cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.117cf
title: Data from: AmpuBase: a transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae)

description: Background: Gastropoda, with approximately 80,000 living species, is the
 largest class of Mollusca. Among gastropods, apple snails (family
 Ampullariidae) have members that are widely distributed in tropical and
 subtropical freshwater ecosystems and are ecologically and economically
 important. They exhibit various morphological and physiological
 adaptations to their respective habitats, which make them ideal candidates
 for studying adaptation, population divergence, speciation, and
 larger-scale patterns of diversity, including biogeography of native and
 invasive populations. The limited availability of genomic data, however,
 hinders in-depth ecological and evolutionary studies of these non-model
 organisms. Results: Using Illumina Hiseq platforms, we sequenced 1,220
 million reads for seven species of apple snails. Together with the RNA-Seq
 data of two apple snails, we conducted de novo transcriptome assembly of
 eight species covering five genera of Ampullariidae, including
 representatives of the Old World and New World lineages. There were 20,730
 to 35,828 unigenes with predicted open read frames for the eight species,
 with N50 (shortest sequence length at 50% of the unigenes) ranging from
 1,320 to 1,803 bp. 69.7 % to 80.2 % of these unigenes were functionally
 annotated by searching against databases of NCBI’s non-redundant, Gene
 Ontology and Kyoto Encyclopaedia of Genes and Genomes. With these data we
 developed AmpuBase, a relational database that features online BLAST for
 DNA/protein sequences, keyword search for unigenes/functional terms, and
 download functions for sequences and whole transcriptomes. Conclusions: In
 summary, we have generated comprehensive transcriptome data for multiple
 ampullariid genera and species, and created a publicly accessible database
 with a user-friendly interface to facilitate future basic and applied
 studies on ampullariids, and comparative molecular studies with other
 invertebrates.
description: Ampullaridae_alignmentThree genes alignment file of 38 ampullariidsAmpullariidae_alignment.nexEightsp_alignmentThree genes alignment file of eight targeted speciesAmpullariids transcriptomeAssembled transcriptomes of eight ampullariids
DOI: 10.5061/dryad.pf58510
title: Data from: Efficiency of genomic prediction across two Eucalyptus nitens seed orchards with different selection histories

description: Genomic selection is expected to enhance the genetic improvement of forest
 tree species by providing more accurate estimates of breeding values
 through marker-based relationship matrices compared with pedigree-based
 methodologies. When adequately robust genomic prediction models are
 available, an additional increase in genetic gains can be made possible
 with the shortening of the breeding cycle through elimination of the
 progeny testing phase and early selection of parental candidates. The
 potential of genomic selection was investigated in an advanced Eucalyptus
 nitens breeding population focused on improvement for solid wood
 production. A high-density SNP chip (EUChip60K) was used to genotype 691
 individuals in the breeding population, which represented two seed
 orchards with different selection histories. Phenotypic records for growth
 and form traits at age six, and for wood quality traits at age seven were
 available to build genomic prediction models using GBLUP which were
 compared to the traditional pedigree-based alternative using BLUP. GBLUP
 demonstrated that breeding value accuracy would be improved and
 substantial increases in genetic gains towards solid wood production would
 be achieved. Cross-validation within and across two different seed
 orchards indicated that genomic predictions would likely benefit in terms
 of higher predictive accuracy from increasing the size of the training
 data sets through higher relatedness and better utilization of LD
description: Data_for_DRYADCompressed file containing genomic information, pedigree and phenotypic data used in the analysis
DOI: 10.5061/dryad.s296n
title: Data from: Unlocking the vault: next generation museum population genomics

description: Natural history museum collections provide unique resources for
 understanding how species respond to environmental change, including the
 abrupt, anthropogenic climate change of the past century. Ideally,
 researchers would conduct genome-scale screening of museum specimens to
 explore the evolutionary consequences of environmental changes, but to
 date such analyses have been severely limited by the numerous challenges
 of working with the highly degraded DNA typical of historic samples. Here
 we circumvent these challenges by using custom, multiplexed, exon-capture
 to enrich and sequence ~11,000 exons (~4Mb) from early 20th century museum
 skins. We used this approach to test for changes in genomic diversity
 accompanying a climate-related range retraction in the alpine chipmunks
 (Tamias alpinus) in the high Sierra Nevada area of California, USA. We
 developed robust bioinformatic pipelines that rigorously detect and
 filter-out base misincorporations in DNA derived from skins, most of which
 likely resulted from post-mortem damage. Furthermore, to accommodate
 genotyping uncertainties associated with low-medium coverage data, we
 applied a recently developed probabilistic method to call SNPs and
 estimate allele frequencies and the joint site frequency spectrum. Our
 results show increased genetic subdivision following range retraction, but
 no change in overall genetic diversity at either non-synonymous or
 synonymous sites. This case study showcases the advantages of integrating
 emerging genomic and statistical tools in museum collection-based
 population genomic applications. Such technical advances greatly enhance
 the value of museum collections, even where a pre-existing reference is
 lacking, and points to a broad range of potential applications in
 evolutionary and conservation biology.
description: Tamias alpinus (the
 Alpine chipmunks) exon capture probe designTargeted exons were
 derived from 6,249 protein-coding genes with a target size totaling 4Mb,
 and spanned a wide range of evolutionary rates in the genome (Bi et al.
 2012). In addition to the T. alpinus exons, we targeted the ~16 kb T.
 alpinus complete mitochondrial genome and 350 bp from the consensus
 Spermophilus (S. fulvus, S. major, and S. pygmaeus) SRY gene to assess
 empirical error rates and potential sample contamination (Bi et al. 2012).
 We also selected seven nuclear genes (acrosin, acp5, cmyc, rag-1, anon,
 zan, and zp2) previously sequenced in Tamias (6,031 bp total), which were
 used as positive controls in post-capture qPCR assays to determine the
 initial enrichment quality.033283_D_Fasta_20110329.txtTamias alpinus (the Alpine chipmunks) annotated transcriptsThe Tamias alpinus transcriptome was annotated using the BLASTX algorithm and a database of human, mouse, rat, and thirteen-lined ground squirrel proteins.T.alpinus_annotated_transcripts.txt
DOI: 10.5061/dryad.g3375
title: Data from: Kicking Triturus arntzeni when it’s down: large-scale nuclear genetic data confirm that newts from the type locality are genetically admixed

description: We collected nuclear DNA data (52 markers) with next-generation sequencing
 for nine Triturus newt specimens, including the holotype and two of the
 paratypes of T. arntzeni, from the type locality at Vrtovać in eastern
 Serbia. We compare these data to a reference set composed of the four
 crested newt species distributed in eastern Serbia namely T. cristatus, T.
 dobrogicus, T. ivanbureschi and T. macedonicus to determine to which of
 these species the newts from the type locality of T. arntzeni should be
 attributed. The majority of alleles in individuals from Vrtovać is derived
 from T. macedonicus, but a considerable number of T. ivanbureschi alleles
 is also present; alleles typical for T. cristatus and T. dobrogicus are
 found at low frequency. Accordingly, we interpret Vrtovać as a T.
 macedonicus – T. ivanbureschi hybrid population, albeit not composed of F1
 hybrids but of genetically admixed individuals derived through multiple
 generations of backcrossing. The data support the notion that the name T.
 arntzeni should not be applied to a species newly distinguished in T.
 karelinii sensu lato (to which the name T. ivanbureschi has been given).
 We conclude that because of the hybrid nature of the individuals from
 Vrtovać, the name T. arntzeni should be placed not only in the synonymy of
 T. macedonicus but also in the synonymy of T. ivanbureschi. In this study
 we demonstrate that next-generation sequencing can provide high quality
 data for type material with degraded DNA and therefore can play an
 important role in taxonomy.
description: 1 -
 FASTQ_IonTorrentRaw Ion Torrent reads in
 FASTQ format2 -
 SAM_alignmentsBWA alignments in SAM
 format3 -
 VCF_raw_SNP_reportsRaw SNP reports in VCF
 format4 -
 Filtered_SNP_reportFiltered SNP report used
 to construct consensus sequences5 -
 Number_readsNumber of reads per
 individual per marker6 -
 Genotypic_dataTable containing data in
 genotypic format7 -
 Allelic_variantsAllelic variants per
 marker8 -
 Reconstructed_sequences_FASTAFASTA files of
 reconstructed sequences9 -
 BAPS_inputBAPS input file (GENEPOP
 format)10 -
 Structure_inputStructure input
 file11 -
 BAPS_Structure_outputThe BAPS and Structure
 output12 -
 NewHybrids_inputNewHybrids input
 file13 -
 Alle_proportionTable with distribution
 of T. ivanbureschi and T. macedonicus alleles in newts from the T.
 arntzeni type locality
DOI: 10.5281/zenodo.18380066
title: labeobarbus_sandersi_spades_01.fasta.gz
DOI: 10.5281/zenodo.18380065
title: labeobarbus_sandersi_spades_01.fasta.gz
DOI: 10.5061/dryad.1414v
title: Data from: PHRAPL: phylogeographic inference using approximate likelihoods

description: The demographic history of most species is complex, with multiple
 evolutionary processes combining to shape the observed patterns of genetic
 diversity. To infer this history, the discipline of phylogeography has (to
 date) used models that simplify the historical demography of the focal
 organism, for example by assuming or ignoring ongoing gene flow between
 populations or by requiring a priori specification of divergence history.
 Since no single model incorporates every possible evolutionary process,
 researchers rely on intuition to choose the models that they use to
 analyze their data. Here, we describe an approximate likelihood approach
 that reduces this reliance on intuition. PHRAPL allows users to calculate
 the probability of a large number of complex demographic histories given a
 set of gene trees, enabling them to identify the most likely underlying
 model and estimate parameters for a given system. Available model
 parameters include coalescence time among populations or species, gene
 flow, and population size. We describe the method and test its performance
 in model selection and parameter estimation using simulated data. We also
 compare model probabilities estimated using our approximate likelihood
 method to those obtained using standard analytical likelihood. The method
 performs well under a wide range of scenarios, although this is sometimes
 contingent on sampling many loci. In most scenarios, as long as there are
 enough loci and if divergence among populations is sufficiently deep,
 PHRAPL can return the true model in nearly all simulated replicates.
 Parameter estimates from the method are also generally accurate in most
 cases. PHRAPL is a valuable new method for phylogeographic model selection
 and will be particularly useful as a tool to more extensively explore
 demographic model space than is typically done or to estimate parameters
 for complex models that are not readily implemented using current methods.
 Estimating relevant parameters using the most appropriate demographic
 model can help to sharpen our understanding of the evolutionary processes
 giving rise to phylogeographic patterns.
description: SupplementaryMaterials_PHRAPL_tutorialA detailed tutorial for using PHRAPLJackson.etal_SystBio_SupplementaryMaterials_phrapl_vignette.htmlSupplementaryMaterials_FiguresSupplemental figuresJackson.etal_SystBio_SupplementaryFigures.pdfSupplementaryMaterials_MethodsSupplemental methodsJackson.etal_SystBio_SupplementaryMethods.pdfSupplementalMaterials_Data&ScriptsDatasets simulated and scripts used for this paperJackson.etal_Data&Scripts.zip
DOI: 10.5061/dryad.q4p27mb
title: Data from: Phylogenomics supports incongruence between ecological specialization and taxonomy in a charismatic clade of buck moths

description: Local adaptation can be a fundamental component of speciation, but its
 dynamics in relation to gene flow are not necessarily straightforward.
 Herbivorous taxa with localized host plant or habitat specialization
 across their geographic range are ideal models for investigating the
 patterns and constraints of local adaptation and its impact on
 diversification. The charismatic, day-flying moths of the Hemileuca maia
 species complex (Lepidoptera: Saturniidae) are such taxa, as they are
 geographically-widespread, exhibit considerable ecological and
 morphological variability and host and habitat specificity, but apparently
 lack genetic differentiation across their range. Here, we use genome-wide
 single nucleotide polymorphisms to assess relationships and population
 structure of this group across North America, and investigate the scales
 where genomic divergence correlates with adaptive ecological
 characteristics. In contrast to previous genetic studies of the group, we
 find broad- and fine-scale genetic differentiation between lineages, which
 is at odds with various levels of taxonomic description and recognition of
 conservation units. Furthermore, ecological specialization only explains
 some fine-scale genetic differentiation, and across much of the group’s
 range, local adaptation is apparently occurring in the face of strong gene
 flow. These results provide unprecedented insight into drivers of
 speciation in this group, the relationship between taxonomy and
 genomics-informed species boundaries, and conservation management of
 internationally-protected entities. Broadly, this system provides a model
 for understanding how local adaptation in an herbivore can arise and be
 maintained in the face of apparently strong gene flow, and the importance
 of geographic isolation in generating genomic divergence, despite a lack
 of ecological divergence.
description: phylogenetic
 datasetphylogenetic dataset
 input file (119 taxa, 903,168 bp alignment)phylo.phypopulation genetic datasetpopulation genetic dataset input file (119 individuals, 2,111 SNPs)popgen.strFigures S1-S2Figures S1-S2: Detailed STRUCTURE results, and fully-labeled phylogenetic trees/networksSupplementary_Material.pdfTableS1_S2Tables S1 and S2
DOI: 10.5061/dryad.7m2q041
title: Data from: The reproductive biology of two poorly known relatives of the fig (Ficus) and insights into the evolution of the fig syconium.

description: We conducted the first detailed investigation of the floral architecture
 and reproductive biology of two species from the genus Dorstenia, which
 are poorly known relatives of Ficus (Moraceae). Our aims were to extend
 and refine knowledge of the understudied genus Dorstenia and to explore
 possible insights into the evolution of the fig syconium. We characterised
 four key stages of floral development using light microscopy, scanning
 electron microscopy and histological staining. Reproductive biology was
 found to be complex and species-specific. Both study species are
 monoecious and produce an inflorescence of minute male and female flowers.
 Protogyny, associated with a spatial separation of male and female flowers
 and asynchronous stamen development, was species-specific, as was seed
 set. Our results reveal novel insights into the complex reproductive
 biology of an under-studied genus in the family Moraceae. We propose that
 exploring the reproductive biology of Dorstenia and other poorly known
 Ficus relatives will provide insights into the evolution of the fig
 syconium – the unique reproductive structure of this economically and
 ecologically important genus.
description: TableTableFigure
 Images.pptx
DOI: 10.5061/dryad.8kb37
title: Data from: Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

description: Background: Genomic selection (GS) in forestry can substantially reduce
 the length of breeding cycle and increase gain per unit time through early
 selection and greater selection intensity, particularly for traits of low
 heritability and late expression. Affordable next-generation sequencing
 technologies made it possible to genotype large numbers of trees at a
 reasonable cost. Results: Genotyping-by-sequencing was used to genotype
 1,126 Interior spruce trees representing 25 open-pollinated families
 planted over three sites in British Columbia, Canada. Four imputation
 algorithms were compared (mean value (MI), singular value decomposition
 (SVD), expectation maximization (EM), and a newly derived, family-based
 k-nearest neighbor (kNN-Fam)). Trees were phenotyped for several yield and
 wood attributes. Single- and multi-site GS prediction models were
 developed using the Ridge Regression Best Linear Unbiased Predictor
 (RR-BLUP) and the Generalized Ridge Regression (GRR) to test different
 assumption about trait architecture. Finally, using PCA, multi-trait GS
 prediction models were developed. The EM and kNN-Fam imputation methods
 were superior for 30 and 60% missing data, respectively. The RR-BLUP GS
 prediction model produced better accuracies than the GRR indicating that
 the genetic architecture for these traits is complex. GS prediction
 accuracies for multi-site were high and better than those of single-sites
 while multi-site predictability produced the lowest accuracies reflecting
 type-b genetic correlations and deemed unreliable. The incorporation of
 genomic information in quantitative genetics analyses produced more
 realistic heritability estimates as half-sib pedigree tended to inflate
 the additive genetic variance and subsequently both heritability and gain
 estimates. Principle component scores as representatives of multi-trait GS
 prediction models produced surprising results where negatively correlated
 traits could be concurrently selected for using PCA2 and PCA3.
 Conclusions: The application of GS to open-pollinated family testing, the
 simplest form of tree improvement evaluation methods, was proven to be
 effective. Prediction accuracies obtained for all traits greatly support
 the integration of GS in tree breeding. While the within-site GS
 prediction accuracies were high, the results clearly indicate that
 single-site GS models ability to predict other sites are unreliable
 supporting the utilization of multi-site approach. Principle component
 scores provided an opportunity for the concurrent selection of traits with
 different phenotypic optima.
description: PhenotypesTree ID (Site, Family, Tree), height, diameter, volume, velocity, Resistograph, Xray (wood density), MoE (modulus of elasticity)SNP MI 30%Genotyping-by-sequence imputated SNP file with 30% missing data using the mean imputation methodSNP MI 60%Genotyping-by-sequence imputated SNP file with 60% missing data using the mean imputation method
DOI: 10.5061/dryad.815qq
title: Data from: Identifying anatomical origins of coexisting oscillations in the cortical microcircuit

description: Oscillations are omnipresent in neural population signals, like multi-unit
 recordings, EEG/MEG, and the local field potential. They have been linked
 to the population firing rate of neurons, with individual neurons firing
 in a close-to-irregular fashion at low rates. Using a combination of
 mean-field and linear response theory we predict the spectra generated in
 a layered microcircuit model of V1, composed of leaky integrate-and-fire
 neurons and based on connectivity compiled from anatomical and
 electrophysiological studies. The model exhibits low- and high-γ
 oscillations visible in all populations. Since locally generated
 frequencies are imposed onto other populations, the origin of the
 oscillations cannot be deduced from the spectra. We develop an universally
 applicable systematic approach that identifies the anatomical circuits
 underlying the generation of oscillations in a given network. Based on a
 theoretical reduction of the dynamics, we derive a sensitivity measure
 resulting in a frequency-dependent connectivity map that reveals
 connections crucial for the peak amplitude and frequency of the observed
 oscillations and identifies the minimal circuit generating a given
 frequency. The low-γ peak turns out to be generated in a sub-circuit
 located in layer 2/3 and 4, while the high-γ peak emerges from the
 inter-neurons in layer 4. Connections within and onto layer 5 are found to
 regulate slow rate fluctuations. We further demonstrate how small
 perturbations of the crucial connections have significant impact on the
 population spectra, while the impairment of other connections leaves the
 dynamics on the population level unaltered. The study uncovers connections
 where mechanisms controlling the spectra of the cortical microcircuit are
 most effective.
description: py.tarThe folder includes all
 script necessary to reproduce the figures in the associated publication.
 All or selected figures are created by the file create_figures.py.
 Simulation data are stored i the sub-folder data/. The sub-folder
 meanfield/ includes the files creating data for the analytical
 predictions. Before they can be executed please follow the installation
 instructions in meanfield/README.txt.
DOI: 10.5061/dryad.35v02
title: Data from: Development of genomic resources for Nothofagus species using next-generation sequencing data

description: Using next-generation sequencing, we developed the first whole-genome
 resources for two hybridizing Nothofagus species of the Patagonian forests
 that crucially lack genomic data, despite their ecological and industrial
 value. A de novo assembly strategy combining base quality control and
 optimization of the putative chloroplast gene map yielded ~32 000 contigs
 from 43% of the reads produced. With 12.5% of assembled reads, we covered
 ~96% of the chloroplast genome and ~70% of the mitochondrial gene content,
 providing functional and structural annotations for 112 and 52 genes,
 respectively. Functional annotation was possible on 15% of the contigs,
 with ~1750 potentially novel nuclear genes identified for Nothofagus
 species. We estimated that the new resources (13.41 Mb in total) included
 ~4000 gene regions representing ~6.5% of the expected genic partition of
 the genome, the remaining contigs potentially being nongenic DNA. A
 high-quality single nucleotide polymorphisms resource was developed by
 comparing various filtering methods, and preliminary results indicate a
 strong conservation of cpDNA genomes in contrast to numerous exclusive
 nuclear polymorphisms in both species. Finally, we characterized 2274
 potential simple sequence repeat (SSR) loci, designed primers for 769 of
 them and validated nine of 29 loci in 42 individuals per species.
 Nothofagus obliqua had more alleles (4.89) on average than N. nervosa
 (2.89), 8 SSRs were efficient to discriminate species, and three were
 successfully transferred in three other Nothofagus species. These
 resources will greatly help for future inferences of demographic, adaptive
 and hybridizing events in Nothofagus species, and for conserving and
 managing natural populations.
description: Nothofagus_assemblies