cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3d6g1
title: Data from: Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation

description: Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater
 fishes that have a puzzling biogeographical disjunction across southern
 Australia. Current understanding of pygmy perch phylogenetic relationships
 suggests past east-west migrations across a vast expanse of now arid
 habitat in central southern Australia, a region lacking contemporary
 rivers. Pygmy perches also represent a threatened group with confusing
 taxonomy and potentially cryptic species diversity. Here, we present the
 first study of the evolutionary history of pygmy perches based on
 genome-wide information. Data from 13,991 ddRAD loci and a concatenated
 sequence of 1,075,734 bp were generated for all currently described and
 potentially cryptic species. Phylogenetic relationships, biogeographic
 history and cryptic diversification were inferred using a framework that
 combines phylogenomics, species delimitation and estimation of divergence
 times. The genome-wide phylogeny clarified the biogeographic history of
 pygmy perches, demonstrating multiple east-west events of divergence
 within the group across the Australian continent. These results also
 resolved discordance between nuclear and mitochondrial data from a
 previous study. In addition, we propose three cryptic species within a
 southwestern species complex. The finding of potentially new species
 demonstrates that pygmy perches may be even more susceptible to ecological
 and demographic threats than previously thought. Our results have
 substantial implications for improving conservation legislation of pygmy
 perch lineages, especially in southwestern Western Australia.
description: Concatenated_4381lociConcatenated alignment of 4,361 ddRAD loci (strict dataset)Concatenated_13991lociConcatenated alignment of 13,991 ddRAD loci (relaxed dataset)
DOI: 10.15468/dl.mtxf3e
title: Occurrence Download

description: A dataset containing 121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-180 -60,-70 -60,-70 70,-180 70,-180 -60))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (e9f60bdb-217d-4b4e-a22a-2781321220a1, 28eb1a3f-1c15-4a95-931a-4af90ecb574d, 2538e1c8-ae3c-4812-b6aa-ca9aa53ba277, bf0d80b3-46da-4e60-b1cf-39f2320acb43, c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f, 1928bdf0-f5d2-11dc-8c12-b8a03c50a862)",
 "TaxonKey is Balaenoptera edeni",
 "Year 2000-2026"
 ]
}

 The dataset includes 121 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000475-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j7245
title: Data from: An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

description: Salmonids are an important cultural and ecological resource exhibiting
 near worldwide distribution between their native and introduced range.
 Previous research has generated linkage maps and genomic resources for
 several species as well as genome assemblies for two species. We first
 leveraged improvements in mapping and genotyping methods to create a dense
 linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling
 family data from different sources. We successfully mapped 14,620 SNP loci
 including 2,336 paralogs in subtelomeric regions. This improved map was
 then used as a foundation to integrate genomic resources for gene
 annotation and population genomic analyses. We anchored a total of 286
 scaffolds from the Atlantic salmon genome to the linkage map to provide a
 framework for the placement 11,728 Chinook salmon ESTs. Previously
 identified thermotolerance QTL were found to co-localize with several
 candidate genes including HSP70, a gene known to be involved in thermal
 response, as well as its inhibitor. Multiple regions of the genome with
 elevated divergence between populations were also identified, and
 annotation of ESTs in these regions identified candidate genes for fitness
 related traits such as stress response, growth, and behavior.
 Collectively, these results demonstrate the utility of combining genomic
 resources with linkage maps to enhance evolutionary inferences.
description: Genotypes for female
 consensus map formatted for LepMapThis file contains
 genotypes for haploid and diploid families used to create the female
 consensus linkage map. Description of data is in the ReadMe
 file.HapDipFemConsensus.linkageGenotypes for male diploid map formatted for LepMapDipMale.linkage contains the genotypes used to produce the diploid male map in McKinney et al. 2015. Description of data is in the ReadMe file.DipMale.linkageLocusNamingKeyLocusNamingKey.xlsx provides a lookup table to convert locus names used in HapDipFemConsensus.linkage and DipMale.linkage to the names presented in the linkage maps in McKinney et al. 2015.
DOI: 10.5061/dryad.7kt3h
title: Data from: Anticipating the emergence of infectious diseases

description: In spite of medical breakthroughs, the emergence of pathogens continues to
 pose threats to both human and animal populations. We present candidate
 approaches for anticipating disease emergence prior to large-scale
 outbreaks. Through use of ideas from the theories of dynamical systems and
 stochastic processes we develop approaches which are not specific to a
 particular disease system or model, but instead have general
 applicability. The indicators of disease emergence detailed in this paper
 can be classified into two parallel approaches: a set of early-warning
 signals based around the theory of critical slowing down and a
 likelihood-based approach. To test the reliability of these two approaches
 we contrast theoretical predictions with simulated data. We find good
 support for our methods across a range of different model structures and
 parameter values.
description: anticipating_emergenceAll code used to simulate time series data, analyse data and create figures for the paper
DOI: 10.5061/dryad.7sj8s
title: Data from: "De novo assembled transcriptome of organs involved in reproduction in an endangered endemic Iberian cyprinid fish (Squalius pyrenaicus)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

description: Sex determination systems are diverse, especially among fish, and include
 genetic and/or environmental components. Unexpectedly for such a basic
 aspect of development, sex determination systems change rapidly during
 evolution and gonadal fate is not ultimate, being actively maintained
 lifelong. Here, sequences of expressed genes involved in maintenance of
 gonad identity and reproduction processes were obtained through
 transcriptome assembly of the brain-gonadal axis tissues of a freshwater
 fish inhabiting highly variable environments, the gonochoristic Iberian
 fish Squalius pyrenaicus. Through Illumina total RNA-sequencing, male and
 female transcriptomes of brain and gonad tissues were assembled with
 Trans-ABySS software and merged to produce a more comprehensive S.
 pyrenaicus transcriptome. Coding sequences (CDS) predicted by TransDecoder
 were annotated using blastx. By means of read mapping against the
 reference transcriptome and CDS datasets, using Bowtie2, the accuracy of
 read mapping was assessed. This first endemic Iberian cyprinid
 transcriptome of organs involved in reproduction processes may serve as a
 valuable genomic resource for studying sexual mechanisms and other aspects
 of evolution, such as speciation and responses to environmental changes,
 and may be a useful tool for conservation studies since S. pyrenaicus is
 an endangered species.
description: ORFs blast hits
 (1)S.
 pyrenaicus ORFs blastx hits identified against NCBI non-redundant protein
 databasetabela_anotacao_contigs_blast_geneID_1.xlsxPredicted coding sequences GO annotation (1)GO terms in DAVID “all” category associated to the CDS datasettabela_anotacao_go_1.xlsxReference transcriptome blast hitsS. pyrenaicus reference transcriptome blastx hits identified against NCBI non-redundant protein databasetabela_anotacao_contigs_blast_geneID_transcriptome_1.xlsxReference transcriptome sequencesS. pyrenaicus de novo assembled transcriptome with Trans-ABySS softwarepp_contigs_nonRedudant.fa.bz2ORFs sequencesS. pyrenaicus transcriptome coding sequences (CDS) predicted by TransDecoder softwarepp_contigs_nonRedudant_transdecoder_cds_nonRedudant.fa.bz2
DOI: 10.5061/dryad.7v81b
title: Data from: Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians

description: Recently, microbiologists have focused on characterizing the probiotic
 role of skin bacteria for amphibians threatened by the fungal disease
 chytridiomycosis. However, the specific characteristics of microbial
 diversity required to maintain health or trigger disease are still not
 well understood in natural populations. We hypothesized that seasonal and
 developmental transitions affecting susceptibility to chytridiomycosis
 could also alter the stability of microbial assemblages. To test our
 hypothesis, we examined patterns of skin bacterial diversity in two
 species of declining amphibians (Lithobates yavapaiensis and
 Eleutherodactylus coqui) affected by the pathogenic fungus
 Batrachochytrium dendrobatidis (Bd). We focused on two important
 transitions that affect Bd susceptibility: ontogenetic (from juvenile to
 adult) shifts in E. coqui and seasonal (from summer to winter) shifts in
 L. yavapaiensis. We used a combination of community-fingerprinting
 analyses and 16S rRNA amplicon sequencing to quantify changes in bacterial
 diversity and assemblage composition between seasons and developmental
 stages, and to investigate the relationship between bacterial diversity
 and pathogen load. We found that winter-sampled frogs and juveniles, two
 states associated with increased Bd susceptibility, exhibited higher
 diversity compared with summer-sampled frogs and adult individuals. Our
 findings also revealed that hosts harbouring higher bacterial diversity
 carried lower Bd infections, providing support for the protective role of
 bacterial communities. Ongoing work to understand skin microbiome
 resilience after pathogen disturbance has the potential to identify key
 taxa involved in disease resistance.
description: LongoetalRSOS.tarThis archive contains four files: (1) mapping file, (2) OTU table, (3) split libraries using the forward sequence read, and (4) tree file.
DOI: 10.5061/dryad.6dq3r10
title: Data from: Evaluating the costs and benefits of marsh-management strategies while accounting for uncertain sea-level rise and ecosystem response

description: Prioritization of marsh-management strategies is a difficult task as it
 requires a manager to evaluate the relative benefits of each strategy
 given uncertainty in future sea-level rise and in dynamic marsh response.
 A modeling framework to evaluate the costs and benefits of management
 strategies while accounting for both of these uncertainties has been
 developed. The base data for the tool are high-resolution
 uncertainty-analysis results from SLAMM (the Sea-Level Affecting Marshes
 Model) under different adaptive-management strategies. These results are
 combined with an ecosystem-valuation assessment from stakeholders. Model
 results and stakeholder values are linked together using "utility
 functions" that characterize the relationship between stakeholder
 values and geometric metrics such as "marsh area," marsh
 edge," or "marsh width." The expected-value of each
 site's ecosystem benefits can then be calculated and compared using
 estimated costs for each strategy. Estimates of optimal marsh-management
 strategies may then be produced, maximizing the "ecosystem benefits
 per estimated costs" ratio.
description: NYSERDA_SLAMM_DMMTThis data repository contains all of the data files required to run the Dynamic Marsh Management Tool (DMMT) as described in the manuscript “Evaluating the costs and benefits of marsh-management strategies while accounting for uncertain sea-level rise and ecosystem response.”
DOI: 10.5061/dryad.4bm23
title: Data from: Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

description: The unicellular protozoan parasite Leishmania causes the neglected
 tropical disease leishmaniasis, affecting 12 million people in 98
 countries. In South America where the Viannia subgenus predominates, so
 far only L. (Viannia) braziliensis and L. (V.) panamensis have been
 sequenced, assembled and annotated as reference genomes. Addressing this
 deficit in molecular information can inform species typing,
 epidemiological monitoring and clinical treatment. Here, L. (V.) naiffi
 and L. (V.) guyanensis genomic DNA was sequenced to assemble these two
 genomes as draft references from short sequence reads. The methods used
 were tested using short sequence reads for L. braziliensis M2904 against
 its published reference as a comparison. This assembly and annotation
 pipeline identified 70 additional genes not annotated on the original
 M2904 reference. Phylogenetic and evolutionary comparisons of L.
 guyanensis and L. naiffi with ten other Viannia genomes revealed four
 traits common to all Viannia: aneuploidy, 22 orthologous groups of genes
 absent in other Leishmania subgenera, elevated TATE transposon copies, and
 a high NADH-dependent fumarate reductase gene copy number. Within the
 Viannia, there were limited structural changes in genome architecture
 specific to individual species: a 45 Kb amplification on chromosome 34 was
 present in all bar L. lainsoni, L. naiffi had a higher copy number of the
 virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had
 a possible minichromosome derived from the 3’ end of chromosome 34. This
 combination of genome assembly, phylogenetics and comparative analysis
 across an extended panel of diverse Viannia has uncovered new insights
 into the origin and evolution of this subgenus and can help improve
 diagnostics for leishmaniasis surveillance.
description: Leishmania guyanensis
 LgCL085 genome sequence filesLeishmania guyanensis
 LgCL085 genome sequence filesLguyanensis_LgCL085_genome.fa.gzLeishmania guyanensis LgCL085 chromosome annotation filesLeishmania guyanensis LgCL085 chromosome annotation filesLGCL085-chromosomes-all-13-new.embl.gzLeishmania guyanensis LgCL085 bin contig annotation filesLeishmania guyanensis LgCL085 bin contig annotation filesLGCL085-bin-all-13-new.embl.gzLeishmania naiffi LnCL223 genome sequence filesLeishmania naiffi LnCL223 genome sequence filesLnaiffi_LnCL223_genome.fa.gzLeishmania naiffi LnCL223 chromosome annotation filesLeishmania naiffi LnCL223 chromosome annotation filesLNCL223-chromosomes-all-6-new.embl.gzLeishmania naiffi LnCL223 bin contig annotation filesLeishmania naiffi LnCL223 bin contig annotation filesLNCL223-bin-all-6-new.embl.gzFigure-1-high-resolutionFigure-1-high-resolutionFigure-1.pdfSupplementary-TablesSupplementary-TablesLnaiffi-Lguyanensis-SupplTables-141217.xlsxSupplementary-DataSupplementary-DataLnaiffi-Lguyanensis-SupplData-141217.docx
DOI: 10.5061/dryad.4p7t2
title: Data from: The adaptive potential of Populus balsamifera L. to phenology requirements in a warmer global climate

description: The manner in which organisms adapt to climate change informs both a
 broader understanding of the evolution of biodiversity as well as plans
 for future conservation and mitigation. We apply common garden and
 association mapping approaches to quantify genetic variance and identify
 loci affecting bud flush and bud set, traits that define a tree’s season
 for height growth, in the boreal forest tree Populus balsamifera L.
 (balsam poplar). Using data from 478 genotypes grown in each of two common
 gardens, one near the southern edge and another near the northern edge of
 P. balsamifera’s range, we found that broad-sense heritability for bud
 flush and bud set was generally high (H2 &gt; 0.5 in most cases),
 suggesting that abundant genetic variation exists for phenological
 response to changes in the length of the growing season. To identify the
 molecular genetic basis of this variation, we genotyped trees for 346
 candidate single nucleotide polymorphisms (SNPs) from 27 candidate genes
 for the CO/FT pathway in poplar. Mixed model analyses of variance
 identified SNPs in 10 genes to be associated with variation either bud
 flush or bud set. Multiple SNPs within FRIGIDA were associated with bud
 flush, whereas multiple SNPs in LEAFY and GIGANTEA 5 were associated with
 bud set. Although there was strong population structure in trait variance,
 except at the most northern populations the geographic distribution of
 multilocus SNP genotypes was widespread, indicating that geographic
 regions may harbor sufficient diversity in functional genes to facilitate
 adaption to future climatic conditions in many populations.
description: RefSNP_annotation_Dryad_KellerOlsonPoplarRefSNPDataSNP data used to develop Q and A matrices.A_matrixPopPopStructureK matrix for association mappingCandidateSNPSPhenotypes_OlsonEtAl2012
DOI: 10.5061/dryad.92c60
title: Data from: Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis)

description: Sex chromosomes have evolved independently in phylogenetically diverse
 flowering plant lineages. The genes governing sex determination in
 dioecious species remain unknown, but theory predicts that the linkage of
 genes influencing male and female function will spur the origin and early
 evolution of sex chromosomes. For example, in an XY system, the origin of
 an active Y may be spurred by the linkage of female suppressing and male
 promoting genes. Garden asparagus (Asparagus officinalis) serves as a
 model for plant sex chromosome evolution, given that it has recently
 evolved an XX/XY sex chromosome system. In order to elucidate the
 molecular basis of gender differences and sex determination, we used
 RNA-sequencing (RNA-Seq) to identify differentially expressed genes
 between female (XX), male (XY) and supermale (YY) individuals. We
 identified 570 differentially expressed genes, and showed that
 significantly more genes exhibited male-biased than female-biased
 expression in garden asparagus. In the context of anther development, we
 identified genes involved in pollen microspore and tapetum development
 that were specifically expressed in males and supermales. Comparative
 analysis of genes in the Arabidopsis thaliana, Zea mays and Oryza sativa
 anther development pathways shows that anther sterility in females
 probably occurs through interruption of tapetum development before
 microspore meiosis.
description: Asparagus officinalis
 transcriptome assemblyRaw garden asparagus
 transcriptome assembly for Harkess et al. (2015). Transcripts were
 digitally normalized to 30X and assembled in Trinity (r2012-10-05). All
 raw RNA-seq reads can be found in NCBI BioProject
 259909.Asparagus_officinalis.trinity.fa.bz2
DOI: 10.15468/dl.zk8k3s
title: Occurrence Download

description: A dataset containing 1323 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "TaxonKey is Myioborus pictus",
 "Year 1000-2026"
 ]
}

 The dataset includes 1323 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000477-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.17448.84488
title: Pearlman updates with table of contents.pdf
DOI: 10.5061/dryad.2v77j
title: Data from: The impacts of oil palm on recent deforestation and biodiversity loss

description: Palm oil is the most widely traded vegetable oil globally, with demand
 projected to increase substantially in the future. Almost all oil palm
 grows in areas that were once tropical moist forests, some of them quite
 recently. The conversion to date, and future expansion, threatens
 biodiversity and increases greenhouse gas emissions. Today, consumer
 pressure is pushing companies toward deforestation-free sources of palm
 oil. To guide interventions aimed at reducing tropical deforestation due
 to oil palm, we analysed recent expansions and modelled likely future
 ones. We assessed sample areas to find where oil palm plantations have
 recently replaced forests in 20 countries, using a combination of
 high-resolution imagery from Google Earth and Landsat. We then compared
 these trends to countrywide trends in FAO data for oil palm planted area.
 Finally, we assessed which forests have high agricultural suitability for
 future oil palm development, which we refer to as vulnerable forests, and
 identified critical areas for biodiversity that oil palm expansion
 threatens. Our analysis reveals regional trends in deforestation
 associated with oil palm agriculture. In Southeast Asia, 45% of sampled
 oil palm plantations came from areas that were forests in 1989. For South
 America, the percentage was 31%. By contrast, in Mesoamerica and Africa,
 we observed only 2% and 7% of oil palm plantations coming from areas that
 were forest in 1989. The largest areas of vulnerable forest are in Africa
 and South America. Vulnerable forests in all four regions of production
 contain globally high concentrations of mammal and bird species at risk of
 extinction. However, priority areas for biodiversity conservation differ
 based on taxa and criteria used. Government regulation and voluntary
 market interventions can help incentivize the expansion of oil palm
 plantations in ways that protect biodiversity-rich ecosystems.
description: Vijay_et_al_2016_oilpalmContains shapefile and georeferenced TIFFs from the paper.
DOI: 10.5281/zenodo.18381156
title: ZAMONAVIY LIBOSLARDA QUROQ TEXNIKASINI  QO'LLASH

description: Ushbu maqola  quroqchilik  san’atining  o‘ziga xos  jihatlari  bilan bog‘liq  an’analar  va  zamonaviy liboslarda  quroq texnikasini  qo‘llash va  liboslar  yaratish yoki bezash borasida  mulohazalar keltirilgan. Shuningdek,  xotin-qizlarni hunarga o‘rgatish,  ularni tadbirkorlik bilan shug‘ullanishga  yo‘naltirish  orqali mehnat resurslari samaradorligini  oshirishga qaratilgan.
DOI: 10.5281/zenodo.18381157
title: ZAMONAVIY LIBOSLARDA QUROQ TEXNIKASINI  QO'LLASH

description: Ushbu maqola  quroqchilik  san’atining  o‘ziga xos  jihatlari  bilan bog‘liq  an’analar  va  zamonaviy liboslarda  quroq texnikasini  qo‘llash va  liboslar  yaratish yoki bezash borasida  mulohazalar keltirilgan. Shuningdek,  xotin-qizlarni hunarga o‘rgatish,  ularni tadbirkorlik bilan shug‘ullanishga  yo‘naltirish  orqali mehnat resurslari samaradorligini  oshirishga qaratilgan.