cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mg86j
title: Data from: Evolutionary renovation of L/M opsin polymorphism confers a fruit discrimination advantage to ateline New World monkeys

description: New World monkeys exhibit prominent color vision variation due to allelic
 polymorphism of the long-to-middle wavelength (L/M) opsin gene. The known
 spectral variation of L/M opsins in primates is broadly determined by
 amino acid composition at three sites: 180, 277 and 285 (the “three-sites”
 rule). However, two L/M opsin alleles found in the black-handed spider
 monkeys (Ateles geoffroyi) are known exceptions, presumably due to novel
 mutations. The spectral separation of the two L/M photopigments is 1.5
 times greater than expected based on the “three-sites” rule. Yet the
 consequence of this for the visual ecology of the species is unknown, as
 is the evolutionary mechanism by which spectral shift was achieved. In the
 present study, we first examine L/M opsins of two other Atelinae species,
 the long-haired spider monkeys (A. belzebuth) and the common woolly
 monkeys (Lagothrix lagotricha). By a series of site-directed mutagenesis,
 we show that a mutation Y213D (tyrosine to aspartic acid at site 213) in
 the ancestral opsin of the two alleles enabled N294K, which occurred in
 one allele of the ateline ancestor, and increased the spectral separation
 between the two alleles. Second, by modeling the chromaticity of dietary
 fruits and background leaves in a natural habitat of spider monkeys, we
 demonstrate that chromatic discrimination of fruit from leaves is
 significantly enhanced by these mutations. This evolutionary renovation of
 L/M opsin polymorphism in atelines illustrates a previously unappreciated
 dynamism of opsin genes in shaping primate color vision.
description: LMopsin_alignmentA "sequential" (fasta) format of the sequence alignment of L/M opsin genes on which all the analyses in this article is basedAbsorptionSpectraThe dark, light and dark-light difference absorption spectra averaged among multiple measurements for each of intact and mutagenized opsinsreflectanceThe reflectance spectra for the fruits and leavesJND_WilcoxonThe R analysis code fileJND_summaryThe R analysis input file
DOI: 10.5061/dryad.2rm60
title: Data from: Generic and subtribal relationships in Neotropical Cymbidieae (Orchidaceae) based on matK/ycf1 plastid data

description: Relationships among all subtribes of Neotropical Cymbidieae (Orchidaceae)
 were estimated using combined matK/ycf1 plastid sequence data for 289
 taxa. The matrix was analyzed using RAxML. Bootstrap (BS) analyses yield
 100% BS support for all subtribes except Stanhopeinae (87%). Generic
 relationships within subtribes are highly resolved and are generally
 congruent with those presented in previous studies and as summarized in
 Genera Orchidacearum. Relationships among subtribes are largely
 unresolved. The Szlachetko generic classification of Maxillariinae is not
 supported. A new combination is made for Maxillaria cacaoensis J.T.Atwood
 in Camaridium.
description: Cymbidieae matK/ycf1
 combined matrixAligned matK/ycf1 matrix
 for 288 individuals of Cymbidieae plus one outgroup; NEXUS
 file.Cymbidieae COMB
 nonint.nexCymbid GB and vouchers
 MASTERTable of voucher
 specimens and GenBank numbers for Cymbidieae analysis.
DOI: 10.5061/dryad.4108h
title: Data from: Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

description: The measurement of species diversity represents a powerful tool for
 assessing the impacts of human activities on marine ecosystems.
 Traditionally, the impact of fish farming on the coastal environment is
 evaluated by monitoring the dynamics of macrobenthic infaunal populations.
 However, taxonomic sorting and morphology-based identification of the
 macrobenthos demands highly trained specialists and is extremely
 time-consuming and costly, what makes it unsuitable for large-scale
 biomonitoring efforts involving numerous samples. Here, we propose to
 alleviate this laborious task by developing protist metabarcoding tools
 based on next-generation sequencing (NGS) of environmental DNA and RNA
 extracted from sediment samples. In this study, we analysed the response
 of benthic foraminiferal communities to the variation of environmental
 gradients associated with salmon farms in Scotland. We investigated the
 foraminiferal diversity based on ribosomal minibarcode sequences generated
 by the Illumina NGS technology. We compared the molecular data with
 morphospecies counts and with environmental gradients, including distance
 to cages and Redox used as a proxy for sediment oxygenation. Our study
 revealed high variations between foraminiferal communities collected in
 the vicinity of fish farms and at distant locations. We found evidence for
 alpha diversity loss in strongly impacted sites, especially visible in the
 RNA data. We also detected some candidate bioindicator foraminiferal
 species. Based on this proof-of-concept study, we conclude that NGS
 metabarcoding using foraminifera and other protists has considerable
 potential to become a new tool for surveying the impact of aquaculture and
 other industrial activities in the marine environment.
description: SFA114_OBAN_ISUsThe file is a fasta file containing the individual sequence units (ISUs) obtained after the stringent quality filtering, assembly, demultiplexing and dereplication steps described in the paper. The paired-end reads from large forward and reverse fastq files were treated using a custom C language program. The 5 fields of each underscore-separated ISU header represent from the first to the last field: the project alphanumeric ID ('SFA114'), the project name ('OBAN'), the type of molecule ('DNA' of 'RNA'), the sample ID number ('1' - '45') and the number of reads of the ISU.normalized_OTUs_readsFor each OTU (lines) are indicated the number of reads found in each sample (columns). The taxonomic assignment of each OTU is indicated in the first column. The sample names are indicated in the first line.Morphological_countsNumber of foraminifera morphospecies counted in the 45 sequenced sediment samples. For each species identifed based on morphological characters (lines), the counts are detailed for each sample (column in spreadsheet "Species") or summed across samples (spreadsheet "final counts").
DOI: 10.5061/dryad.pg2kb
title: Data from: Transcriptional markers of sub-optimal nutrition in developing Apis mellifera nurse workers

description: Background: Honey bees (Apis mellifera) contribute substantially to the
 worldwide economy and ecosystem health as pollinators. Pollen is essential
 to the bee’s diet, providing protein, lipids, and micronutrients. The
 dramatic shifts in physiology, anatomy, and behavior that accompany normal
 worker development are highly plastic and recent work demonstrates that
 development, particularly the transition from nurse to foraging roles, is
 greatly impacted by diet. However, the role that diet plays in the
 developmental transition of newly eclosed bees to nurse workers is poorly
 understood. To further understand honey bee nutrition and the role of diet
 in nurse development, we used a high-throughput screen of the
 transcriptome of 3 day and 8 day old worker bees fed either honey and
 stored pollen (rich diet) or honey alone (poor diet) within the hive. We
 employed a three factor (age, diet, age x diet) analysis of the
 transcriptome to determine whether diet affected nurse worker physiology
 and whether poor diet altered the developmental processes normally
 associated with aging. Results: Substantial changes in gene expression
 occurred due to starvation. Diet-induced changes in gene transcription
 occurring in younger bees were largely a subset of those occurring in
 older bees, but certain signatures of starvation were only evident 8 day
 old workers. Of the 18,542 annotated genes in the A. mellifera genome,
 0.7% (126 genes) exhibited differential expression due to poor diet at 3d
 of age compared with 81% (15,001 genes) that differed due to poor diet at
 8d of age. Of the genes that were differentially expressed in young or old
 pollen deprived bees, poor diet caused more frequent down-regulation of
 gene expression in younger bees compared to older bees. In addition, the
 age-related physiological changes that accompanied early adult development
 differed due to the diet these young adult bees were fed. More frequent
 down-regulation of gene expression was observed in developing bees fed a
 poor diet compared to an adequate diet. Functional analyses also show that
 the physiological and developmental processes occurring in well-fed bees
 are vastly different than those occurring in pollen deprived bees. These
 data support the hypothesis that poor diet causes normal age-related
 development to go awry. Conclusion: Poor nutrition has major consequences
 for the expression of genes underlying the physiology and age-related
 development of nurse worker bees. More work is certainly needed to fully
 understand the consequences of starvation and the complex biology of
 nutrition and development in this system, but the genes identified in the
 present study provide a starting point for understanding the consequences
 of poor diet and for mitigating the economic costs of colony starvation.
description: Table_S4_large_table_of_expression_data_-_checked_-_final
DOI: 10.5061/dryad.p25vn
title: Data from: Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

description: DNA barcoding is an efficient method to identify specimens and to detect
 undescribed/cryptic species. Sanger sequencing of individual specimens is
 the standard approach in generating large-scale DNA barcode libraries and
 identifying unknowns. However, the Sanger sequencing technology is, in
 some respects, inferior to next-generation sequencers, which are capable
 of producing millions of sequence reads simultaneously. Additionally,
 direct Sanger sequencing of DNA barcode amplicons, as practiced in most
 DNA barcoding procedures, is hampered by the need for relatively
 high-target amplicon yield, coamplification of nuclear mitochondrial
 pseudogenes, confusion with sequences from intracellular endosymbiotic
 bacteria (e.g. Wolbachia) and instances of intraindividual variability
 (i.e. heteroplasmy). Any of these situations can lead to failed Sanger
 sequencing attempts or ambiguity of the generated DNA barcodes. Here, we
 demonstrate the potential application of next-generation sequencing
 platforms for parallel acquisition of DNA barcode sequences from hundreds
 of specimens simultaneously. To facilitate retrieval of sequences obtained
 from individual specimens, we tag individual specimens during PCR
 amplification using unique 10-mer oligonucleotides attached to DNA
 barcoding PCR primers. We employ 454 pyrosequencing to recover full-length
 DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run
 (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence
 reads for each individual specimen. The sequences produced are full-length
 DNA barcodes for all but one of the included specimens. In a subset of
 samples, we also detected Wolbachia, nontarget species, and heteroplasmic
 sequences. Next-generation sequencing is of great value because of its
 protocol simplicity, greatly reduced cost per barcode read, faster
 throughout and added information content.
description: 454 Pyrosequencing-plate
 17.454Reads-set1 unique
 names.fasta454 Pyrosequencing-plate
 23.454Reads-set2 unique
 names.fastaSanger sequences Plate
 1Plate
 1.fastaSanger sequences Plate
 2Plate
 2.fastaTree_file
DOI: 10.5061/dryad.bc8pc
title: Data from: Rapid and accurate taxonomic classification of insect (Class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

description: Current methods to identify unknown insect (class Insecta) cytochrome c
 oxidase (COI barcode) sequences often rely on difficult to define
 thresholds of distances, sequence similarity cutoffs, or monophyly. Most
 methods do not provide a measure of confidence for the taxonomic
 assignments they provide. The aim of this study is to use a naïve Bayesian
 classifier (Wang et al., 2007) to automate unsupervised taxonomic
 assignments for large batches of insect COI sequences such as data
 obtained from environmental barcoding using next generation sequencing
 platforms. This method provides rank-flexible taxonomic assignments with
 an associated bootstrap support value and it is faster than the
 BLAST-based methods commonly used in environmental sequence surveys. We
 have developed and rigorously tested the performance of three different
 training sets using leave-one-out cross-validation, two field datasets,
 and targeted testing of Lepidoptera, Diptera, and Mantodea sequences
 obtained from the Barcode of Life Data system. We found that type I error
 rates, incorrect taxonomic assignments with a high bootstrap support, were
 already relatively low but could be lowered further by ensuring that all
 query taxa are actually present in the reference database. Choosing
 bootstrap support cutoffs according to query length and summarizing
 taxonomic assignments to more inclusive ranks can also help to reduce
 error while retaining the maximum number of assignments. Additionally, we
 highlight gaps in the taxonomic and geographic representation of insects
 in public sequence databases that will require further work by taxonomists
 to improve the quality of assignments generated using any method.
description: Canadian benthos Fasta
 filesFasta files for the
 benthos insect datasets from Fredericton, New Brunswick, Canada: 1) ~ 100
 bp fragments (454), 2) ~ 200 bp fragments (454), 3) ~ 600 bp reference
 (Sanger) sequences.CanadianBenthosFastas.zipTraining the naive Bayesian classifierContains the Fasta and taxonomy files needed to train the Ribosomal Database Project naive Bayesian classifier three different ways: 1) GenBank-genus, 2) GenBank-barcode, 3) GenBank-family.TrainingTheClassifier.zipCustomizing the Insecta taxonomy used with the classifierContains three tab-delimited taxonomy files that can be used to help customize the taxonomic scheme used by the naive Bayesian classifier: 1) GenBank-genus, 2) GenBank-barcode, 3) GenBank-family. One of these files, should be used with one of the two provided Perl scripts to generate a taxonomy file in the format required by the Ribosomal Database Project naive Bayesian classifier during training: 1) make_NBC_taxonomy.plx, 2) make_NBC_taconomy_family.plx.CustomizingInsectaTaxonomy.zipMalaise insect datasetFasta file of Malaise insect data set, see also Gibson et al. (in prep).malaise.fasta
DOI: 10.5061/dryad.v134j
title: Data from: Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening

description: Fruit ripening is the summation of changes rendering fleshy fruit tissues
 attractive and palatable to seed dispersing organisms. For example, sugar
 content is influenced by plastid numbers and photosynthetic activity in
 unripe fruit and later by starch and sugar catabolism during ripening.
 Tomato fruit are sinks of photosynthate, yet unripe green fruit contribute
 significantly to the sugars that ultimately accumulate in the ripe fruit.
 Plastid numbers and chlorophyll content are influenced by numerous
 environmental and genetic factors and are positively correlated with
 photosynthesis and photosynthate accumulation. GOLDEN2-LIKE (GLK)
 transcription factors regulate plastid and chlorophyll levels. Tomato
 (Solanum lycopersicum), like most plants, contains two GLKs (i.e., GLK1
 and GLK2/UNIFORM). Mutant and transgene analysis demonstrated that these
 genes encode functionally similar peptides, though differential expression
 renders GLK1 more important in leaves, while GLK2 is predominant in fruit.
 A latitudinal gradient of GLK2 expression influences the typical uneven
 coloration of green and ripe wild-type fruit. Transcriptome profiling
 revealed a broader fruit gene expression gradient throughout development.
 The gradient influenced general ripening activities beyond plastid
 development and was consistent with the easily observed yet poorly studied
 ripening gradient present in tomato and many fleshy fruits.
description: tpc118794Supplemental
 DS1Supplemental Data File
 1tpc118794Supplemental
 DS2Supplemental Data File
 2tpc118794Supplemental
 DS3Supplemental Data File
 3tpc118794Supplemental
 DS4Supplemental Data File
 4tpc118794SupplementalSupplemental Figures and Tables
DOI: 10.5061/dryad.40nk2
title: Data from: Sex chromosome turnover contributes to genomic divergence between incipient stickleback species

description: Sex chromosomes turn over rapidly in some taxonomic groups, where closely
 related species have different sex chromosomes. Although there are many
 examples of sex chromosome turnover, we know little about the functional
 roles of sex chromosome turnover in phenotypic diversification and genomic
 evolution. The sympatric pair of Japanese threespine stickleback
 (Gasterosteus aculeatus) provides an excellent system to address these
 questions: the Japan Sea species has a neo-sex chromosome system resulting
 from a fusion between an ancestral Y chromosome and an autosome, while the
 sympatric Pacific Ocean species has a simple XY sex chromosome system.
 Furthermore, previous quantitative trait locus (QTL) mapping demonstrated
 that the Japan Sea neo-X chromosome contributes to phenotypic divergence
 and reproductive isolation between these sympatric species. To investigate
 the genomic basis for the accumulation of genes important for speciation
 on the neo-X chromosome, we conducted whole genome sequencing of males and
 females of both the Japan Sea and the Pacific Ocean species. No
 substantial degeneration has yet occurred on the neo-Y chromosome, but the
 nucleotide sequence of the neo-X and the neo-Y has started to diverge,
 particularly at regions near the fusion. The neo-sex chromosomes also
 harbor an excess of genes with sex-biased expression. Furthermore, genes
 on the neo-X chromosome showed higher non-synonymous substitution rates
 than autosomal genes in the Japan Sea lineage. Genomic regions of higher
 sequence divergence between species, genes with divergent expression
 between species, and QTL for inter-species phenotypic differences were
 found not only at the regions near the fusion site, but also at other
 regions along the neo-X chromosome. Neo-sex chromosomes can therefore
 accumulate substitutions causing species differences even in the absence
 of substantial neo-Y degeneration.
description: Brain microarray
 datamRNA from whole brain
 without pituitary glands were analyzed with Agilent
 microarray.Brain.xlsxTestis microarraymRNA from testis were analyzed with Agilent microarray.Testis.xlsExpression_designProbe sequences for expression microarray.CGH_designProbe sequence of comparative genome hybridization array.
DOI: 10.5061/dryad.q0v43
title: Data from: Trait compensation and sex-specific aging of performance in male and female professional basketball players

description: Phenotypic traits are often influenced by dynamic resource allocation
 trade-offs which, when occurring over the course of individual lifespans,
 may manifest as trait aging. Although aging is studied for a variety of
 traits that are closely tied to reproduction or reproductive effort, the
 aging of multiple traits related to fitness in other ways are less well
 understood. We took advantage of almost 30 years of data on human
 whole-organism performance in the National Basketball Association (U.S.A.)
 to examine trends of aging in performance traits associated with scoring.
 Given that patterns of aging differ between sexes in other animal species,
 we also analysed a smaller dataset on players in the Women's National
 Basketball Association to test for potential sex differences in the aging
 of comparable traits. We tested the hypothesis that age-related changes in
 a specific aspect of overall performance can be compensated for by
 elevated expression of another, related aspect. Our analyses suggest that
 the aging of performance traits used in basketball is generally
 characterised by senescence in males, whereas age-related changes in
 basketball performance are less evident in females. Our data also indicate
 a different rate of senescence of different performance traits associated
 with scoring over a male's lifetime.
description: NBA
 dataThese are the data used
 for the modeling of overall points scored by sex and age (NBA all) and of
 point type by sex and age (NBA points)NBA
 all.xlsx
DOI: 10.82294/dvnwu94hx
title: COPUS. Territorio: Cartagena. Sector: Cultura. 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 Cultura (educación informal) en la ciudad de Cartagena.
DOI: 10.5061/dryad.h7pm2
title: Data from: Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii

description: Singlet oxygen is a highly toxic and inevitable byproduct of oxygenic
 photosynthesis. The unicellular green alga Chlamydomonas reinhardtii is
 capable of acclimating specifically to singlet oxygen stress, but the
 retrograde signaling pathway from the chloroplast to the nucleus mediating
 this response is unknown. Here we describe a mutant, singlet oxygen
 acclimation knocked-out 1 (sak1), that lacks the acclimation response to
 singlet oxygen. Analysis of genome-wide changes in RNA abundance during
 acclimation to singlet oxygen revealed that SAK1 is a key regulator of the
 gene expression response during acclimation. The SAK1 gene encodes an
 uncharacterized protein with a domain conserved among chlorophytes and
 present in some bZIP transcription factors. The SAK1 protein is located in
 the cytosol, and it is induced and phosphorylated upon exposure to singlet
 oxygen, suggesting that it is a critical intermediate component of the
 retrograde signal transduction pathway leading to singlet oxygen
 acclimation.
description: Total genes
 RNA-seqThis spreadsheet shows
 all the genes found by RNA-seq and their counts (RPKM) in all four
 samples, WT-mock, WT-Rose Bengal, sak1-mock, sak1-Rose Bengal. Each column
 shows results from a single sequencing lane, each sample was loaded on two
 lanes.TotalGeneCounts2.xlsx