cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j1pt126
title: Data from: Random heteropolymers preserve protein function in foreign environments

description: The successful incorporation of active proteins into synthetic polymers
 could lead to a new class of materials with functions found only in living
 systems. However, proteins rarely function under the conditions suitable
 for polymer processing. On the basis of an analysis of trends in protein
 sequences and characteristic chemical patterns on protein surfaces, we
 designed four-monomer random heteropolymers to mimic intrinsically
 disordered proteins for protein solubilization and stabilization in
 non-native environments. The heteropolymers, with optimized composition
 and statistical monomer distribution, enable cell-free synthesis of
 membrane proteins with proper protein folding for transport and
 enzyme-containing plastics for toxin bioremediation. Controlling the
 statistical monomer distribution in a heteropolymer, rather than the
 specific monomer sequence, affords a new strategy to interface with
 biological systems for protein-based biomaterials.
description: Sequence simulation of
 random heteropolymerThe file contains
 simulated sequences of random heteropolymers and block length histogram
 analysis.Sequence
 Simulation.zipSurface
 AnalysisSurface analysis of
 water soluble proteins as a function of surface
 chemistryEnzyme-Polymer
 SimulationSimulation of
 protein-random heteropolymer complex in solutions
DOI: 10.5061/dryad.2tp53gr
title: Data from: Neopterygian phylogeny: the merger assay

description: The phylogenetic relationships of the recently described genus
 †Ticinolepis from the Middle Triassic of Monte San Giorgio are explored
 through cladistic analyses of the so far largest morphological data set
 for fossil actinopterygians, including representatives of the crown
 neopterygian clades Halecomorphi, Ginglymodi, and Teleostei, and merging
 the lists of characters from previously published systematic studies
 together with newly proposed characters. †Ticinolepis is retrieved as the
 most basal Ginglymodi and our results support the monophyly of Teleostei
 and Holostei, as well as Halecomorphi and Ginglymodi within the latter
 clade. The patterns of relationships within these clades mostly agree with
 previous studies, though a few important differences require future
 research. According to our results, ionoscopiforms are not monophyletic,
 caturids are not amiiforms and leptolepids and luisiellids form a
 monophyletic clade. Our phylogenetic hypothesis confirms the rapid
 radiation of the holostean clades Halecomorphi and Ginglymodi during the
 Early and Middle Triassic and the radiation of pholidophoriform teleosts
 during the Late Triassic. Crown-group Halecomorphi have an enormous ghost
 lineage throughout most of the Mesozoic, but ginglymodians and teleosts
 show a second radiation during the Early Jurassic. The crown-groups of
 Halecomorphi, Ginglymodi and Teleostei originated within parallel events
 of radiation during the Late Jurassic.
description: Data matrix Neopterygian
 phylogeny: the merger assay. LopezArbarello-SfercoCharacter-taxon matrix
 of Neopterygian phylogeny: the merger assay. (99 species - 339
 morphological characters).Neopterygii_LopezArbarello-Sferco.nexStrict consensus treeStrict consensus tree of 24 most parsimonious trees. Equal weighted analysis.SCT_equal_weight.jpgMPT Equal weighted analysis24 most parsimonious trees. Equal weighted analysis.MPT_equal_weight.treMPT implied weighting k3Most parsimonious tree obtained in the analysis under implied weighting using a constant (k-value) of 3 (k3).MPT_implied_weighting_k3.treMPT implied weighting k8Most parsimonious tree obtained in the analysis under implied weighting using a constant (k-value) of 8 (k8).MPT_implied_weighting_k8.tre
DOI: 10.5061/dryad.s1v3801
title: Data from: Local interactions and self-organized spatial patterns stabilize microbial cross-feeding against cheaters

description: Mutualisms are ubiquitous, but models predict they should be susceptible
 to cheating. Resolving this paradox has become relevant to synthetic
 ecology: cooperative cross-feeding, a nutrient exchange mutualism, has
 been proposed to stabilize microbial consortia. Previous attempts to
 understand how cross-feeders remain robust to non-producing cheaters have
 relied on complex behavior (e.g., cheater punishment) or group selection.
 Using a stochastic spatial model, we demonstrate two novel mechanisms that
 can allow cross-feeders to outcompete cheaters, rather than just escape
 from them. Both mechanisms work through the spatial segregation of the
 resources, which prevents individual cheaters from acquiring the resources
 they need to reproduce. First, if microbe dispersal is low but resources
 are shared widely, then the cross-feeders self-organize into stable
 spatial patterns. Here the cross-feeders can build up where the resource
 they need is abundant, and send their resource to where their partner is,
 separating resources at regular intervals in space. Second, if dispersal
 is high but resource sharing is local, then random variation in population
 density creates small-scale variation in resource density, separating the
 resources from each other by chance. These results suggest that
 cross-feeding may be more robust than previously expected and offer
 strategies to engineer stable consortia.
description: Data for
 publicationThis contains the data
 used to make Fig. 2, and all of the appendix figures. It can be analyzed
 using the Matlab code in the code_for_paper document.ssm_data.zipCode for paperThis is a zip file that contains all of the code needed to run the simulations described in our paper, and everything needed to analyze it and recreate the figures. It includes a README.code_for_JRSI.zip
DOI: 10.5061/dryad.1719
title: Data from: No effect of environmental heterogeneity on the maintenance of genetic variation in wing shape in Drosophila melanogaster

description: Theory suggests that heterogeneous environments should maintain more
 genetic variation within populations than homogeneous environments, yet
 experimental evidence for this effect in quantitative traits has been
 inconsistent. To examine the effect of heterogeneity on quantitative
 genetic variation, we maintained replicate populations of Drosophila
 melanogaster under treatments with constant temperatures, temporally
 variable temperature, or spatially variable temperature with either
 panmictic or limited migration. Despite observing differences in fitness
 and divergence in several wing traits between the environments, we did not
 find any differences in the additive genetic variance for any wing traits
 among any of the treatments. Although we found an effect of gene flow
 constraining adaptive divergence between cages in the limited migration
 treatment, it did not tend to increase within-population genetic variance
 relative to any of the other treatments. The lack of any clear and
 repeatable patterns of response to heterogeneous vs. homogeneous
 environments across several empirical studies suggests that a single
 general mechanism for the maintenance of standing genetic variation is
 unlikely; rather, the relative importance of putative mechanisms likely
 varies considerably from one trait and ecological context to another.
description: Wing landmarks and
 traits for parents and offspringyeamanchenwhitlock2010rawdata.csv
DOI: 10.5061/dryad.vr61ks2
title: Data from: Multi-level patterns in population genetics: variogram series detects a hidden isolation-by- distance- dominated structure of Scandinavian brown bears Ursus arctos

description: 1. Large-scale pattern-oriented approaches are useful to understand the
 multi-level processes that shape the genetic structure of a population.
 Matching the scales of patterns and putative processes is both a key to
 success and a challenge. 2. We have developed a simple statistical
 approach, based on variogram analysis, that identifies multiple spatial
 scales where the population pattern, in this case genetic structure, have
 highest expression (i.e. the spatial scales at which the strength of
 patterning of isolation-by-distance (IBD) residual variance reached
 maximum) from empirical data and, thus, at which scales it should be
 studied relative to the underlying processes. The approach is applicable
 to any spatially explicit pairwise data, including genetic, morphological
 or ecological distance or similarity of individuals, populations and
 ecosystems. To exemplify possible applications of this approach, we
 analysed microsatellite genotypes of 1,530 brown bears from Sweden and
 Norway. 3. The variogram approach identified two scales at which
 population structure was strongest, thus indicating two different
 scale-dependent processes: home-rangerelated processes at scales
 &lt;35 km, and subpopulation division at scales &gt;98 km. On the
 basis of this, we performed a scale-explicit analysis of genetic structure
 using DResD analysis and compared the results with those obtained by the
 Bayesian clustering implemented in structure. 4. We found that the genetic
 cluster identified in central Scandinavia by Structure is caused by IBD,
 with distinct gene flow barriers to the south and north. We discuss
 possible applications and research perspectives to further develop the
 approach.
description: Three tab-delimited
 matrices of genetic distances of brown bears, method validation and
 demonstrative dataThe data package consist
 of a zip-file, containing three tab-delimited matrices of genetic
 distances. The matrices are described in the supplementary data file S4,
 found in the supplemental information tab in the online version of the
 article and as README file associated with the data package:
 1."IBD_corrected_gen_distance_shuffled_in_50km.txt" = genetic
 distances corrected for IBD from the simulation fo small scale free
 dispersion; 2."IBD_corrected_genetic_distance_empirical.txt" =
 empirical matrix of genetic distances corrected for IBD;
 3."IBD_corrected_genetic_distance_resampled.txt" = genetic
 distances corrected for IBD and randomised over study area; scenario of
 globally even IBD.Archive.zip
DOI: 10.5061/dryad.9mc8j51
title: Data from: The evolution of floral signals in relation to range overlap in a clade of California Jewelflowers (Streptanthus s.l.)

description: Because of their function as reproductive signals in plants, floral traits
 experience distinct selective pressures related to their role in
 speciation, reinforcement, and prolonged coexistence with close relatives.
 However, few studies have investigated whether population-level processes
 translate into detectable signatures at the macroevolutionary scale. Here,
 we ask whether patterns of floral trait evolution and range overlap across
 a clade of California Jewelflowers reflect processes hypothesized to shape
 floral signal differentiation at the population level. We found a pattern
 of divergence in floral scent composition across the clade such that close
 relatives had highly disparate floral scents given their age. Accounting
 for range overlap with close relatives explained additional variation in
 floral scent over time, with sympatric species pairs having diverged more
 than allopatric species pairs given their age. However, three other floral
 traits (flower size, scent complexity, and flower color) did not fit these
 patterns, failing to deviate from a null Brownian Motion model of
 evolution. Together, our results suggest that selection for divergence
 among close relatives in the composition of floral scents may play a key,
 sustained role in mediating speciation and coexistence dynamics across
 this group, and that signatures of these dynamics may persist at the
 macroevolutionary scale.
description: consensus_treeTrimmed majority-rule consensus tree that was constructed using the full post-burnin distribution from Cacho et al., 2014 and consensus branch lengths calculated using the least squares method via the ‘consensus.edges’ function in the package “phytools.”1000_trees1,000 trimmed trees randomly drawn from the posterior distribution of Cacho et al., 2014.DataR_codeCode for running analysesCode_dryad.R
DOI: 10.5061/dryad.d1m830t
title: Data from: The rise of the ruling reptiles and ecosystem recovery from the Permian-Triassic mass extinction

description: One of the key faunal transitions in Earth history occurred after the
 Permo-Triassic mass extinction (ca. 252.2 Ma), when the previously obscure
 archosauromorphs (which include crocodylians, dinosaurs, and birds) become
 the dominant terrestrial vertebrates. Here, we place all known middle
 Permian–early Late Triassic archosauromorph species into an explicit
 phylogenetic context, and quantify biodiversity change through this
 interval. Our results indicate the following sequence of diversification:
 a morphologically conservative and globally distributed post-extinction
 ‘disaster fauna’; a major but cryptic and poorly sampled phylogenetic
 diversification with significantly elevated evolutionary rates; and a
 marked increase in species counts, abundance, and disparity
 contemporaneous with global ecosystem stabilisation some 5 million years
 after the extinction. This multiphase event transformed global ecosystems,
 with far-reaching consequences for Mesozoic and modern faunas.
description: Ezcurra and Butler
 Supplementary Data 1 Character listEzcurra and Butler
 Supplementary Data 2 Raw MatrixEzcurra and Butler
 Supplementary Data 3 Occurence and temporal dataEzcurra and Butler
 Supplementary Data 4 Matrix for phenotypic ratesEzcurra and Butler
 Supplementary Data 5 MPTsEzcurra and Butler
 Supplementary Data 6 Script to calculate phylogenetic
 diversity4
DOI: 10.5061/dryad.8q0p192
title: Data from: Ectopic fat obesity presents the greatest risk for incident type 2 diabetes: a population-based longitudinal study

description: Objectives: Obesity is a risk factor for type 2 diabetes mellitus. Among
 obesity, visceral fat obesity, and ectopic fat obesity, it has been
 unclear which has the greatest effect on incident diabetes. Methods: In
 this historical cohort study of 8430 men and 7034 women, we investigated
 the effect of obesity phenotypes on incident diabetes. Obesity, visceral
 fat obesity, and ectopic fat obesity were defined as body mass index
 ≥25 kg/m2, waist circumference ≥90 cm in men or ≥80 cm in women, and
 having fatty liver diagnosed by abdominal ultrasonography, respectively.
 We divided the participants into eight groups according to the presence or
 absence of the three obesity phenotypes. Results: During the median 5.8
 years follow-up for men and 5.1 years follow-up for women, 286 men and 87
 women developed diabetes. Compared to the non-obese group, the hazard
 ratios (HRs) of incident diabetes in the only-obesity, only-visceral fat
 obesity, only-ectopic fat obesity groups, and with all-three types of
 obesity group were 1.85 (95%CI 1.06–3.26, p = 0.05) in men and 1.79
 (0.24–13.21, p = 0.60) in women, 3.41 (2.51–4.64, p &lt; 0.001) in men
 and 2.30 (0.87–6.05, p = 0.12) in women, 4.74 (1.91–11.70,
 p &lt; 0.001) in men and 13.99 (7.23–27.09, p &lt; 0.001) in women
 and 10.5 (8.02–13.8, p &lt; 0.001) in men and 30.0 (18.0–50.0,
 p &lt; 0.001) in women. Moreover, the risk of incident diabetes of the
 groups with ectopic fat obesity were almost higher than that of the four
 groups without ectopic fat obesity. Conclusion: Ectopic fat obesity
 presented the greatest risk of incident type 2 diabetes.
description: Data set of Ectopic fat
 obesity presents the greatest risk for incident type 2 diabetes: a
 population-based longitudinal study.Data set Int J
 Obesity.xlsx
DOI: 10.5061/dryad.1hn0951
title: Data from: Genome-wide single nucleotide polymorphism scan suggests adaptation to urbanization in an important pollinator, the red-tailed bumblebee (Bombus lapidarius L.)

description: Urbanization is considered a global threat to biodiversity; the growth of
 cities results in an increase in impervious surfaces, soil and air
 pollution, fragmentation of natural vegetation, invasion of non-native
 species along with numerous environmental changes, including the heat
 island phenomenon. The combination of these effects constitutes a
 challenge for both the survival and persistence of many native species,
 whilst also imposing altered selective regimes. Here, using 110,314 single
 nucleotide polymorphisms (SNPs) generated by restriction-site associated
 DNA sequencing (RAD-seq), we investigated the genome-wide effects of
 urbanization on putative neutral and adaptive genomic diversity in a major
 insect pollinator, Bombus lapidarius, collected from nine German cities
 and nine paired rural sites. Overall, genetic differentiation among sites
 was low and there was no obvious genome-wide genetic structuring,
 suggesting absence of strong effects of urbanization on gene flow. We
 nevertheless identified several loci under directional selection, a subset
 of which was associated with urban land use, including the percentage of
 impervious surface, surrounding each sampling site. Overall, our results
 provide evidence of local adaptation to urbanization in the face of gene
 flow in a highly mobile insect pollinator.
description: VCF_file
DOI: 10.5061/dryad.qf737c2
title: Data from: Host plant distributions and climate interact to affect the predicted geographic distribution of a neotropical termite

description: Species distribution models (SDMs) have been widely used in the scientific
 literature. The majority of SDMs use climate data or other abiotic
 variables to forecast the potential distribution of a species in
 geographic space. Biotic interactions can affect the predicted spatial
 distribution of a species in many ways across multiple spatial scales, and
 incorporating these predictors in an SDM is a current topic in the
 scientific literature. Constrictotermes cyphergaster is a widely
 distributed termite in the Neotropics. This termite species nests in
 plants and more frequently nests in some arboreal species. Thus, this
 species is an excellent model to evaluate the influence of biotic
 interactions in SDMs. We evaluate the influences of climate and the
 geographic distribution of host plants on the potential distribution of C.
 cyphergaster. Three correlative models (MaxEnt) were built to predict the
 geographic distribution of the termite: (1) climate data, (2) biotic data
 (i.e., the geographic distribution of host plants), and (3) climate and
 biotic data. The models that were generated indicate that the potential
 geographic distribution of C. cyphergaster is concentrated in the Cerrado
 and Caatinga regions. In addition, path analysis and multiple regression
 revealed the importance of the direct effects of biological interactions
 in the geographic distribution of the termite, while climate affected the
 distribution of the termite mainly through indirect effects by influencing
 the geographic distributions of host plants. The current study endorses
 the importance of including biological interactions in SDMs. We recommend
 using biotic predictors in SDM studies of insect species, mainly because
 insects have important environmental services and biotic interaction data
 can improve the macroecological studies of this group.
description: Species occurrence
 dataOccurrence points
 (geographic coordinates) of termite Constrictotermes cyphergaster and
 eigth plants (Annona crassiflora, Aspidosperma pyrifolium, Caesalpinia
 pyramidalis, Caryocar brasiliense, Croton blanchetianus, Plathymenia
 reticulata, Pilosocereus gounellei, Qualea grandifloraspecies_coordinates.csvPrincipal Coordinates of Neighbour MatricesSuitabilities of the models generated by MaxEntPCNMs.txt
DOI: 10.5281/zenodo.18339503
title: Atoll biodiversity and environments: an AI-ready, interactive data portal for Indo-Pacific atolls

description: This FAIR² data portal provides harmonized information on biodiversity and environments for Indo-Pacific atolls. It collates species inventories using best available data for six terrestrial guilds (arthropods, birds, land crabs, native mammals, vascular plants, reptiles), and integrates biogeographic descriptors, land and reef habitat classifications, oceanographic variables, climate metrics, human population data, and information on historical military use. Outputs from models trained on these data are also provided, such as estimated breeding seabird population sizes for each atoll. In total, the different data layers provide information for all 310 Indo-Pacific atolls with permanent, emergent landforms, and comprise 90 standardized variables and 4,215 species records digitized from 677 literature sources, with species catalogues linked to GBIF, BOLD, and NCBI databases via unique taxon identifiers. The portal adheres to FAIR² principles (Findable, Accessible, Interoperable, Reusable, AI-readiness, Responsible AI) to support reproducible environmental analyses and machine-learning workflows. While biodiversity data coverage varies geographically and both environmental and biodiversity data lack temporal replication, the dataset provides the first centralized, interoperable baseline for information on atoll biotic and physical systems, enabling a framework for additional data layers, cross-layer analyses and supporting research, conservation, climate-risk assessment, and policy.
DOI: 10.5281/zenodo.18339504
title: Atoll biodiversity and environments: an AI-ready, interactive data portal for Indo-Pacific atolls

description: This FAIR² data portal provides harmonized information on biodiversity and environments for Indo-Pacific atolls. It collates species inventories using best available data for six terrestrial guilds (arthropods, birds, land crabs, native mammals, vascular plants, reptiles), and integrates biogeographic descriptors, land and reef habitat classifications, oceanographic variables, climate metrics, human population data, and information on historical military use. Outputs from models trained on these data are also provided, such as estimated breeding seabird population sizes for each atoll. In total, the different data layers provide information for all 310 Indo-Pacific atolls with permanent, emergent landforms, and comprise 90 standardized variables and 4,215 species records digitized from 677 literature sources, with species catalogues linked to GBIF, BOLD, and NCBI databases via unique taxon identifiers. The portal adheres to FAIR² principles (Findable, Accessible, Interoperable, Reusable, AI-readiness, Responsible AI) to support reproducible environmental analyses and machine-learning workflows. While biodiversity data coverage varies geographically and both environmental and biodiversity data lack temporal replication, the dataset provides the first centralized, interoperable baseline for information on atoll biotic and physical systems, enabling a framework for additional data layers, cross-layer analyses and supporting research, conservation, climate-risk assessment, and policy.