cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m463f7k
title: Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

description: Modern tomatoes have narrow genetic diversity limiting their improvement
 potential. We present a tomato pan-genome constructed using genome
 sequences of 725 phylogenetically and geographically representative
 accessions, revealing 4,873 genes absent from the reference genome.
 Presence/absence variation analyses reveal substantial gene loss and
 intense negative selection of genes and promoters during tomato
 domestication and improvement. Lost or negatively selected genes are
 enriched for important traits, especially disease resistance. We identify
 a rare allele in TomLoxC promoter selected against during domestication.
 QTL mapping and analysis of transgenic plants reveal a novel role for
 TomLoxC in apocarotenoid production, which contributes to desirable tomato
 flavor. In orange-stage fruit, accessions harboring both the rare and
 common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than
 those homozygous for either, and are resurgent in modern tomatoes. The
 tomato pan-genome adds depth and completeness to the reference genome, and
 is useful for future biological discovery and breeding.
description: SNPs called from the
 RNA-Seq data of RILsSNPs called from the
 RNA-Seq data of RILs and their two parents, S. lycopersicum breeding line
 NC EBR-1 and S. pimpinellifolium accession LA2093. The file is in vcf
 format.RIL_SNPs.vcf.gzTomato non-reference genome sequencesNon-reference genome sequences of tomato pan-genomeTomato_NonRef.fa.gzgene models in non-reference genomegene models annotated in the non-reference sequences of the tomato pan-genome, in gff3 formatTomato_NonRef.gff.gz
DOI: 10.5281/zenodo.18390447
title: Input data for Coalispr

description: Datasets to illustrate the use of Coalispr, a Python tool to clean up (small) RNA sequencing results. Coalispr can visualize over 100 bedgraphs in one panel and helps to retrieve read counts from associated alignment files without reliance on reference features like GTF annotations. The archives contain bedgraphs (also in processed form), reference data, bam-alignment files for counting, and descriptions for experiments, ncRNAs and genes.
description: Datasets of STAR-mapped RNA-seq reads for analysis with Coalispr as described in the essay "Bio informatics: Integrate negative controls to get the good data." Preparation and analysis are detailed in the tutorials "Cryptococcus siRNAs", and "Mouse miRNAs".

Unprocessed fungal datasets were retrieved from GEO GSE128009 and GSE43363 and have been published by Dumesic et al. 2013 (DOI 10.1016/j.cell.2013.01.046) and Burke et al. 2019 (DOI 10.1534/g3.119.400330). Additional resources were gene-annotations from Wallace et.al 2020 (DOI 10.1093/nar/gkaa060) and data at GEO GSE133125.

Mouse data have been described in Sarshad et al. 2018 (DOI 10.1016/j.molcel.2018.07.020) and raw miRNA sequencing reads were kindly provided by the corresponding author, Markus Hafner.
description: The version of Coalispr released in January 2026 (v0.9.6) requires newer versions of the  configurartion files. These are in the archive 'Replacement_files'; see the NOTE for more information.
DOI: 10.5061/dryad.bq091cg
title: Data from: Origin of angiosperms and the puzzle of the Jurassic gap

description: Angiosperms are by far the most species-rich clade of land plants, but
 their origin and early evolutionary history remain poorly understood. We
 reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid
 genomes representing 85% of extant families and all orders. With a
 well-resolved plastid tree and 62 fossil calibrations, we dated the origin
 of the crown angiosperms to the Upper Triassic, with major angiosperm
 radiations occurring in the Jurassic and Lower Cretaceous. This estimated
 crown age is substantially earlier than that of unequivocal angiosperm
 fossils, and the difference is here termed the ‘Jurassic angiosperm gap’.
 Our time-calibrated plastid phylogenomic tree provides a highly relevant
 framework for future comparative studies of flowering plant evolution.
description: Data from: Origin of
 Angiosperms and the Puzzle of the Jurassic GapSequence alignments
 underlying analyses and all trees.2881_Sequence_alignments.rarData from: Origin of Angiosperms and the Puzzle of the Jurassic GapSequence alignments underlying analyses and all trees.2881_trees.rar
DOI: 10.5061/dryad.bh0pj76
title: Data from: Opportunities to integrate herders’ indicators into formal rangeland monitoring: an example from Mongolia

description: Despite increasing calls for knowledge integration around the world,
 traditional knowledge is rarely used in formal, Western science-based
 monitoring and resource management. To better understand indicators
 herders use and their relationship to researcher-measured indicators, we
 conducted in-depth field interviews with 26 herders in three ecological
 zones of Mongolia. We asked each herder to 1) assess the overall condition
 of three different sites located along a livestock-use gradient from their
 winter camp using a numeric scale, 2) describe the indicators they used in
 their assessment, and 3) explain what caused their pastures to remain
 healthy or become degraded. At each site, we collected field data on
 vegetation variables and compared these with herders’ ratings and
 indicators using linear regression. We used classification and ordination
 to understand how herders’ assessment scores related to plant community
 composition, and determine how well multivariate analysis of factors
 determining plant community composition aligned with herders’ observations
 of factors causing rangeland change. Across all ecological zones, herders
 use indicators similar to those used in formal monitoring. Herders’
 assessment scores correlated significantly and positively with measured
 total foliar cover in all three ecological zones, and with additional
 measured variables in the steppe and desert steppe. Ordination revealed
 that herder assessment scores were correlated with the primary ordination
 axis in each zone, and the main factors driving plant community
 composition in each zone were the same as those identified by herders as
 the primary causes of rangeland change in that zone. These results show
 promise for developing integrated indicators and monitoring protocols and
 highlight the importance of developing a common language of monitoring
 terminology shared by herders, government monitoring agencies, and
 researchers. We propose a new model for integrating herder knowledge and
 participation into formal monitoring in Mongolia, with implications for
 rangelands and pastoral people globally. We suggest practical ways of
 involving herders in formal monitoring that have potential broad
 application for promoting local and indigenous people’s participation in
 implementing international agreements such as the UN Convention to Combat
 Desertification and the UN Convention on Biological Diversity, both of
 which call for involvement of local people and indigenous/traditional
 knowledges.
description: Data_Herders indicators
 for formal monitoring_DryadVegetation data was
 collected in the field during the summers in 2011 and 2012. Herders
 interview was conducted in the field during summer
 2013.
DOI: 10.5061/dryad.1t2513c
title: Data from: A dynamic model of facilitation on environmental stress gradients

description: Theories based on competition for resources in animals and other
 non-sessile organisms rarely consider the role of facilitative
 interactions. Yet these interactions are important for community assembly,
 especially under stressful environments (e.g. the stress-gradient
 hypothesis, SGH). To make an explicit link between species interaction
 theory and SGH patterns, I used a classic resource competition model
 promoting coexistence between a beneficiary and its facilitator sharing a
 common resource along a stress gradient. I compared model outcomes for two
 fundamentally different mechanisms of facilitation (alleviation of
 resource vs. non-resource stress), and also tested the effect of a
 reciprocal cost of facilitation from the beneficiary. I then tested
 model's biological relevance using experimental data from two tuber
 moth species (Lepidoptera, Gelechiidae) for which facilitation in resource
 access was previously established. Simulation outcomes revealed that both
 the mode of facilitation and the incorporation of facilitation costs
 affected the shape of the facilitation-stress relationship. These
 predictions are in line with current SGH observations and experiments on
 both plants and animals and reconcile the frequently reported variability
 of this relationship in nature. Moreover, a sensitivity analysis of
 model's parameters confirmed the robustness of the modelling
 framework to uncover the mechanisms responsible for observed species
 interaction–stress patterns. Finally, when parameterized with tuber moth
 demographic data, model's results corresponded to observed
 interaction outcomes along resource stress gradients. Overall, having a
 common model for plants and animals may simplify assumptions in SGH
 studies, allow contrasting the shapes of different consumer-resource
 relationships and specifying the conditions that favour one type of
 interaction outcome over another.
description: Code for a dynamic model
 of facilitationCODE TO RUN THE MODEL
 DESCRIBED IN DANGLES (2019) OIKOSDynamic_model_facilitation_Dangles.R
DOI: 10.5061/dryad.3m5116g
title: Data from: Predicting the ecological impacts of an alien invader: experimental approaches reveal the trophic consequences of competition

description: 1.Ecological theory on the trophic impacts of invasive fauna on native
 competitors is equivocal. While increased inter‐specific competition can
 result in coexisting species having constricted and diverged trophic
 niches, the competing species might instead increase their niche sizes to
 maintain energy intakes. Empirical experiments can test invasion theory on
 competitive interactions and niche sizes across different spatial scales
 and complexity. 2.The consequences of increased inter‐specific competition
 from a model alien fish Leuciscus idus were tested on two taxonomically
 and trophically similar native fishes, Squalius cephalus and Barbus
 barbus. Competitive interactions were tested in tank aquaria using
 comparative functional responses (CFRs) and cohabitation trials. The
 consequences of these competitive interactions for the trophic niche sizes
 and positions of the fishes were tested in pond mesocosms. 3.CFRs revealed
 that compared to B. barbus, L. idus had significantly higher attack and
 consumption rates; cohabitation trials revealed B. barbus growth rates
 were depressed in sympatry with L. idus. For L. idus and S. cephalus,
 differences in their functional response parameters and growth rates were
 not significant. 4.Pond mesocosms used stable isotope metrics to quantify
 shifts in the trophic niche sizes of the fishes between allopatry and
 sympatry using a substitutive experimental design. Isotopic niches were
 smaller and more divergent in sympatric paired species than predicted by
 their allopatric treatments, suggesting trophic impacts from
 inter‐specific competition. However, an all‐species sympatric treatment
 revealed similar niche sizes with allopatry. This maintenance of niche
 sizes in the presence of all species potentially resulted from the
 buffering of direct competitive effects of the species‐pairs by indirect
 effects. 5.Experimental predictions from tank aquaria assisted the
 interpretation of the constricted and diverged trophic niches detected in
 the paired‐species sympatric treatments of the pond mesocosms. However,
 the all‐species sympatric treatment of this experiment revealed greater
 complexity in the outcomes of the competitive interactions within and
 between the species. These results have important implications for
 understanding how alien species integrate into food webs and influence the
 trophic relationships between native species.
description: Britton et al. data
 predicting invadersData for
 'Predicting the ecological impacts of an alien invader: experimental
 approaches reveal the trophic consequences of
 competition'
DOI: 10.5281/zenodo.15323195
title: CaWoSched

description: For instructions on compiling see the README.md file in the code/ folder.
DOI: 10.5061/dryad.2qh4k34
title: Data from: Selection for novel metabolic capabilities in Salmonella enterica

description: Bacteria are known to display extensive metabolic diversity and many
 studies have shown that they can use an extensive repertoire of small
 molecules as carbon- and energy sources. However, it is less clear to what
 extent a bacterium can expand its existing metabolic capabilities by
 acquiring mutations that, for example, rewire its metabolic pathways. To
 investigate this capability and potential for evolution of novel
 phenotypes, we sampled large populations of mutagenized Salmonella
 enterica to select very rare mutants that can grow on minimal media
 containing 124 low molecular weight compounds as sole carbon sources. We
 found mutants growing on 18 of these novel carbon sources, and identified
 the causal mutations that allowed growth for four of them. Mutations that
 relieve physiological constraints or increase expression of existing
 pathways were found to be important contributors to the novel phenotypes.
 For the remaining 14 novel phenotypes, whole genome sequencing of
 independent mutants and genetic analysis suggested that these novel
 metabolic phenotypes result from a combination of multiple mutations. This
 work, by virtue of identifying the genetic and mechanistic basis for new
 metabolic capabilities, sheds light on the properties of adaptive
 landscapes underlying the evolution of novel phenotypes.
description: WGS_fastq_Deoxy_D_glucoseFastq files obtained from whole genome sequencing of mutants growing on 2-Deoxy-D-glucose as sole carbon source. Each mutant was paired end sequenced using Illumina's Miseq. Thus there are two fastq files per mutant. Each file name has a DA number designating the strain, and description of the strain can be obtained from the supplementary table 3 of the manuscript.WGS_fastq_valineFastq files obtained from whole genome sequencing of mutants growing on valine as sole carbon source. Each mutant was paired end sequenced using Illumina's Miseq. Thus there are two fastq files per mutant. Each file name has a DA number designating the strain, and description of the strain can be obtained from the supplementary table 3 of the manuscript.WGS_fastq_ErythroseFastq files obtained from whole genome sequencing of mutants growing on erythrose as sole carbon source. Each mutant was paired end sequenced using Illumina's Miseq. Thus there are two fastq files per mutant. Each file name has a DA number designating the strain, and description of the strain can be obtained from the supplementary table 3 of the manuscript.WGS_fastq_D-adonitolFastq files obtained from whole genome sequencing of mutants growing on D-adonitol as sole carbon source. Each mutant was paired end sequenced using Illumina's Miseq. Thus there are two fastq files per mutant. Each file name has a DA number designating the strain, and description of the strain can be obtained from the supplementary table 3 of the manuscript.
DOI: 10.5061/dryad.39pt227
title: Data from: Netted crop covers reduce honey bee foraging activity and colony strength in a mass flowering crop

description: The widespread use of protective covers in horticulture represents a novel
 landscape-level change, presenting challenges for crop pollination. Honey
 bees (Apis mellifera L) are pollinators of many crops, but their behaviour
 can be affected by conditions under covers. To determine how netting crop
 covers can affect honey bee foraging dynamics, colony health, and
 pollination services, we assessed the performance of 52 nucleus honey bee
 colonies in five covered and six uncovered kiwifruit orchards. Colony
 strength was estimated pre- and post- introduction, and the foraging of
 individual bees (including pollen-, nectar-, and naïve foragers) was
 monitored in a subset of the hives fitted with RFID readers.
 Simultaneously, we evaluated pollination effectiveness by measuring flower
 visitation rates and the number of seeds produced after single honey bee
 visits. Honey bee colonies under cover exhibited both an acute loss of
 foragers and changes in the behaviour of successful foragers. Under cover,
 bees were four times less likely to return after their first trip outside
 the hive. Consequently, the number of adult bees in hives declined at a
 faster rate in these orchards, with colonies losing on average 1,057 ± 274
 of their bees in under two weeks. Bees that did forage under cover
 completed fewer trips provisioning their colony, failing to re-enter after
 a few short-duration trips. These effects are likely to have implications
 for colony health and productivity. We also found that bee density
 (bees/thousand flowers) and visitation rates to flowers were lower under
 cover, however we did not detect a resultant change in pollination. Our
 findings highlight the need for environment-specific management techniques
 for pollinators. Improving honey bee orientation under covers and
 increasing our understanding of the effects of covers on bee nutrition and
 brood rearing should be primary objectives for maintaining colonies and
 potentially improving pollination in these systems.
description: Data for honey bee
 foraging activity, colony strength and pollination in covered vs uncovered
 kiwifruit orchardsData used in - Netted crop
 covers reduce honey bee foraging activity and colony strength in a
 mass.zip
DOI: 10.5061/dryad.b7g95d2
title: Data from: Leading-edge vortices over swept-back wings with varying sweep geometries

description: Micro air vehicles are used in a myriad of applications, such as
 transportation and surveying. Their performance can be improved through
 study of wing designs and lift generation techniques including
 leading-edge vortices (LEVs). Observation of natural fliers, e.g., birds
 and bats, has shown that LEVs are a major contributor to lift during
 flapping flight, and the common swift (Apus apus) has been observed to
 generate LEVs during gliding flight. We hypothesize that non-linear
 swept-back wings generate a vortex in the leading-edge region, which can
 augment the lift in a similar manner to linear swept-back wings (i.e.,
 delta wing) during gliding flight. Particle image velocimetry experiments
 were performed in a water flume to compare flow over two wing geometries:
 one with a non-linear sweep (swift-like wing) and one with a linear sweep
 (delta wing). Experiments were performed at three spanwise planes and
 three angles of attack at a chord-based Reynolds number of 26,000.
 Streamlines, vorticity, swirling strength, and Q criterion, were used to
 identify LEVs. The results show similar LEV characteristics for delta and
 swift-like wing geometries. These similarities suggest that sweep
 geometries other than a linear sweep (i.e., delta wing) are capable of
 creating LEVs during gliding flight.
description: Experimental
 DataPIV velocity
 measurements in .vec and .mat formats - see readme.m inside the zip
 file.OpenScience_Data.zip
DOI: 10.5061/dryad.9v60c13
title: Data from: Genetic variation and possible origins of weedy rice found in California

description: Control of weeds in cultivated crops is a pivotal component in successful
 crop production allowing higher yield and higher quality. In rice‐growing
 regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed
 related to cultivated rice which infests rice fields. With populations
 across the globe evolving a suite of phenotypic traits characteristic of
 weeds and of cultivated rice, varying hypotheses exist on the origin of
 weedy rice. Here, we investigated the genetic diversity and possible
 origin of weedy rice in California using 98 simple sequence repeat (SSR)
 markers and an Rc gene‐specific marker. By employing phylogenetic
 clustering analysis, we show that four to five genetically distinct
 biotypes of weedy rice exist in California. Analysis of population
 structure and genetic distance among individuals reveals diverse
 evolutionary origins of California weedy rice biotypes, with ancestry
 derived from indica, aus, and japonica cultivated rice as well as possible
 contributions from weedy rice from the southern United States and wild
 rice. Because this diverse parentage primarily consists of weedy, wild,
 and cultivated rice not found in California, most existing weedy rice
 biotypes likely originated outside California.
description: SampleDescriptionList of rice genotypes used in genetic study, genotype source, grain attributes, and presence or absence of 14-basepair deletion in Rc gene.GeneticMarkersDistribution and allele variation of 98 microsatellite markers and 1 Rc gene-specific marker among 96 weedy, cultivated and wild rices. Microsatellite marker primer sequences are most accessible from the Gramene database (http://archive.gramene.org/markers/microsat/) but were published in: International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800. The Rc marker is published in Subudhi et al. 2012: Subudhi, P.K, Parco, A., Singh, P.K., De Leon, T., Karan, R., Biradar, H., Cohn, M.A., Brar, D.S., & Sasaki, T. (2012) Genetic architecture of seed dormancy in US weedy rice in different genetic backgrounds. Crop Science 52: 2564-2575.GeneticDataGenotype data from 99 genetic markers described in the file GeneticMarkers.csv for 96 rice samples described in the file SampleDescription.csv. Data contains codominant marker data with two columns for each locus and one line per sample. Alleles are numbered 1 through n for each marker. Missing data is coded as 0.
DOI: 10.5061/dryad.5q66f0n
title: Data from: Temporal intraspecific trait variability drives responses of functional diversity to inter-annual aridity variation in grasslands

description: Inter-annual climate variation alters functional diversity through
 intraspecific trait variability and species turnover. We examined these
 diversity elements in three types of grasslands in Northern China,
 including two temperate steppes and an alpine meadow. We evaluated the
 differences in community-weighted means (CWM) of plant traits and
 functional dispersion (FDis) between two years with contrasting aridity in
 the growing season. Four traits were measured: specific leaf area (SLA),
 leaf dry matter content (LDMC), leaf nitrogen concentration (LNC) and the
 maximum plant height (H). CWM for SLA of the alpine meadow increased in
 the dry year while that of the temperate steppe in Qinghai showed opposing
 trends. CWM of LDMC in two temperate steppes became higher and CWM of LNC
 in all grasslands became lower in the dry year. Compared with the wet
 year, FDis of LDMC in the alpine meadow and FDis of LNC in the temperate
 steppe in Qinghai decreased in the dry year. FDis of H was higher in the
 dry year for two temperate steppes. Only in the temperate steppe in
 Qinghai did the multi-FDis of all traits experience a significant increase
 in the dry year. Most of the changes in CWM and FDis between two years
 were explained by intraspecific trait variation rather than shifts in
 species composition. This study highlights that temporal intraspecific
 trait variation contributes to functional responses to environmental
 changes. Our results also suggest it would be necessary to consider
 habitat types when modelling ecosystem responses to climate changes, as
 different grasslands showed different response patterns.
description: plant functional traits
 and relative aboveground biomassThis sheet contains
 traits and relative aboveground biomass of each species in three
 grasslands over two years.data.Temporal intraspecific
 trait variability drives responses of functional diversity to inter-annual
 aridity variation in grasslands.xlsx