cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p2ngf1vm5
title: Soil inoculation alters leaf metabolic profiles in genetically identical plants

description:  Abiotic and biotic properties of soil can influence growth and
 chemical composition of plants. Although it is well-known that soil
 microbial composition can vary greatly spatially, how this variation
 affects plant chemical composition is poorly understood. We grew
 genetically identical Jacobaea vulgaris in sterilized
 soil inoculated with live soil collected from four natural grasslands and
 in 100% sterilized soil. Within each grassland we sampled eight plots,
 totalling 32 different inocula. Two samples per plot were collected,
 leading to three levels of spatial variation: within plot, between and
 within grasslands. The leaf metabolome was analysed with 1H
 Nuclear magnetic resonance spectroscopy (NMR) to investigate if
 inoculation altered the metabolome of plants and how this varied between
 and within grasslands. Inoculation led to changes in metabolomics profiles
 of J. vulgaris in two out of four sites. Plants grown in
 sterilized and inoculated soils differed in concentrations of malic acid,
 tyrosine, trehalose and two pyrrolizidine alkaloids (PA). Metabolomes of
 plants grown in inoculated soils from different sites varied in glucose,
 malic acid, trehalose, tyrosine and in one PA. The metabolome of plants
 grown in soils with inocula from the same site was more similar than with
 inocula from distant sites. We show that soil influences leaf metabolomes.
 Performance of aboveground insects often depends on chemical composition
 of plants. Hence our results imply that soil microbial communities, via
 affecting aboveground plant metabolomes, can impact aboveground
 plant-insect food chains but that it is difficult to make general
 predictions due to spatial variation in soil microbiomes.  
description: see manuscript for detailed descripton
DOI: 10.5061/dryad.fn2z34tps
title: Denitrification performance of pseudomonas fluorescens Z03 immobilized by GO modified PVA-SA gel bead at low temperature

description: Experimental data monitoring results.
DOI: 10.5061/dryad.95x69p8f9
title: Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes

description: Sex chromosomes have evolved from the same autosomes multiple times across
 vertebrates, suggesting that selection for recombination suppression has
 acted repeatedly and independently on certain genetic backgrounds. Here,
 we perform comparative genomics of a bird clade (larks and their sister
 lineage; Alaudidae and Panuridae) where multiple sex chromosome–autosome
 fusions appear to have formed expanded sex chromosomes. We detected the
 largest known avian sex chromosome (195.3 Mbp) and show that it originates
 from fusions between parts of four avian chromosomes: Z, 3, 4A and 5.
 Within these four chromosomes, we found evidence by using phylogenetic
 inference of five evolutionary strata where recombination had been
 suppressed at different time points, and showed that stratum age explained
 the divergence rate of Z–W gametologs. Next, we analysed chromosome
 content and found that chromosome 3 was significantly enriched for genes
 with predicted sex-related functions. Finally, we demonstrate extensive
 homology to sex chromosomes in other vertebrate lineages: chromosomes Z,
 3, 4A and 5 have independently evolved into sex chromosomes in fish (Z),
 turtles (Z, 5), lizards (Z, 4A), mammals (Z, 4A) and frogs (Z, 3, 4A, 5).
 Our results provide insights in and support for repeated evolution of sex
 chromosomes in vertebrates. 
description: This dataset contains genome assemblies for the following
 species: Alauda arvensis, Alauda razae, Eremophila alpestris and Panurus
 biarmicus. The DNA used for these assemblies was extracted som a single
 adult male per species, and paired-end sequenced (150 base pairs) on an
 Illumina HiSeqX machine. The sequence data was assembled using Spades
 v3.5.0 using kmer lengths 21,33,55,77 and 127 and setting --careful. The
 assemblies contains scaffolds longer than 1000 base pairs. 
 The data was generated for the study "Sex chromosome evolution in
 vertebrates supported by expanded avian sex chromosomes"
 by Hanna Sigeman, Suvi Ponnikas, Pallavi Chauhan, Elisa Dierickx, M. de L. Brooke and Bengt Hansson.  More information can be found in the manuscript. The raw reads used for the genome assemblies can be found on the NCBI Sequence Read Archive under the Bioproject accession PRJNA578893.
DOI: 10.5061/dryad.d2547d7zf
title: Chemical evidence of preserved collagen in a 54-million-year-old fish vertebrae

description: Collagens are the most abundant protein in the animal kingdom. Collagens
 form the structural framework of connective tissues such as bones, tendons
 and skin and play important biomechanical role in supporting tissue
 functions. The preservation of collagen in deep time is a topic of intense
 debate. Here we provide indisputable evidence of the presence of collagen
 in Early Eocene fish vertebrae using online pyrolysis-comprehensive two
 dimensional gas chromatography-time-of-flight mass spectrometry and
 immunofluorescence studies. The presence of cyclic dipeptides such as
 diketodipyrrole, 2,5-diketopiperazine of proline-proline and
 2,5-diketopiperazine of proline-glycine along with other nitrogen-bearing
 molecules in the pyrolysis products of the studied fossils unequivocally
 demonstrate that collagen can withstand degradation and diagenetic
 alteration. Immunofluorescence study also confirms the presence of
 collagen-I in the fossilized fish vertebrae. The present findings suggest,
 contrary to common opinion, that the preservation of collagen in
 fossilized soft tissues is not rare. We propose that one of the essential
 factors controlling preservation of collagen is the establishment of a
 suitable microenvironment within the fossil inhibiting diagenetic
 alteration including microbial decay.
description: Supplemental material for the associated article in
 <em>Palaeontology</em>.
DOI: 10.5061/dryad.rn8pk0p5k
title: Odors of non‐predatory species help prey moderate their risk assessment

description: Prey use contemporary information to update their risk estimation, and
 accordingly, optimize their anti-predator reactions. Conceptualization of
 this process is largely focused on information that reflects predator
 activity. We aimed to complement this unilateral view by testing whether
 prey also use cues of non-predatory species to update their risk
 perception. We focused our investigation on the desert isopod Hemilepistus
 reaumuri that reacts defensively to excavated soil mounds, even in the
 absence of direct predator cues. We located in the field 18 isopod burrows
 and surrounded each with six soil mounds. One mound remained odourless,
 and the other five were supplemented with odours of a major isopod
 predator, the golden scorpion, and four sympatric species that do not prey
 on isopods, but excavate soil. Isopods augmented their defensive responses
 toward mounds supplemented by scorpion odours and lessened their
 anti-predator reactions toward mounds with odours of herbivore rodents.
 Isopods’ responses to the odours of the two insectivorous species that do
 not eat isopods were similar to the reaction towards the odourless control
 mounds. Our results suggest that prey use non-predatory species cues to
 moderate their risk estimation. Therefore, we need to consider this
 potentially important source of information in studies of predator-prey
 interactions. Our findings also indicate cues of non-predatory species may
 not be adequate as control treatments to predator cues.
DOI: 10.82294/dvnwkjq5v
title: Entrevistas semiestructuradas. Territorio: Cali. Sector: Cultura. Año: 2025

description: A partir de un proceso de acompañamiento situado, se recopilaron testimonios por medio de entrevistas semiestructuradas durante el año 2025, las cuales indagaron sobre 4 categorías que describían la práctica en educación artística de docentes, cultores, sabedores de la enseñanza del arte, que hacían parte de los programas de formación en educación artística y cultural del sector Cultura (educación informal) en la ciudad de Cali.
DOI: 10.5061/dryad.np5hqbzp6
title: LeWoS: A universal leaf‐wood classification method to facilitate the 3D modelling of large tropical trees using terrestrial LiDAR

description: 1. Leaf-wood separation in terrestrial LiDAR data is a prerequisite for
 non-destructively estimating biophysical forest properties such as
 standing wood volumes and leaf area distributions. Current methods have
 not been extensively applied and tested on tropical trees. Moreover, their
 impacts on the accuracy of subsequent wood volume retrieval were rarely
 explored. 2. We present LeWoS, a new fully automatic tool to automate the
 separation of leaf and wood components, based only on geometric
 information at both the plot and individual tree scales. This data-driven
 method utilizes recursive point cloud segmentation and regularization
 procedures. Only one parameter is required, which makes our method easily
 and universally applicable to data from any LiDAR technology and forest
 type. 3. We conducted a two-fold evaluation of the LeWoS method on an
 extensive data set of 61 tropical trees. We first assessed the point-wise
 classification accuracy, yielding a score of 0.91 ± 0.03 in average.
 Secondly, and for the first time, we evaluated the impact of the proposed
 method on 3D tree models by cross-comparing estimates in wood volume and
 branch length with those based on manually separated wood points. This
 comparison showed similar results, with relative biases of less than 9%
 and 21% on volume and length, respectively. 4. LeWoS allows an automated
 processing chain for non-destructive tree volume and biomass estimation
 when coupled with 3D modelling methods. The average processing time on a
 laptop was 90s for 1 million points. We provide LeWoS as an open source
 tool with an end-user interface, together with a large data set of
 labelled 3D point clouds from contrasting forest structures. This study
 closes the gap for stand volume modelling in tropical forests where leaf
 and wood separation remain a crucial challenge.
description: Manually labelled point clouds.
 Format: x, y, z, leaf/wood label (1 for wood,
 0 for leaf)
DOI: 10.5061/dryad.rjdfn2z67
title: Data from: Bayesian modelling reveals host genetics associated with rumen microbiota jointly influence methane emission in dairy cows

description: Reducing methane emissions from livestock production is of great
 importance for the sustainable management of the Earth’s environment.
 Rumen microbiota play an important role in producing biogenic methane.
 However, knowledge of how host genetics influences variation in ruminal
 microbiota and their joint effects on methane emission is limited. We
 analyzed data from 750 dairy cows, using a Bayesian model to
 simultaneously assess the impact of host genetics and microbiota on host
 methane emission. We estimated that host genetics and microbiota explained
 24% and 7%, respectively, of variation in host methane levels. In this
 Bayesian model, one bacterial genus explained up to 1.6% of the total
 microbiota variance. Further analysis was performed by a mixed linear
 model to estimate variance explained by host genomics in abundances of
 microbial genera and operational taxonomic units (OTU). Highest estimates
 were observed for a bacterial OTU with 33%, for an archaeal OTU with 26%,
 and for a microbial genus with 41% heritability. However, after multiple
 testing correction for the number of genera and OTUs modelled, none of the
 effects remained significant. We also used a mixed linear model to test
 effects of individual host genetic markers on microbial genera and OTUs.
 In this analysis, genetic markers inside host genes ABS4 and DNAJC10 were
 found associated with microbiota composition. We show that a Bayesian
 model can be utilized to model complex structure and relationship between
 microbiota simultaneously and their interaction with host genetics on
 methane emission. The host genome explains a significant fraction of
 between-individual variation in microbial abundance. Individual microbial
 taxonomic groups each only explain a small amount of variation in methane
 emissions. The identification of genes and genetic markers suggests that
 it is possible to design strategies for breeding cows with desired
 microbiota composition associated with phenotypes.
description: Please see the methods part of the paper
DOI: 10.5061/dryad.j9kd51c7j
title: Data from: Differential patterns of floristic phylogenetic diversity across a post‐glacial landscape

description: Aim In this study, we explored spatial patterns of phylogenetic diversity
 (PD) and endemism in the flora of Norway and tested hypothesized
 post‐glacial environmental drivers of PD, including temperature,
 precipitation, edaphic factors and time since glacial retreat. Location
 Norway. Taxon Vascular plants (Trachaeophyta). Methods We produced a
 multi‐locus maximum‐likelihood (ML) phylogeny using a combination of newly
 produced DNA sequences from herbarium specimens and sequences available
 from public repositories. We combined the phylogeny with species
 occurrence data to estimate PD and phylogenetic endemism across Norway,
 using a spatial randomization to judge statistical significance. We used
 multiple‐model inference to identify environmental variables that
 contributed the most to the patterns of PD. Finally, we estimated
 phylogenetic turnover and used this to identify Norwegian plant
 assemblages in terms of composition and evolutionary history. Results Our
 ML phylogeny contained 87% of all currently described native Norwegian
 vascular plants. Assemblages were phylogenetically overdispersed in warmer
 and wetter regions of Norway, as well as in regions with a longer
 post‐glacial history. In cold and dry regions, plant assemblages were
 phylogenetically clustered, and characterized by neo‐endemism, while the
 mild and wet regions were characterized by both paleo‐ and neo‐endemism.
 PD was positively correlated with summer temperature and habitat
 heterogeneity, and peaked in the southeast of Norway. Main conclusions
 Both contemporary ecological factors (climate and habitat heterogeneity),
 and post‐glacial history seem to have shaped the phylogenetic structure of
 the flora of Norway. The flora in the far north of Norway appear to be a
 result of recent diversification while the coastal regions are assemblages
 of deeper lineages. Our results suggest that there is an evolutionary
 signal in the distribution of the Norwegian vascular flora.
description: Occurrence data for the native Norwegian vascular plant species
 obtained from the Global Biodiversity Information Facility (GBIF).
 The dataset contains 3,597,865 occurrences.
DOI: 10.5061/dryad.h9w0vt4db
title: Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry

description: Color pattern mimicry in Heliconius butterflies is a classic case study of
 complex trait adaptation via selection on a few large effect genes.
 Association studies have linked color pattern variation to a handful of
 noncoding regions, yet the presumptive cis-regulatory elements (CREs) that
 control color patterning remain unknown. Here we combine chromatin assays,
 DNA sequence associations, and genome editing to functionally characterize
 5 cis-regulatory elements of the color pattern gene optix. We were
 surprised to find that the cis-regulatory architecture of optix is
 characterized by pleiotropy and regulatory fragility, where deletion of
 individual cis-regulatory elements has broad effects on both color pattern
 and wing vein development. Remarkably, we found orthologous cis-regulatory
 elements associate with wing pattern convergence of distantly related
 comimics, suggesting that parallel coevolution of ancestral elements
 facilitated pattern mimicry. Our results support a model of color pattern
 evolution in Heliconius where changes to ancient, multifunctional
 cis-regulatory elements underlie adaptive radiation.
DOI: 10.5061/dryad.nzs7h44mp
title: Variation in community structure of gall-inducing insects associated with a tropical plant supports the hypothesis of competition in stressful habitats

description: Environmental factors act as drivers of species coexistence or
 competition. Mesic environments favor the action of parasites and
 predators on gall communities, while the factors that determine the
 structure of gall communities in xeric environments remain unknown. We
 evaluated the structure of gall communities along an environmental
 gradient defined by intrinsic plant characteristics, soil fertility and
 aridity, and investigated the role of competition as a structuring force
 of gall communities in xeric environments. We created null models to
 compare observed and simulated patterns of co-occurrence of galls and used
 the C-score index to assess community aggregation or segregation. We used
 the NES C-score (standardized C-score) to compare patterns of
 co-occurrence with parameters of environmental quality. Xeric environments
 had poorer and more arid soils and more-sclerophyllous plants than mesic
 environments, which was reflected in the distribution patterns of gall
 communities. Values of the C-score index revealed a segregated
 distribution of gall morphospecies in xeric environments, but a random
 distribution in mesic environments. The low availability of resources for
 oviposition and the high density of gallers in xeric environments
 reinforce interspecific competition as an important structuring force for
 gall communities in these environments.
description: This study was developed at seven sites with the presence of a population of <i>C. langsdorfii</i>, each located in a different plant formation. The sites were chosen to include a gradient of environmental stress, ranging from dry environments, such as rupestrian grasslands and ironstone outcrops, to humid environments, such as Atlantic forest and riparian forest. The distance between sampling areas ranges from 90 to 500 km. We obtained meteorological data for each of the studied sites for the 24 months preceding the study — a period corresponding to vegetative investment by each plant.
DOI: 10.15139/s3/gbxgv6
title: Data Management and Sharing Plan for: Multi-Site Neuroimage Harmonization for Personalized Brain Disorder Analysis

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.jwstqjq4v
title: Climate structures bison dietary quality and composition at the continental scale

description: These data are generated from bison fecal material collected in the summer
 of 2018. Samples have been analyzed for dietary quality (NIRS
 spectroscopy), dietary composition (NGS metabarcoding with c-h trnL
 primers), and elemental concentration (ICP‐AES).
DOI: 10.5061/dryad.dbrv15dx1
title: TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

description: Alu retrotransposons account for more than 10% of the human genome, and
 insertions of these elements create structural variants segregating in
 human populations. Such polymorphic Alu are powerful markers to understand
 population structure, and they represent variants that can greatly impact
 genome function, including gene expression. Accurate genotyping of Alu and
 other mobile elements has been challenging. Indeed, we found that Alu
 genotypes previously called for the 1000 Genomes Project are sometimes
 erroneous, which poses significant problems for phasing these insertions
 with other variants that comprise the haplotype. To ameliorate this issue,
 we introduce a new pipeline -- TypeTE -- which genotypes Alu insertions
 from whole-genome sequencing data. Starting from a list of polymorphic
 Alus, TypeTE identifies the hallmarks (poly-A tail and target site
 duplication) and orientation of Alu insertions using local re-assembly to
 reconstruct presence and absence alleles. Genotype likelihoods are then
 computed after re-mapping sequencing reads to the reconstructed alleles.
 Using a ‘gold standard’ set of PCR-based genotyping of &gt;200 loci,
 we show that TypeTE improves genotype accuracy from 83% to 92% in the 1000
 Genomes dataset. TypeTE can be readily adapted to other retrotransposon
 families and brings a valuable toolbox addition for population genomics.
DOI: 10.5061/dryad.x95x69pd8
title: Data from: The genomic impact of historical hybridization with massive mitochondrial DNA introgression

description: Background: The extent to which selection determines interspecific
 patterns of genetic exchanges enlightens the role of adaptation in
 evolution and speciation. Often reported extensive interspecific
 introgression could be selection-driven, but also result from demographic
 processes, especially in cases of invasive species replacements, which can
 promote introgression at their front. Because invasion and selective
 sweeps similarly mold variation, population genetics evidence for
 selection can only be gathered in an explicit demographic framework. The
 Iberian hare, Lepus granatensis, displays in its northern range extensive
 mitochondrial DNA introgression from L. timidus, an arctic/boreal species
 that it replaced locally after the last glacial maximum. We use
 whole-genome sequencing to infer geographic and genomic patterns of
 nuclear introgression and fit a neutral model of species replacement with
 hybridization, allowing us to evaluate how selection influenced
 introgression genome-wide, including for mtDNA. Results: Although the
 average nuclear and mtDNA introgression patterns are strongly contrasted,
 they fit a single neutral model of post-glacial invasive replacement of
 timidus by granatensis. Outliers of elevated introgression include several
 genes related to immunity, spermatogenesis, and mitochondrial metabolism.
 Introgression is reduced on the X-chromosome and in low recombining
 regions. Conclusion: General nuclear and mtDNA patterns of introgression
 can be explained by purely demographic processes. Hybrid incompatibilities
 and interplay between selection and recombination locally modulate levels
 of nuclear introgression. Selection promoted introgression of some genes
 involved in conflicts, either interspecific (parasites) or possibly
 cytonuclear. In the latter case, nuclear introgression could mitigate the
 potential negative effects of alien mtDNA on mitochondrial metabolism and
 male-specific traits.
description: Hare (<em>Lepus</em>) pseudo-reference genome built
 through iterative mapping of sequencing reads from <em>Lepus
 timidus</em>, <em>Lepus granatensis</em> and
 <em>Lepus americanus</em> on the European rabbit
 (<em>Oryctolagus cuniculus</em>) genome template (available
 from
 ftp://ftp.ensembl.org/pub/release-80/fasta/oryctolagus_cuniculus/dna/).