremely lengthy AT‐repeat regions. The entirety of the small
 single copy region (SSC) of A. canadense and A. sieboldii var. sieboldii
 has been incorporated into the inverted repeat regions (IR), and the SSC
 of A. delavayi is only 14 bp long. All sampled Asarum plastomes share an
 inversion of a large portion of the large single copy region (LSC) such
 that trnE‐UUC is adjacent to the LSC‐IR boundary. Conclusions: Plastome
 divergence in Asarum appears to be consistent with trends seen in highly
 rearranged plastomes of the monocots and eudicots. We propose that
 plastome instability in Asarum is due to repetitive motifs that serve as
 recombinatory substrates and reduce genome stability.
description: Magnoliids_alignment25 Magnoliid plastomes, with a single IR region removed, aligned using MAFFT and processed using Gblocks.Asaroideae_alignmentAsaroideae plastomes, with a single IR region removed, aligned using MAFFT and processed using Gblocks.trnH_alignmenttrnH(GUG) from plastomes and mitochondrial genomes throughout the Piperales aligned using MAFFT and processed using Gblocks.
DOI: 10.5061/dryad.873bn
title: Data from: Comparison of the immune response during acute and chronic Staphylococcus aureus infection

description: Staphylococcus aureus bacteria are able to grow in a planktonic state that
 is associated with acute infections and in biofilms that are associated
 with chronic infections. Acute infections, such as skin infections, are
 often self-limiting. However, chronic infections, such as implant
 infections, can be difficult to clear and may require surgical
 intervention. The host immune response may contribute to the different
 outcomes often associated with these two disease types. We used proteomic
 arrays and two murine models for an initial, descriptive characterization
 of the contribution of the host immune response to outcomes of acute
 versus chronic S. aureus disease. We compared the immune responses between
 a model of self-limiting skin and soft tissue infection caused by the
 planktonic form of S. aureus versus a model of surgical mesh implant
 infection, which we show to be caused by a bacterial biofilm. The
 significantly altered host cytokines and chemokines were largely different
 in the two models, with responses diminished by 21 days post-implantation
 in surgical mesh infection. Because bacterial levels remained constant
 during the 21 days that the surgical mesh infection was followed, those
 cytokines that are significantly increased during chronic infection are
 not likely effective in eradicating biofilm. Comparison of the levels of
 cytokines and chemokines in acute versus chronic S. aureus infection can
 provide a starting point for evaluation of the role of specific immune
 factors that are present in one disease manifestation but not the other.
description: Sample
 arraysRepresentative Mouse XL
 cytokine arrays for SSTI, Day 7 biofilm, and day 21 biofilm
 infections.Fold change calculations
 for Mouse XL Cytokine ArraysEach tab contains raw
 densitometry data for Mouse XL Cytokine arrays performed on samples from
 skin and soft tissue infection, 7 day mesh infection, or 21 day mesh
 infection. Fold changes for each of three array sets per infection
 (infected/uninfected) were used to calculate the mean log2 fold change for
 each cytokine and chemokine(reported in Supplemental Table 2 of
 paper).consolidated raw data used in
 paper.xls
DOI: 10.5061/dryad.d3h31
title: Data from: A rich diversity of opercle bone shape among teleost fishes

description: The opercle is a prominent craniofacial bone supporting the gill cover in
 all bony fish and has been the subject of morphological, developmental,
 and genetic investigation. We surveyed the shapes of this bone among 110
 families spanning the teleost tree and examined its pattern of occupancy
 in a principal component-based morphospace. Contrasting with expectations
 from the literature that suggest the local morphospace would be only
 sparsely occupied, we find primarily dense, broad filling of the
 morphological landscape, indicating rich diversity. Phylomorphospace plots
 suggest that dynamic evolution underlies the observed spatial patterning.
 Evolutionary transits through the morphospaces are sometimes long, and
 occur in a variety of directions. The trajectories seem to represent both
 evolutionary divergences and convergences, the latter supported by
 convevol analysis. We suggest that that this pattern of occupancy reflects
 the various adaptations of different groups of fishes, seemingly
 paralleling their diverse marine and freshwater ecologies and life
 histories. Opercle shape evolution within the acanthomorphs, spiny
 ray-finned fishes, appears to have been especially dynamic.
description: Kimmel DRYAD deposits
 PLOS ONEThe ReadMe file contains
 a synopsis of data used for the Figures and Tables in the
 paper
DOI: 10.5061/dryad.2g2m7
title: Data from: Hydrothermally synthesized PZT film grown in highly concentrated KOH solution with large electromechanical coupling coefficient for resonator

description: This paper presents a study of lead zirconate titanate (PZT) films
 hydrothermally grown on a dome-shaped titanium diaphragm. Few articles in
 the literature address the implementation of hydrothermal PZT films on
 curved-diaphragm substrates for resonators. In this study, a 50-μm-thick
 titanium sheet is embossed using balls of designed dimensions to shape a
 dome-shaped cavity array. Through single-process hydrothermal synthesis,
 PZT films are grown on both sides of the processed titanium diaphragm with
 good adhesion and uniformity. The hydrothermal synthesis process involves
 a high concentration of potassium hydroxide solution and excess amounts of
 lead acetate and zirconium oxychloride octahydrate. Varied deposition
 times and temperatures of PZT films are investigated. The grown films are
 characterized by X-ray diffraction and scanning electron microscopy. The
 10-μm-thick PZT dome-shaped resonators with 60- and 20-μm-thick supporting
 layers are implemented and further tested. Results for both resonators
 indicate that large electromechanical coupling coefficients and a series
 resonance of 95 MHz from 14 MHz can be attained. The device is connected
 to a complementary metal–oxide–semiconductor integrated circuit for
 analysis of oscillator applications. The oscillator reaches a Q value of
 6300 in air. The resonator exhibits a better sensing stability when loaded
 with water when compared with air.
description: 15xrd_codesXRD-data file
DOI: 10.5061/dryad.q24m6
title: Data from: Kinship underlies costly cooperation in Mosuo villages

description: The relative importance of social evolution theories such as kin
 selection, direct reciprocity and needs-based transfers in explaining
 real-world cooperation is the source of much debate. Previous field
 studies of cooperation in human communities have revealed variability in
 the extent to which each of these theories drive human sociality in
 different contexts. We conducted multivariate social network analyses
 predicting costly cooperation—labouring on another household’s farm—in
 128,082 dyads of Mosuo farming households in southwest China. Through
 information-theoretic model selection, we tested the roles played by
 genealogical relatedness, affinal relationships (including reproductive
 partners), reciprocity, relative need, wealth, household size, spatial
 proximity, and gift-giving in an economic game. The best-fitting models
 included all factors, along with interactions between relatedness and (i)
 reciprocity, (ii) need, (iii) the presence of children in another
 household, and (iv) proximity. Our results show how a real-world form of
 cooperation was driven by kinship. Households tended to help kin in need
 (but not needy non-kin) and travel further to help spatially distant
 relatives. Households were more likely to establish reciprocal
 relationships with distant relatives and non-kin but not with closer kin;
 closer kin cooperated regardless of reciprocity. These patterns of
 kin-driven cooperation show the importance of inclusive fitness in
 understanding human social behaviour.
description: Dyadic data used in
 analysisAnonymised dataset
 containing household dyads.mosuo dyads -
 anon.csv