cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8pd11
title: Data from: Comparative study of the validity of three regions of 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community

description: The nuclear 18S-rRNA gene has been used as a metabarcoding marker in
 massively parallel sequencing (MPS)-based environmental surveys for
 plankton biodiversity research. However, different hypervariable regions
 have been used in different studies, and their utility has been debated
 among researchers. In this study, detailed investigations into 18S-rRNA
 were carried out; we investigated the effective number of sequences
 deposited in international nucleotide sequence databases (INSDs), the
 amplification bias, and the amplicon sequence variability among the three
 variable regions, V1–3, V4–5 and V7–9, using in silico polymerase chain
 reaction (PCR) amplification based on INSDs. We also examined the primer
 universality and the taxonomic identification power, using MPS-based
 environmental surveys in the Sea of Okhotsk, to determine which region is
 more useful for MPS-based monitoring. The primer universality was not
 significantly different among the three regions, but the number of
 sequences deposited in INSDs was markedly larger for the V4–5 region than
 for the other two regions. The sequence variability was significantly
 different, with the highest variability in the V1–3 region, followed by
 the V7–9 region, and the lowest variability in the V4–5 region. The
 results of the MPS-based environmental surveys showed significantly higher
 identification power in the V1–3 and V7–9 regions than in the V4–5 region,
 but no significant difference was detected between the V1–3 and V7–9
 regions. We therefore conclude that the V1–3 region will be the most
 suitable for future MPS-based monitoring of natural eukaryote communities,
 as the number of sequences deposited in INSDs increases.
description: EnvironmentalSurvey.tar.gzAnalysis commands and results of environmental surveys by 454 massively parallel 18S amplicon sequencing of eukaryote community sampled at Monbetsu.EstimationOfPCRSuccessRates.tar.gzAnalysis commands and results for estimating PCR success rates and amplicon sequence variability.EstimationOfEffectiveNumberOfSequences.tar.gzAnalysis commands and results of estimation of effective number of registered sequences.
DOI: 10.5061/dryad.5mv53
title: Data from: Evidence for an active rare biosphere within freshwater protists community

description: Studies on the active rare biosphere at the RNA level are mainly focused
 on Bacteria and Archaea and fail to include the protists, which are
 involved in the main biogeochemical cycles of the earth. In this study,
 the richness, composition and activity of the rare protistan biosphere
 were determined from a temporal survey of two lakes by pyrosequencing. In
 these ecosystems, the always rare OTUs represented 77.2% of the total OTUs
 and 76.6% of the phylogenetic diversity. From the various phylogenetic
 indices computed, the phylogenetic units (PUs) constituted exclusively by
 always rare OTUs were discriminated from the other PUs. Therefore, the
 rare biosphere included mainly taxa that are distant from the reference
 databases compared to the dominant ones. In addition, the rarest OTUs
 represented 59.8% of the active biosphere depicted by rRNA and the
 activity (rRNA:rDNA ratio) increased with the rarity. The high rRNA:rDNA
 ratio determined in the rare fraction highlights that some protists were
 active at low abundances and contribute to ecosystem functioning.
 Interestingly, the always rare and active OTUs were characterized by
 seasonal changes in relation with the main environmental parameters
 measured. In conclusion, the rare eukaryotes represent an active, dynamic
 and overlooked fraction in the lacustrine ecosystems.
description: Clean pyrosequencing
 dataThese sequences were
 checked against the following quality criteria: (i) no Ns, (ii) quality
 score ≥ 23 according to the PANGEA process (Giongo et al., 2010), (iii) a
 minimum sequence length of 200 bp, and (iv) no sequencing error in the
 forward primer. The scripts used were quality.pl and preprocess.pl
 implemented in the pipeline PANAM
 (http://code.google.com/p/panam-phylogenetic-annotation /downloads /list)
 described more in detail in the related paper (Taib et al.
 2013).pooled_sample_Seq.fastaTable1_dataSimilarity and phylogenetic indices determined for each phylogenetic units (PUs) presented in the table 1Phylogeny_fasttree_filesThis compressed file aggregates the FastTree files (newick format) generated by the script panam.plsynthese_OTU_RNA_DNAOTUs with the taxonomies, the DNA and RNA abundances (tab delimited)
DOI: 10.5061/dryad.p928v
title: Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs

description: Accurately delimiting species boundaries is a non-trivial undertaking that
 can have significant effects on downstream inferences. We compared the
 efficacy of commonly-used species delimitation methods (SDMs) and a
 population genomics approach based on genome-wide single nucleotide
 polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent
 Frog Complex currently recognized as a single species (Amolops
 larutensis). First, we used morphological, mitochondrial DNA and
 genome-wide SNPs to identify putative species boundaries by implementing
 non-coalescent and coalescent-based SDMs (mPTP, iBPP, BFD*). We then
 tested the validity of putative boundaries by estimating spatiotemporal
 gene flow (fastsimcoal2, ABBA-BABA) to assess the extent of genetic
 isolation among putative species. Our results show that the A. larutensis
 complex runs the gamut of the speciation continuum from highly divergent,
 genetically isolated lineages (mean Fst = 0.9) to differentiating
 populations involving recent gene flow (mean Fst = 0.05; Nm &gt; 5).
 As expected, SDMs were effective at delimiting divergent lineages in the
 absence of gene flow but overestimated species in the presence of marked
 population structure and gene flow. However, using a population genomics
 approach and the concept of species as separately evolving metapopulation
 lineages as the only necessary property of a species, we were able to
 objectively elucidate cryptic species boundaries in the presence of past
 and present gene flow. This study does not discount the utility of SDMs
 but highlights the danger of violating model assumptions and the
 importance of carefully considering methods that appropriately fit the
 diversification history of a particular system.
description: md5mc48p10STRUCTURE file for sNMF analysis and GENODIVE. Filtered using min. depth = 5; missing data = 50%md5mc48p.10.strmd5mc68p.10STRUCTURE file for sNMF analysis and GENODIVE. Filtered using min. depth = 5; missing data = 30%md10mc48p.10STRUCTURE file for sNMF analysis and GENODIVE. Filtered using min. depth = 10; missing data = 50%md10mc68p.10STRUCTURE file for sNMF analysis and GENODIVE. Filtered using min. depth = 10; missing data = 30%16S.ND1.concatenated.nexconcatenated mitochondrial sequence matrix for MrBayes.Concatenated.mrbayes2.nexsNMF analysisExample R script for the sNMF analysisLEA.Rmd5mc48_final_noinvariantSNP input file for maximum likelihood phylogenetic analysis after filtering for invariant and non-binary sitesmd5mc48p.10Input file for ABBA-BABA analysis. Min depth = 5; missing data = 50%snapp.7spInput file for SNAPP
DOI: 10.5061/dryad.pb5vv
title: Data from: Opsins have evolved under the permanent heterozygote model: insights from phylotranscriptomics of Odonata

description: Gene duplication plays a central role in adaptation to novel environments
 by providing new genetic material for functional divergence and evolution
 of biological complexity. Several evolutionary models have been proposed
 for gene duplication to explain how new gene copies are preserved by
 natural selection, but these models have rarely been tested using
 empirical data. Opsin proteins, when combined with a chromophore, form a
 photopigment that is responsible for the absorption of light, the first
 step in the phototransduction cascade. Adaptive gene duplications have
 occurred many times within the animal opsins’ gene family, leading to
 novel wavelength sensitivities. Consequently, opsins are an attractive
 choice for the study of gene duplication evolutionary models. Odonata
 (dragonflies and damselflies) have the largest opsin repertoire of any
 insect currently known. Additionally, there is tremendous variation in
 opsin copy number between species, particularly in the
 long-wavelength-sensitive (LWS) class. Using comprehensive
 phylotranscriptomic and statistical approaches, we tested various
 evolutionary models of gene duplication. Our results suggest that both the
 blue-sensitive (BS) and LWS opsin classes were subjected to strong
 positive selection that greatly weakens after multiple duplication events,
 a pattern that is consistent with the permanent heterozygote model. Due to
 the immense interspecific variation and duplicability potential of opsin
 genes among odonates, they represent a unique model system to test
 hypotheses regarding opsin gene duplication and diversification at the
 molecular level.
description: Opsin
 Alignment1Multiple sequence COBALT
 alignment putative Odonata and Ephemeroptera opsin protein sequences
 including homologous opsin sequences from mollusks
 (outgroup).Alignment1.fastaOpsin Alignment2Multiple sequence COBALT alignment of putative Odonata and Ephemeroptera opsin protein sequences including homologous opsin sequences from mollusks (outgroup). All partial opsin sequences (&lt; 1056 bp and &lt; 7 transmembrane domains) were excluded.Alignment2.fastaOpsin Alignment3Multiple sequence COBALT alignment of putative Odonata and Ephemeroptera opsin protein sequences including homologous opsin sequences from mollusks (outgroup) combined with opsins identified in (Futahashi et al. 2015).Alignment3.fastaBayesian "diffusion" modelNaive Bayesian model of selection "diffusion" written in R programming language.Bayesian_diffusion_model.rTranscriptome Trinity assembliesTranscriptome Trinity assemblies. NCBI accession numbers of raw RNA-seq libraries that were used to assemble transcriptomes: SRR2164542 SRR2164543 SRR2164551 SRR2164552 SRR2157378 SRR2157379 SRR2157380 SRR2157381 SRR2157382 SRR2157383 SRR2164544 SRR2164545 SRR2157367 SRR2164546 SRR2164547 SRR2164548 SRR2157371 SRR2157372 SRR2164549 SRR2164550transcriptomes.tgz
DOI: 10.5061/dryad.6p2n6
title: Data from: Heritable gene expression differences between apomictic clone members in Taraxacum officinale: insights into early stages of evolutionary divergence in asexual plants

description: Background: Asexual reproduction has the potential to enhance deleterious
 mutation accumulation and to constrain adaptive evolution. One source of
 mutations that can be especially relevant in recent asexuals is activity
 of transposable elements (TEs), which may have experienced selection for
 high transposition rates in sexual ancestor populations. Predictions of
 genomic divergence under asexual reproduction therefore likely include a
 large contribution of transposable elements but limited adaptive
 divergence. For plants empirical insight into genome divergence under
 asexual reproduction remains limited. Here, we characterize expression
 divergence between clone members of a single apomictic lineage of the
 common dandelion (Taraxacum officinale) to contribute to our knowledge of
 genome evolution under asexuality. Results: Using RNA-Seq, we show that
 about one third of heritable divergence within the apomictic lineage is
 driven by TEs and TE-related gene activity. In addition, we identify
 non-random transcriptional differences in pathways related to acyl-lipid
 and abscisic acid metabolisms which might reflect functional divergence
 within the apomictic lineage. We analyze SNPs in the transcriptome to
 assess genetic divergence between the apomictic clone members and reveal
 that heritable expression differences between the accessions are not
 explained simply by genome-wide genetic divergence. Conclusion: The
 present study depicts a first effort towards a more complete understanding
 of apomictic plant genome evolution. We identify abundant TE activity and
 ecologically relevant functional genes and pathways affecting heritable
 within-lineage expression divergence. These findings offer valuable
 resources for future work looking at epigenetic silencing and
 Cis-regulation of gene expression with particular emphasis on the effects
 of TE activity on asexual species’ genome.
description: de novo transcriptome
 assembly of dandelion leaf tissueIllumina sequencing
 Trinity assemblyTrinity.fastaField experiment raw count tableraw count of reads mapping the reference transcriptome using RSEM (semi-natural field experiment)F_Trinity_genes.counts.matrixGreenhouse experiment raw count tableraw count of reads mapping the reference transcriptome using RSEM (greenhouse experiment)GH_Trinity_genes.counts.matrix
DOI: 10.15468/avebmp
title: THE HUDSONIAN CURLEW

description: This dataset contains the digitized treatments in Plazi based on the original book chapter Lath. (1843): THE HUDSONIAN CURLEW. In: The birds of America: from drawings made in the United States and their territories. New York: J. B. Chevalier: 42-47, DOI: 10.5281/zenodo.18317323
DOI: 10.5061/dryad.f1782h7
title: Data from: Genomewide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication

description: Studies of genetic diversity among phenotypically distinct crop landraces
 improve our understanding of fruit evolution and genome structure under
 domestication. Chile peppers (Capsicum spp. L.) are economically valuable
 and culturally important species, and extensive phenotypic variation among
 landraces exists in southern Mexico, a center of C. annuum diversity. We
 collected 103 chile pepper seed accessions from 22 named landraces across
 27 locations in southern Mexico. We genotyped these accessions with
 genotyping-by-sequencing (GBS), yielding 32,623 filtered single-nucleotide
 polymorphisms. Subsequently, we genotyped 32 additional C. annuum
 accessions from a global collection for comparison to the Mexican
 collection. Within the Mexican collection, genetic assignment analyses
 showed clear genetic differentiation between landraces and clarified the
 unique nature of the Tusta landrace. Further clustering analyses indicated
 that the largest fresh-use Chile de Agua, and dry-use Costeño landraces
 were part of separate clades, indicating that these two landraces likely
 represent distinct populations. The global accessions showed considerable
 admixture and limited clustering, which may be due to the collapse of
 use-type divisions outside of Central America. The separation of the
 Mexican landraces in part by fruit morphology related to use, highlights
 the relevance of this use-type morphological diversity for plant breeders
 and the utility of fruit development variation for evolutionary
 biologists.
description: Full Mexican Chile
 Pepper Collection Genotype TableGenotype table in
 variant call format for all 32,623 SNPs identified in the Mexican chile
 pepper collection of this study. Includes genotypes from both plants in
 each population.mexPep_mexCollection_allPlants.vcfGenotype table for entire chile pepper collectionGenotype table for entire chile pepper collection, in variant call format. Includes one individual per each accession, and only SNPs of sufficient quality, for comparison between the chile pepper collection from Mexico and the global collection.mexPep_fullCollection_OnePerAcc.vcf
DOI: 10.5061/dryad.q5tm5
title: Data from: A genetic legacy of introgression confounds phylogeny and biogeography in oaks

description: Oaks (Quercus L.) have long been suspected to hybridize in nature, and
 widespread genetic exchange between morphologically defined species is
 well documented in two- to six-species systems, but the phylogenetic
 consequences of hybridization in oaks have never been demonstrated in a
 phylogenetically diverse sample. Here, we present phylogenomic analyses of
 a ca 30 Myr clade that strongly support morphologically defined species
 and the resolution of novel clades of white oaks; however, historical
 hybridization across clade boundaries is detectable and, undiagnosed,
 would obscure the imprint of biogeographic history in the phylogeny.
 Phylogenetic estimation from restriction-site-associated DNA sequencing
 data for 156 individuals representing 81 species supports two successive
 intercontinental disjunctions of white oaks: an early vicariance between
 the Eurasian and American white oaks, and a second, independent radiation
 represented by two relictual species. A suite of subsampled and
 partitioned analyses, however, supports a more recent divergence of the
 Eurasian white oaks from within the American white oaks and suggests that
 historic introgression between the Eurasian white oaks and a now-relictual
 lineage biases concatenated phylogenetic estimates. We demonstrate how
 divergence and reticulation both influence our understanding of the timing
 and nature of diversification and global colonization in these
 ecologically and economically important taxa.
description: Complete RAD dataset in
 phylip format (zipped).Complete concatenated
 phylogenetic dataset ( min. 4 individuals per locus) in phylip format.
 Clustered via PyRAD at 90% similarity within and among
 samples.c90d6m4p3.phy.gzZipped ".loci" file.Locus-delimited dataset (".loci) output from PyRAD for entire RAD dataset.c90d6m4p3.loci.gzncsc90d6m4p3.nexComplete RAD dataset (min. 4 individuals per locus) in interleaved nexus format.Taxa partitionTaxa partition in nexus format for use in SVDq analysis implemented in PAUP 4a150. To be used in conjunction with RAD dataset in nexus format.svdtax.txt
DOI: 10.5061/dryad.m3n87
title: Data from: Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerata L.) through transcriptome analysis

description: Orchardgrass (Dactylis glomerata L.) is a long-lived, cool-season forage
 grass that is commonly used for hay production. Despite its economic
 importance, orchardgrass genome remains relatively unexplored. In this
 study, we used Illumina RNA sequencing to identify gene-associated
 molecular markers, including simple sequence repeats (SSRs) and single
 nucleotide polymorphisms (SNPs), as well as heat stress-induced
 differentially expressed genes (DEGs) in two orchardgrass genotypes,
 ‘Baoxing’ (heat resistant) and ‘01998’ (heat susceptible). Approximately
 163 million high-quality trimmed reads were generated from 207 million raw
 reads using the Illumina HiSeq 2000 platform. A total of 126 846 unigenes
 were obtained after de novo assembly of the trimmed reads, and 40 078
 unigenes were identified as coding sequences (CDSs). Based on the
 assembled unigenes, 669 300 high-quality SNPs, including 416 099
 transitions and 257 736 transversions, were contained in 75 875 unigenes.
 In addition, a total of 8475 microsatellites were detected in 7764
 unigenes. When placed under heat stress, the total number of DEGs in
 ‘Baoxing’ (3527) was higher than in ‘01998’ (2649), indicating that in
 comparison with heat-susceptible ‘01998’, heat-resistant ‘Baoxing’ seems
 to have more unigenes that respond to heat stress. The high-throughput
 transcriptome sequencing of orchardgrass under heat stress provides useful
 information for gene identification and for the development of SNP and SSR
 molecular markers. The comparison of DEGs under different periods of heat
 stress allowed us to identify a wealth of candidate DEGs that can be
 further analysed in order to determine the genetic mechanisms underlying
 heat tolerance in orchardgrass.
description: SNPs
 uploadSNPs for all the samples
 of orchardgrassSSR
 uploadSSR for all samples of
 orchardgrasunigene
 uploadThe unigene is the final
 DNA sequence assemblyGenotyping results for
 SSR validationSNP
 validationAligned sequences for SNP
 validation.docxThe results of qRT-PCR
 for validated genesReadcount_FPKMDifferential_analysis_results
DOI: 10.5061/dryad.9d12p
title: Data from: Genome-wide SNPs resolve a key conflict between sequence and allozyme data to confirm another threatened candidate species of river blackfishes (Teleostei: Percichthyidae: Gadopsis)

description: Conflicting results from different molecular datasets have long confounded
 our ability to characterise species boundaries. Here we use genome-wide
 SNP data and an expanded allozyme dataset to resolve conflicting
 systematic hypotheses on an enigmatic group of fishes (Gadopsis, river
 blackfishes, Percichthyidae) restricted to southeastern Australia.
 Previous work based on three sets of molecular markers: mtDNA, nuclear
 intron DNA and 51 allozyme loci was unable to clearly resolve the status
 of a putative fifth candidate species (SWV) within Gadopsis marmoratus.
 Resolving the taxonomic status of candidate species SWV is particularly
 critical as based on IUCN criteria this taxon would be considered
 Critically Endangered. After all filtering steps we retained a subset of
 10,862 putatively unlinked SNP loci for population genetic and
 phylogenomic analyses. Analyses of SNP loci based on maximum likelihood,
 fastSTRUCTURE and DAPC were all consistent with the previous and updated
 allozyme results supporting the validity of the candidate Gadopsis species
 SWV. Immediate conservation actions should focus on preventing take by
 anglers, protection of water resources to sustain perennial reaches and
 drought refuge pools, and aquatic and riparian habitat protection and
 improvement. In addition, a formal morphological taxonomic review of the
 genus Gadopsis is urgently required.
description: Gadopsis_fastStructurefastSTRUCTURE input format for 44 Gadopsis samples and 10,862 unlinked SNPsGadopsis_phylipPhylip input for 44 Gadopsis samples and 17,394 concatenated ddRAD loci (1,541,113 bp)Gadopsis_lociLoci file from 44 Gadopsis samples and 17395 ddRAD lociGadopsis_44_17394.loci