cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.935qb
title: Data from: Ecological fidelity of functional traits based on species presence-absence in a modern mammalian bone assemblage (Amboseli, Kenya)

description: Comparisons between modern death assemblages and their source communities
 have demonstrated fidelity to species diversity across a variety of
 environments and taxonomic groups. However, differential species
 preservation and collection (including body-size bias) in both modern and
 fossil death assemblages may still skew the representation of other
 important ecological characteristics. Here, we move beyond live-dead
 taxonomic fidelity and focus on the recovery of functional ecology (how
 species interact with their ecosystem) at the community level for a
 diverse non-volant mammal community (87 species; Amboseli, Kenya). We use
 published literature to characterize species, using four functional traits
 and their associated categorical attributes (i) dietary mode (11
 attributes; e.g., browser, grazer), (ii) preferred feeding habitat (16
 attributes; e.g., grassland, woodland), (iii) preferred sheltering habitat
 (17 attributes; e.g., grassland, underground cavity), and (iv) activity
 time (7 attributes; e.g., diurnal, nocturnal, nocturnally dominated
 crepuscular). For each functional ecological trait we compare the death
 assemblage's recovered richness and abundance structure of
 constituent functional attributes with those of the source community,
 using Jaccard similarity, Spearman's rho, and the Probability of
 Interspecific Encounter (evenness). We use Monte Carlo simulations to
 evaluate whether these empirical comparisons are significantly different
 from expectations calculated from randomized sampling of species from the
 source community. Results indicate that although the Amboseli death
 assemblage is significantly overrepresented by large-bodied species
 relative to the Amboseli source community, it captures many functional
 dimensions of the ecosystem within expectations of a randomized collection
 of species. Additional resampling simulations and logistic regressions
 further illustrate that the size bias inherent to the Amboseli death
 assemblage is not a major driver of deviations between the functional
 ecological properties of the death assemblage and its source community.
 Finally, the Amboseli death assemblage also enhances our understanding of
 the mammal community by adding nine species and two functional attributes
 previously unknown from the ecosystem.
description: Miller et al 2014
 Paleobiology SOM and AppendicesSupplemental Online
 Materials and Appendices for "Ecological fidelity of functional
 traits based on species presence-absence in a modern mammalian bone
 assemblage (Amboseli, Kenya)."
DOI: 10.5061/dryad.05k14
title: Data from: A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms

description: Symbiotic associations occur in every habitat on earth, but we know very
 little about their evolutionary histories. Current models of trait
 evolution cannot adequately reconstruct the deep history of symbiotic
 innovation, because they assume homogenous evolutionary processes across
 millions of years. Here we use a recently developed, heterogeneous and
 quantitative phylogenetic framework to study the origin of the symbiosis
 between angiosperms and nitrogen-fixing (N2) bacterial symbionts housed in
 nodules. We compile the largest database of global nodulating plant
 species and reconstruct the symbiosis’ evolution. We identify a single,
 cryptic evolutionary innovation driving symbiotic N2-fixation evolution,
 followed by multiple gains and losses of the symbiosis, and the subsequent
 emergence of ‘stable fixers’ (clades extremely unlikely to lose the
 symbiosis). Originating over 100 MYA, this innovation suggests deep
 homology in symbiotic N2-fixation. Identifying cryptic innovations on the
 tree of life is key to understanding the evolution of complex traits,
 including symbiotic partnerships.
description: Werner_NFixFull angiosperm symbiotic N2-fixation database. For full details, please see ReadMe file.WernerNFix_README_Update.txt
DOI: 10.5061/dryad.627ck
title: Data from: Investigating sensitivity of phylogenetic community structure metrics using North American desert bats

description: A relatively recent approach to characterizing structure of natural
 communities is to use phylogenies of species pools to compare patterns of
 relatedness between real and simulated communities. Such an approach can
 provide mechanistic insights into structure. Despite popularity of
 phylogenetic approaches, we do not yet fully understand how phylogenetic
 community structure (PCS) metrics might be impacted by changes to the
 phylogeny or community membership data from which they are calculated. We
 investigate metric sensitivity and examine PCS of bats from the 4 great
 desert regions of North America. We inferred a phylogeny of the regional
 species pool to calculate PCS metrics using community membership data
 delimited using 3 different methods. We also randomized our phylogeny to
 determine how reasonable changes to the tree affect PCS metrics. Overall,
 PCS metrics are quite robust to moderate changes in the phylogeny from
 which they are calculated. These metrics also are fairly insensitive to
 our 3 methods of delimiting communities. Additionally, we found that in
 general, communities are significantly phylogenetically clustered,
 suggesting habitat filtering has been important in community assembly.
description: Capture and collection
 dataGeographic coordinates
 and number of bats captured/collected at sites in North American
 desertsCommunity
 dataCommunity data matrices
 for each delimitation method for each desertTree
 filesTree files used in
 phylogenetic community structure analyses and permuted trees used in
 sensitivity analyses
DOI: 10.5061/dryad.c4s8s
title: Data from: Effects of long term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach

description: In order to understand the fine scale effects of changes in nutrient
 availability on eukaryotic soil microorganisms communities, a multiple
 barcoding approach was used to analyse soil samples from four different
 treatments in a long term fertilization experiment. We performed
 PCR-amplification on soil DNA with primer pairs specifically targeting the
 18S rRNA genes of all eukaryotes and three protist groups (Cercozoa,
 Chrysophyceae-Synurophyceae and Kinetoplastida) as well as the ITS gene of
 fungi and the 23S plastid rRNA gene of photoautotrophic microorganisms.
 Amplicons were pyrosequenced and a total of 88,706 quality filtered reads
 were clustered in to 1,232 operational taxonomic units (OTU) across the
 six datasets. Comparisons of the taxonomic coverage achieved based on
 overlapping assignment of OTUs revealed that half of the eukaryotic taxa
 identified were missed by the universal eukaryotic barcoding marker. There
 was only little differences in OTU richness observed between organic-
 (farmyard manure), mineral- and non-fertilized soils. However, the
 community compositions appeared to be strongly structured by organic
 fertilization in all datasets other than that generated using the
 universal eukaryotic 18S rRNA primers, whereas mineral fertilization had
 only a minor effect. In addition, a co-occurrence based network analysis
 revealed complex potential interaction patterns between OTUs from
 different trophic levels, e.g. between fungivorous flagellates and fungi.
 Our results demonstrate that changes in pH, moisture and organic nutrients
 availability caused shifts in the composition of eukaryotic microbial
 communities at multiple trophic levels.
description: Trimmed_Subsampled_ReadsGood quality reads for all six datasets.Pipeline_output_tablesOTU matrices, taxonomic tables and phylogenetical distances matrices for all six datasets.cer.barcodesBarcodes labeling cercozoan sequences libraries.script_bioinformatic_analyses_cerExample bioinformatic pipeline to analyse the cercozoan dataset raw sequences.script_alternative_clustering_methods_cerAlternative methods to cluster sequences into OTUs.script_threshold_cerExample analysis to determine the clustering threshold approaching species level for a new barcoding marker.script_fig_cerProduce figure output of the previous script.script_diversity_statisticsMain statistical analyses of diversity patterns.soil_parametersAdditional measured soil parameters.script_cooccurence_analysisIdentified non-random co-occurrences and exclusions among all six datasets OTUs.script_phyla_networkIdentified non-random co-occurrences and exclusions among OTUs grouped at phylum level.binCollection of bash and R scripts requested to execute the previous scripts.READMEDescription of all files provided in this data package.
DOI: 10.5061/dryad.qb251
title: Data from: Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

description: The molecular era has fundamentally reshaped our knowledge of the
 evolution and diversification of angiosperms. One outstanding question is
 the phylogenetic placement of Amborella trichopoda Baill., commonly
 thought to represent the first lineage of extant angiosperms. Here, we
 leverage publicly available data and provide a broad coalescent-based
 species tree estimation of 45 seed plants. By incorporating 310 nuclear
 genes, our coalescent analyses strongly support a clade containing
 Amborella plus water lilies (i.e., Nymphaeales) that is sister to all
 other angiosperms across different nucleotide rate partitions. Our results
 also show that commonly applied concatenation methods produce strongly
 supported, but incongruent placements of Amborella: slow-evolving
 nucleotide sites corroborate results from coalescent analyses, while
 fast-evolving sites place Amborella alone as the first lineage of extant
 angiosperms. We further explored the performance of coalescent versus
 concatenation methods using nucleotide sequences simulated on i) the two
 alternate placements of Amborella with branch lengths and substitution
 model parameters estimated from each of the 310 nuclear genes, and ii)
 three hypothetical species trees that are topologically identical except
 with respect to the degree of deep coalescence and branch lengths. Our
 results collectively suggest that the Amborella alone placement inferred
 using concatenation methods is likely misled by fast-evolving sites. This
 appears to be exacerbated by the combination of long branches in stem
 group angiosperms, Amborella, and Nymphaeales with the short internal
 branch separating Amborella and Nymphaeales. In contrast, coalescent
 methods appear to be more robust to elevated substitution rates.
description: Supplementary
 materialThis PDF file includes:
 Figures S1–S11 Tables S1–S8Supplementary_material.pdfS2. Nucleotide alignments of 45 plastid genes in PHYLIP format.plastid.zipS1. Nucleotide alignments of 310 nuclear genes in PHYLIP format.nuclear.zip
DOI: 10.5061/dryad.q827h
title: Data from: The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria

description: C4 photosynthesis represents a most remarkable case of convergent
 evolution of a complex trait, which includes the reprogramming of the
 expression patterns of thousands of genes. Anatomical, physiological, and
 phylogenetic and analyses as well as computational modeling indicate that
 the establishment of a photorespiratory carbon pump (termed C2
 photosynthesis) is a prerequisite for the evolution of C4. However, a
 mechanistic model explaining the tight connection between the evolution of
 C4 and C2 photosynthesis is currently lacking. Here we address this
 question through comparative transcriptomic and biochemical analyses of
 closely related C3, C3-C4, and C4 species, combined with Flux Balance
 Analysis constrained through a mechanistic model of carbon fixation. We
 show that C2 photosynthesis creates a misbalance in nitrogen metabolism
 between bundle sheath and mesophyll cells. Rebalancing nitrogen metabolism
 requires anaplerotic reactions that resemble at least parts of a basic C4
 cycle. Our findings thus show how C2 photosynthesis represents a
 pre-adaptation for the C4 system, where the evolution of the C2 system
 establishes important C4 components as a side effect.
description: Quantitative information
 for Flaveria leaf transcriptome reads mapped in a cross species approach
 onto the reference transcriptome from Arabidopsis
 thaliana.The transcriptomes of
 mature leaves from nine Flaveria species with different type
 photosynthesis (C3, C4 and C3-C4 intermediate) were sequenced by Illumina
 sequencing leading to 30 to 58 million reads per species and experiment.
 Four independent experiments were performed and the reads were mapped in a
 cross species approach onto the minimal set of Arabidopsis thaliana coding
 sequences in the protein space using the BLAST-like alignment tool BLAT.
 In the table the normalized read counts in rpkm (reads per million and
 kilo base) for all Arabidopsis cds are give alongside the TAIR and MapMan
 annotations of the respective Arabidopsis genes.Figure2-source
 data2.xlsx
DOI: 10.5281/zenodo.18390675
title: Genetic variance in spider mites reveals trade-offs: lines with higher growth rate suffer stronger competition but exert stronger reproductive interference
DOI: 10.5061/dryad.40rk0
title: Data from: Stress response or beneficial temperature acclimation: transcriptomic signatures in Antarctic fish (Pachycara brachycephalum)

description: Research on the thermal biology of Antarctic marine organisms has
 increased awareness of their vulnerability to climate change, as a
 flipside of their adaptation to life in the permanent cold and their
 limited capacity to acclimate to variable temperatures. Here, we employed
 a species–specific microarray of the Antarctic eelpout, Pachycara
 brachycephalum to identify long-term shifts in gene expression after 2
 months of acclimation to six temperatures between -1°C and 9°C. Changes in
 cellular processes comprised signalling, post-translational modification,
 cytoskeleton remodelling, metabolic shifts and alterations in the
 transcription as well as translation machinery. The magnitude of
 transcriptomic responses paralleled the change in whole animal
 performance. Optimal growth at 3°C occurred at a minimum in gene
 expression changes indicative of a balanced steady state. The
 up–regulation of ribosomal transcripts at 5°C and above was accompanied by
 the transcriptomic activation of differential protein degradation
 pathways, from proteasome-based degradation in the cold towards lysosomal
 protein degradation in the warmth. From 7°C upwards increasing transcript
 levels representing heat shock proteins and an acute inflammatory response
 indicate cellular stress. Such patterns may contribute to a warm-induced
 energy deficit and a strong weight loss at temperatures above 6°C.
 Together, cold or warm acclimation led to specific cellular rearrangements
 and the progressive development of functional imbalances beyond the
 optimum temperature. The observed temperature–specific expression profiles
 reveal the molecular basis of thermal plasticity and refine present
 understanding of the shape and positioning of the thermal performance
 curve of ectotherms on the temperature scale.
description: animal
 dataThis file contains
 growth and sampling data of fish under study as well as quality parameters
 of RNA samples that were used in the expression
 analysis.animal_data.txtPb_nr_annotated_Blast2GOThis file contains sequence annotations from the nr-database of all represented transcripts on the array. The file can be loaded using the open source software Blast2GO. (http://www.blast2go.com/b2ghome)Pb_swissProt_annotated_Blast2GOThis file contains sequence annotations from the SwissProt-database of all represented transcripts on the array. The file can be loaded using the open source software Blast2GO. (http://www.blast2go.com/b2ghome)
DOI: 10.5281/zenodo.16753844
title: Genetic variance in spider mites reveals trade-offs: lines with higher growth rate suffer stronger competition but exert stronger reproductive interference
DOI: 10.15468/dl.vcqf4q
title: Occurrence Download

description: A dataset containing 2782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is d3f94e8a-bb06-4d2b-89a6-6cd66abfa66c",
 "TaxonKey is Crex crex"
 ]
}

 The dataset includes 2782 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001616-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2nk64
title: Data from: Activation of the Arabidopsis thaliana immune system by combinations of common ACD6 alleles

description: A fundamental question in biology is how multicellular organisms
 distinguish self and non-self. The ability to make this distinction allows
 animals and plants to detect and respond to pathogens without triggering
 immune reactions directed against their own cells. In plants,
 inappropriate self-recognition results in the autonomous activation of the
 immune system, causing affected individuals to grow less well. These
 plants also suffer from spontaneous cell death, but are at the same time
 more resistant to pathogens. Known causes for such autonomous activation
 of the immune system are hyperactive alleles of immune regulators, or
 epistatic interactions between immune regulators and unlinked genes. We
 have discovered a third class, in which the Arabidopsis thaliana immune
 system is activated by interactions between natural alleles at a single
 locus, ACCELERATED CELL DEATH 6 (ACD6). There are two main types of these
 interacting alleles, one of which has evolved recently by partial
 resurrection of a pseudogene, and each type includes multiple functional
 variants. Most previously studies hybrid necrosis cases involve rare
 alleles found in geographically unrelated populations. These two types of
 ACD6 alleles instead occur at low frequency throughout the range of the
 species, and have risen to high frequency in the Northeast of Spain,
 suggesting a role in local adaptation. In addition, such hybrids occur in
 these populations in the wild. The extensive functional variation among
 ACD6 alleles points to a central role of this locus in fine-tuning
 pathogen defenses in natural populations.
description: RADseq data and ACD6
 genotype for Costa Brava accessionsGenotypic information
 obtained by RADseq for 1688 accessions collected in the Costa Brava region
 of Spain in Spring 2012. Reads were processed with SHORE (ver. 0.9) and
 mapped to the reference sequence, Col-0, with BWA, using the default
 parameters and allowing 5% mismatches. All mapped reads were converted
 into BAM format by Samtools (ver. 0.1.18) for further analysis. Single
 nucleotide polymorphism (SNP) genotypes were generated using the
 subprogram UnifiedGenotyper implemented in GATK (ver. 2.3-6). The genotype
 at the ACD6 locus is reported for each individual as well, as determined
 by direct Sanger sequencing of the transmembrane domain of
 ACD6.Todesco_2014_RADseq_and_ACD6genotyping.csv
DOI: 10.82294/dvnazeypk
title: COPUS. Territorio: Cali. Sector: Educación. Año: 2025
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2025 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Educación (educación formal) en la ciudad de Cali.
DOI: 10.5061/dryad.dv4qk
title: Data from: Phylogenetic measures of biodiversity and neo- and paleo-endemism

description: Understanding spatial patterns of biodiversity is critical for
 conservation planning, particularly given rapid habitat loss and
 human-induced climatic change. Diversity and endemism are typically
 assessed by comparing species ranges across regions. However,
 investigation of patterns of species diversity alone misses out on the
 full richness of patterns that can be inferred using a phylogenetic
 approach. Here, using Australian Acacia as an example, we show that the
 application of phylogenetic methods, particularly two new measures,
 relative phylogenetic diversity and relative phylogenetic endemism,
 greatly enhances our knowledge of biodiversity across both space and time.
 We found that areas of high species richness and species endemism are not
 necessarily areas of high phylogenetic diversity or phylogenetic endemism.
 We propose a new method called categorical analysis of neo- and
 paleo-endemism (CANAPE) that allows, for the first time, a clear,
 quantitative distinction between centres of neo- and paleo-endemism,
 useful to the conservation decision-making process.
description: Point_distribution_Australian_Phylogenetic_Diversity_Acacia.csv file with distribution data (herbarium records) for 508 Australian Acacia species, Australia
DOI: 10.5061/dryad.j86v9
title: Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan

description: Wild populations of Atlantic salmon have declined worldwide. While the
 causes for this decline may be complex and numerous, increased mortality
 at sea is predicted to be one of the major contributing factors. Examining
 the potential changes occurring in the genome-wide composition of
 populations during this migration has the potential to tease apart some of
 the factors influencing marine mortality. Here, we genotyped 5568 SNPs in
 Atlantic salmon populations representing two distinct regional genetic
 groups and across two cohorts to test for differential allelic and
 genotypic frequencies between juveniles (smolts) migrating to sea and
 adults (grilses) returning to freshwater after one year at sea. Given the
 complexity of the traits potentially associated with sea mortality, we
 contrasted the outcomes of a single-locus FST based genome scan method
 with a new multi-locus framework to test for genetically-based
 differential mortality at sea. While numerous outliers were identified by
 the single-locus analysis, no evidence for parallel, temporally repeated
 selection was found. In contrast, the multi-locus approach detected
 repeated patterns of selection for a multi-locus group of 34 co-varying
 SNPs in one of the two populations. No significant pattern of selective
 mortality was detected in the other population, suggesting different
 causes of mortality among populations. These results first support the
 hypothesis that selection mainly causes small changes in allele
 frequencies among many co-varying loci rather than a small number of
 changes in loci with large effects. They also point out that moving away
 from the a strict “selective sweep paradigm” towards a multi-locus
 genetics framework may be a more useful approach for studying the genomic
 signatures of natural selection on complex traits in wild populations.
description: Genotypes_PowerMarkerGenotype file for 2923 SNPs retained for analyses performed in the article.Donnees_genet SAS 2923Input file for SAS analysesSAS Discriminant AnalysisSAS analyses ScriptsScript_covariance_allelic_effectScript for covariance of allelic effect analysisDonnees_genet_2923One of two input files for the delta p analysisDelta_PTwo of two input files for delta p analysisScript_Delta pScript for delta p analysis (figure construction)