cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.70sn9
title: Data from: Recovery of native genetic background in admixed Populations Using haplotypes, phenotypes, and pedigree information – using Cika cattle as a case breed

description: The aim of this study was to obtain unbiased estimates of the diversity
 parameters, the population history, and the degree of admixture in Cika
 cattle which represents the local admixed breeds at risk of extinction
 undergoing challenging conservation programs. Genetic analyses were
 performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina
 Bovine SNP50 array data of 76 Cika animals and 531 animals from 14
 reference populations. To obtain unbiased estimates we used short
 haplotypes spanning four markers instead of single SNPs to avoid an
 ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes
 combined with partial pedigree and type trait classification show the
 potential to improve identification of purebred animals with a low degree
 of admixture. Phylogenetic analyses demonstrated unique genetic identity
 of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net
 suggested long and broad phylogenetic connection between Cika and
 Pinzgauer. Unsupervised clustering performed by the admixture analysis and
 two-dimensional presentation of the genetic distances between individuals
 also suggest Cika is a distinct breed despite being similar in appearance
 to Pinzgauer. Animals identified as the most purebred could be used as a
 nucleus for a recovery of the native genetic background in the current
 admixed population. The results show that local well-adapted strains,
 which have never been intensively managed and differentiated into specific
 breeds, exhibit large haplotype diversity. They suggest a conservation and
 recovery approach that does not rely exclusively on the search for the
 original native genetic background but rather on the identification and
 removal of common introgressed haplotypes would be more powerful.
 Successful implementation of such an approach should be based on combining
 phenotype, pedigree, and genome-wide haplotype data of the breed of
 interest and a spectrum of reference breeds which potentially have had
 direct or indirect historical contribution to the genetic makeup of the
 breed of interest.
description: Allele counts in TreeMix
 format and 4-SNP-block haplotypesSimcic_et_al_2015_S1_Dataset.zip
DOI: 10.5061/dryad.73f69
title: Data from: Natural light exposure, sleep and depression among day workers and shiftworkers at Arctic and Equatorial latitudes

description: Objectives: This study aimed to investigate the relationship between
 individual natural light exposure, sleep need, and depression at two
 latitudes, one extreme with a few hours of light per day during winter,
 and the other with equal hours of light and darkness throughout the year.
 Methods: This cross-sectional study included a sample of Brazilian workers
 (Equatorial, n = 488 workers) and a Swedish sample (Arctic, n = 1,273).
 Results: The reported mean total natural light exposure per 4-week cycle
 differed significantly between the Equatorial and Arctic regions. However,
 shiftworkers from both sites reported similar hours of natural light
 exposure. Short light exposure was a predictor for insufficient sleep.
 Conclusion: Reduced exposure to natural light appears to increase the
 perception of obtaining insufficient sleep. Arctic workers were more prone
 to develop depression than Equatorial workers.
description: Marqueze et
 alData collected in the
 field. Adequate description in Readme file.
DOI: 10.5281/zenodo.18387530
title: Widespread seasonal transition in snow effects on vegetation growth across the Tibetan Plateau

description: Code and data for "Widespread seasonal transition in snow effects on vegetation growth across the Tibetan Plateau"
DOI: 10.5281/zenodo.18388489
title: Widespread seasonal transition in snow effects on vegetation growth across the Tibetan Plateau

description: Code and data for "Widespread seasonal transition in snow effects on vegetation growth across the Tibetan Plateau"
DOI: 10.5061/dryad.3q6n0
title: Data from: An ultraviolet floral polymorphism associated with life history drives pollinator discrimination in Mimulus guttatus (Phrymaceae)

description: Premise of the study: Ultraviolet (UV) floral patterns are common in
 angiosperms and mediate pollinator attraction, efficiency, and constancy.
 UV patterns may vary within species, yet are cryptic to human observers.
 Thus, few studies have explicitly described the distribution or ecological
 significance of intraspecific variation in UV floral patterning. Here, we
 describe the geographic distribution and pattern of inheritance of a UV
 polymorphism in the model plant species Mimulus guttatus (Phrymaceae). We
 then test whether naturally occurring UV phenotypes influence pollinator
 interactions within M. guttatus. Methods: We document UV patterns in 18
 annual and 19 perennial populations and test whether UV pattern is
 associated with life history. To examine the pattern of inheritance, we
 conducted crosses within and between UV phenotypes. Finally, we tested
 whether bee pollinators discriminate among naturally occurring UV
 phenotypes in two settings: wild bee communities and captive Bombus
 impatiens. Key results: Within M. guttatus, perennial populations exhibit
 a small bulls-eye pattern, whereas a bilaterally symmetric runway pattern
 occurs mainly in annual populations. Inheritance of UV patterning is
 consistent with a single-locus Mendelian model in which the runway
 phenotype is dominant. Bee pollinators discriminate against unfamiliar UV
 patterns in both natural and controlled settings. Conclusions: We describe
 a widespread UV polymorphism associated with life history divergence
 within Mimulus guttatus. UV pattern influences pollinator visitation and
 should be considered when estimating reproductive barriers between life
 history ecotypes. This work develops a new system to investigate the
 ecology and evolution of UV floral patterning in a species with extensive
 genomic resources.
description: Population Phenotype
 DataThis file contains data
 on the UV pattern of individuals from populations of M. guttatus, M.
 nasutus, and M. laciniatus.Hybrid Reflectance
 DataThis file contains
 standardized reflectance spectra for flowers from F1 hybrids between
 populations of M. guttatusField Pollinator
 TrialsThis file contains data
 from choice trials in wild populations of M. guttatus using the native
 pollinator communityCaptive Pollinator
 TrialsThis file contains data
 from choice trials with captive Bombus impatiens using outbred lines of M.
 guttatus
DOI: 10.82294/dvnf7ausg
title: COPUS. Territorio: Amazonas. Sector: Educación. Año: 2024
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2024 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 el departamento de Amazonas.
DOI: 10.5061/dryad.b6s6q
title: Data from: Heterogeneity of genetic architecture of body size traits in a free-living population

description: Knowledge of the underlying genetic architecture of quantitative traits
 could aid in understanding how they evolve. In wild populations, it is
 still largely unknown whether complex traits are polygenic or influenced
 by few loci with major effect, due to often small sample sizes and low
 resolution of marker panels. Here, we examine the genetic architecture of
 five adult body size traits in a free-living population of Soay sheep on
 St Kilda using 37 037 polymorphic SNPs. Two traits (jaw and weight) show
 classical signs of a polygenic trait: the proportion of variance explained
 by a chromosome was proportional to its length, multiple chromosomes and
 genomic regions explained significant amounts of phenotypic variance, but
 no SNPs were associated with trait variance when using GWAS. In
 comparison, genetic variance for leg length traits (foreleg, hindleg and
 metacarpal) was disproportionately explained by two SNPs on chromosomes 16
 (s23172.1) and 19 (s74894.1), which each explained &gt;10% of the
 additive genetic variance. After controlling for environmental
 differences, females heterozygous for s74894.1 produced more lambs and
 recruits during their lifetime than females homozygous for the common
 allele conferring long legs. We also demonstrate that alleles conferring
 shorter legs have likely entered the population through a historic
 admixture event with the Dunface sheep. In summary, we show that different
 proxies for body size can have very different genetic architecture and
 that dense SNP helps in understanding both the mode of selection and the
 evolutionary history at loci underlying quantitative traits in natural
 populations.
description: Annual fitness
 dryadannual
 fitness dryad.txtLBS data
 dryadcapture data
 dryadskeletal data
 dryadSNP
 data
DOI: 10.15468/dl.pefunz
title: Occurrence Download

description: A dataset containing 38103 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "GadmGid is one of (COL.15.86_2)"
 ]
}

 The dataset includes 38103 records from 130 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001629-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9h569
title: Data from: Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

description: With methods for sequencing thousands of loci for many individuals,
 phylogeographic studies have increased inferential power and the potential
 for applications to new questions. In songbirds, strong patterns of
 inter-chromosomal synteny, the published genome of a songbird and the
 ability to obtain thousands of genetic loci for many individuals permit
 the investigation of differentiation between and diversity within lineages
 across chromosomes. Here, we investigate patterns of differentiation and
 diversity in Certhia americana, a widespread North American songbird,
 using next-generation sequencing. Additionally, we reassess previous
 phylogeographic studies within the group. Based on ~30 million sequencing
 reads and more than 16 000 single-nucleotide polymorphisms in 41
 individuals, we identified a strong positive relationship between genetic
 differentiation and chromosome size, with a negative relationship between
 genetic diversity and chromosome size. A combination of selection and
 drift may explain these patterns, although we found no evidence for
 selection. Because the observed genomic patterns are very similar between
 widespread, allopatric clades, it is unlikely that selective pressures
 would be so similar across such different ecological conditions.
 Alternatively, the accumulation of fixed differences between lineages and
 loss of genetic variation within lineages due to genetic drift alone may
 explain the observed patterns. Due to relatively higher recombination
 rates on smaller chromosomes, larger chromosomes would, on average,
 accumulate fixed differences between lineages and lose genetic variation
 within lineages faster, leading to the patterns observed here in C.
 americana.
description: Consensus
 sequencesConsensus sequences of
 all loci used in analyses. Loci identifier numbers match those of other
 uploaded files.Certhia30_variable_loci.fastaSNPsSNPs of each individual, with the top row containing the identifier locus for each SNP. Individual names match those in the publication. Missing data coded as 0.certhia30.structure.tsvSummary StatisticsOutput of STACKS for the 30% coverage dataset. Populations identified as north or south (lines 1 & 2). Locus ID matches identifiers of other uploaded files. BP indicates location of each SNP (starting at bp 0), allowing placement of SNPs into consensus sequences.certhia30.sumstats.tsv
DOI: 10.6084/m9.figshare.31158640
title: Pain Control in Cats Diagnosed With Neoplasia – A Scoping Review

description: This dataset contains the supplementary materials supporting a scoping review on pharmacological pain management in cats with neoplastic disease.
DOI: 10.6084/m9.figshare.31158640.v1
title: Pain Control in Cats Diagnosed With Neoplasia – A Scoping Review

description: This dataset contains the supplementary materials supporting a scoping review on pharmacological pain management in cats with neoplastic disease.
DOI: 10.5061/dryad.3c7m4
title: Data from: Identification and characterization of Cyprinid Herpesvirus-3 (CyHV-3) encoded microRNAs

description: MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in
 post-transcriptional gene regulation. Some viruses encode their own miRNAs
 and these are increasingly being recognized as important modulators of
 viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a
 highly pathogenic agent that causes acute mass mortalities in carp
 (Cyprinus carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here,
 bioinformatic analyses of the CyHV-3 genome suggested the presence of
 non-conserved precursor miRNA (pre-miRNA) genes. Deep sequencing of small
 RNA fractions prepared from in vitro CyHV-3 infections led to the
 identification of potential miRNAs and miRNA–offset RNAs (moRNAs) derived
 from some bioinformatically predicted pre-miRNAs. DNA microarray
 hybridization analysis, Northern blotting and stem-loop RT-qPCR were then
 used to definitively confirm that CyHV-3 expresses two pre-miRNAs during
 infection in vitro. The evidence also suggested the presence of an
 additional four high-probability and two putative viral pre-miRNAs. MiRNAs
 from the two confirmed pre-miRNAs were also detected in gill tissue from
 CyHV-3-infected carp. We also present evidence that one confirmed miRNA
 can regulate the expression of a putative CyHV-3-encoded dUTPase.
 Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1
 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by
 members of the Alloherpesviridae family, a group distantly related to the
 Herpesviridae family. The discovery of these novel CyHV-3 genes may help
 further our understanding of the biology of this economically important
 virus and their encoded miRNAs may have potential as biomarkers for the
 diagnosis of latent CyHV-3.
description: H361_Unique_Sequence_TagsUnique reads and read counts obtained from deep sequencing of small RNA (~17-25 nt) from Common Carp Brain cells (CCBs) infected with Cyprinid Herpesvirus-3 (CyHV-3) H361 isolate. Fully intact 3’ adapter sequences are trimmed from the 3’ end of each unique read.N076_Unique_Sequence_TagsUnique reads and read counts obtained from deep sequencing of small RNA (~17-25 nt) from Common Carp Brain cells (CCBs) infected with Cyprinid Herpesvirus-3 (CyHV-3) N076 isolate. Fully intact 3’ adapter sequences are trimmed from the 3’ end of each unique read.
DOI: 10.5061/dryad.nb5pq
title: Data from: Temperature-sensitive fitness cost of insecticide resistance in Chinese populations of the diamondback moth Plutella xylostella

description: Alleles conferring a higher adaptive value in one environment may have a
 detrimental impact on fitness in another environment. Alleles conferring
 resistance to pesticides and drugs provide textbook examples of this
 trade-off as, in addition to conferring resistance to these molecules,
 they frequently decrease fitness in pesticide/drug-free environments. We
 show here that resistance to chlorpyrifos, an organophosphate (OP), in
 Chinese populations of the diamondback moth, Plutella xylostella, is
 conferred by two mutations of ace1 – the gene encoding the
 acetylcholinesterase enzyme targeted by OPs – affecting the amino acid
 sequence of the corresponding protein. These mutations were always linked,
 consistent with the segregation of a single resistance allele, ace1R,
 carrying both mutations, in the populations studied. We monitored the
 frequency of ace1R (by genotyping more than 20 000 adults) and the level
 of resistance (through bioassays on more than 50 000 individuals) over
 several generations. We found that the ace1R resistance allele was costly
 in the absence of insecticide and that this cost was likely recessive.
 This fitness costs involved a decrease in fecundity: females from
 resistant strains laid 20% fewer eggs, on average, than females from
 susceptible strains. Finally, we found that the fitness costs associated
 with the ace1R allele were greater at high temperatures. At least two life
 history traits were involved: longevity and fecundity. The relative
 longevity of resistant individuals was affected only at high temperatures
 and the relative fecundity of resistant females – which was already
 affected at temperatures optimal for development – decreased further at
 high temperatures. The implications of these findings for resistance
 management are discussed.
description: Data on ace1
 genotypesvariations of on ace1
 genotypes as affected by temperatures.Data on
 kithe
 variations of ki values corresponding to different generations and
 strainsData on longevity and
 fortilitylongevity and fortility
 in R and S insect strains under different temperatureData on longevity and
 fertility.xlsxData on
 mortalitymortality in R and S
 insect strains under different temperatures
DOI: 10.5061/dryad.q3r3k
title: Data from: A dynamic framework for the study of optimal birth intervals reveals the importance of sibling competition and mortality risks

description: Human reproductive patterns have been well studied, but the mechanisms by
 which physiology, ecology and existing kin interact to affect the life
 history need quantification. Here, we create a model to investigate how
 age-specific interbirth intervals adapt to environmental and intrinsic
 mortality, and how birth patterns can be shaped by competition and help
 between siblings. The model provides a flexible framework for studying the
 processes underlying human reproductive scheduling. We developed a
 state-based optimality model to determine age-dependent and
 family-dependent sets of reproductive strategies, including the state of
 the mother and her offspring. We parameterized the model with realistic
 mortality curves derived from five human populations. Overall, optimal
 birth intervals increase until the age of 30 after which they remain
 relatively constant until the end of the reproductive lifespan. Offspring
 helping each other does not have much effect on birth intervals.
 Increasing infant and senescent mortality in different populations
 decreases interbirth intervals. We show that sibling competition and
 infant mortality interact to lengthen interbirth intervals. In
 lower-mortality populations, intense sibling competition pushes births
 further apart. Varying the adult risk of mortality alone has no effect on
 birth intervals between populations; competition between offspring drives
 the differences in birth intervals only when infant mortality is low.
 These results are relevant to understanding the demographic transition,
 because our model predicts that sibling competition becomes an important
 determinant of optimal interbirth intervals only when mortality is low, as
 in post-transition societies. We do not predict that these effects alone
 can select for menopause.
description: Model source
 codeThis link is to a page
 providing access to code hosted on Zenodo. The Zenodo page also includes a
 link to source code hosted on GitHub.Model data
 filesData files from all
 experiments used to generate figures in the paperibi model
 output.zipAnalysis
 codeThis link is to a page
 providing access to code hosted on Zenodo. The Zenodo page also includes a
 link to analysis code hosted on GitHub.
DOI: 10.5061/dryad.8160
title: Data from: De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques.

description: Next-generation sequencing (NGS) technologies are increasingly applied in
 many organisms, including non-model organisms that are important for
 ecological and conservation purposes. Illumina and 454 sequencing are
 among the most used NGS technologies and have been shown to produce
 optimal results at reasonable costs when used together. Here, we describe
 the combined application of these two NGS technologies to characterize the
 transcriptome of a plant species of ecological and conservation relevance
 for which no genomic resource is available, Scabiosa columbaria. We
 obtained 528,557 reads from a 454 GS-FLX run and a total of 28,993,627
 reads from two lanes of an Illumina GAII single run. After reads trimming,
 the de novo assembly of both types of reads produced 109,630 contigs. Both
 the contigs and the &gt;75 bp remaining singletons were blasted
 against Uniprot/Swissprot database, resulting in 29,676 and 10,515
 significant hits, respectively. Based on sequence similarity with known
 gene products, these sequences represent at least 12,516 unique genes,
 most of which are well covered by contig sequences. In addition, we
 identified 4,320 microsatellite loci, of which 856 had flanking sequences
 suitable for PCR primer design. We also identified 75,054 putative SNPs.
 This annotated sequence collection and the relative molecular markers
 represent a main genomic resource for S. columbaria which should
 contribute to future research in conservation and population biology
 studies. Our results demonstrate the utility of NGS technologies as
 starting point for the development of genomic tools in nonmodel but
 ecologically important species.
description: Supplementary material
 S1Supplementary material
 S2Supplementary material
 S3
DOI: 10.5061/dryad.r8r2k
title: Data from: "You are not what you eat: massive parallel sequencing reveals that gut microbiome is not diet-related in larval Dilophus febrilis (Diptera: Bibionidae)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

description: This article documents the public availability of metagenome sequence data
 from 454 amplicon sequencing of larval dipteran gut (Dilophus febrilis)
 and their potential food sources dwarf shrub litter (Vaccinium
 gaultheroides), grass litter (Dactylis glomerata), and cow dung (Bos
 primigenius taurus).
description: Filtered_dataFiltered data (Pyro Pipeline, OTUs) of 454 amplicon sequencing: D-D: Diptera fed with dwarf-shrub litter, D-G: Diptera fed with grass litter, D-C: Diptera fed with cow dung, DL: Dwarf-shrub litter, GL: Grass litter, CD: Cow dung.