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52 results for “RAD-seq”
Data from: Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference
Restriction site-associated DNA sequencing (RAD-seq) provides high-resolution population genomic data at low cost, and has become an important component in ecological and evolutionary studies. As with all high-throughput technologies, analytic strategies require critical validation to ensure accurate and unbiased interpretation. To test for the impact of bioinformatic data processing on downstream population genetic inferences, we analysed mammalian RAD-seq data (>100 individuals) with 312 combinations of methodology (de novo vs. mapping to references of increasing divergence) and filtering criteria (missing data, HWE, FIS, coverage, mapping, genotype quality). In an effort to identify commonalities and biases in all pipelines, we computed summary statistics (nr. loci, nr. SNP, π, Hetobs, FIS, FST, Ne, m) and compared the results to independent null expectations (isolation-by-distance correlation, expected transition-to-transversion ratio Ts/Tv, Mendelian mismatch rates of known parent-offspring trios). We observed large differences between reference-based and de novo approaches, the former generally calling more SNPs and reducing FIS and Ts/Tv. Data completion levels showed little impact on most summary statistics, and FST estimates were robust across all pipelines. The site-frequency spectrum (SFS) was highly sensitive to the chosen approach as reflected in large variance of parameter estimates across demographic scenarios (single-population bottlenecks and isolation-with-migration model). Null-expectations were best met by reference-based approaches, though contingent on the specific criteria. We recommend RAD-seq studies employ reference-based approaches to a closely related genome, and due to the high stochasticity associated with the pipeline advocate the use of multiple pipelines to ensure robust population genetic and demographic inferences.
Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches
<p>Target enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies. Each method has its own pros and cons. The choice between them is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms in plants. In this study, we employed RAD-seq and Hyb-Seq of Angiosperm 353 genes in phylogenomic and biogeographic studies of <em>Hamamelis</em> (the witch-hazels) and <em>Castanea </em>(chestnuts), two classic examples exhibiting the well-known eastern Asian (EA)-eastern North American (ENA) disjunct distribution, and compared them side by side. Our results showed congruences in phylogenetic inference and divergence time dating between the two data sets obtained through our customized procedures of library preparation and sequence trimming, although they differed in the number of loci and informative sites, the amount of missing data, and sampling within species. We suggest the selection of the two methods based on fund availability and sampling scale. Our phylogenetic analyses of RAD-seq and Hyb-Seq data resulted in well-resolved species relationships, and ancient introgressions were revealed in both genera by D-statistic test and PhyloNet. Biogeographic analyses including fossil data using total evidence-based dated tree and DEC model, applying specific inter-area dispersal probabilities, revealed a complicated history for each genus, indicating multiple intercontinental dispersals and local extinctions in areas outside of the taxa's modern ranges in both the Paleogene and Neogene. The study demonstrates the importance of including fossil taxa for a more accurate reconstruction of biogeographic histories of taxa to understand the EA and ENA floristic disjunction. Our results support an "out of western North America" migration of <em>Castanea</em> but an "out of Asia" migration of <em>Hamamelis</em> during their initial diversification, and the origins of the EA-ENA disjunction in both genera were results of vicariance.</p>
RAD-seq of Ash individuals
<p>Ash (<i>Fraxinus </i>spp.) is one of the most widely distributed tree genera in North America. Populations of ash in the United States and Canada have been decimated by the introduced pest <i>Agrilus planipennis </i>(Coleoptera: Buprestidae; emerald ash borer), having negative impacts on both forest ecosystems and economic interests. The majority of trees succumb to attack by <i>A. planipennis</i>, but some trees have been found to be tolerant to infestation despite years of exposure.</p> <p>Restriction site-associated DNA (RAD) sequencing was used to sequence ash individuals, both tolerant and susceptible to <i>A. planipennis </i>attack, in order to identify single nucleotide polymorphism (SNP) patterns related to tolerance and health declines.</p> <p>Understanding the mechanisms of host tolerance through genome-wide association has the potential to restore populations with cultivars that are able to withstand <i>A. planipennis</i> infestation. We were successful in using RAD-sequencing in order to identify SNPs that could contribute to tolerance of <i>A. planipennis</i>. This was a first step toward uncovering the genetic basis for host tolerance to <i>A. planipennis</i>.</p>
Data from: The phylogeographic history of Megistostegium (Malvaceae) in the dry, spiny thickets of southwestern Madagascar using RAD-seq data and ecological niche modeling.
<p class="MsoCommentText">The spiny thicket of southwestern Madagascar represents an extreme and ancient landscape with extraordinary levels of biodiversity and endemism. Few hypotheses exist for explaining speciation in the region and few plant studies have explored hypotheses for species diversification. Here we investigate three species in the endemic genus <i>Megistostegium </i>(Malvaceae) to evaluate phylogeographic structure and explore the roles of climate, soil and paleoclimate oscillations on population divergence and speciation throughout the region. We combine phylogenetic and phylogeographic inference of RADseq data with ecological niche modeling across space and time. Population structure is concurrent with major rivers in the region and we identify a new, potentially important biogeographic break coincident with several landscape features. Our data further suggests that niches occupied by species and populations differ substantially across their distribution. Paleodistribution modelling provide evidence that past climatic change could be responsible for the current distribution, population structure and maintenance of species in <i>Megistostegium.</i></p>
RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees
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Data from: Identifying patterns of dispersal, connectivity, and selection in the sea scallop, Placopecten magellanicus, using RAD-seq derived SNPs
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Data from: Attack of the PCR clones: rates of clonality have little effect on RAD-seq genotype calls
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Data from: Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals.
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Data from: RAD-seq reveals genetic structure of the F2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression
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RAD-seq of Ash individuals
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The filtered VCF file containing SNPs detected from the Vitis bryoniifolia clade using RAD-seq.
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Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish
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Data from: Misconceptions on missing data in RAD-seq phylogenetics with a deep-scale example from flowering plants
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RAD-seq vcf files for the leaf beetle Gonioctena quinquepunctata sampled across Europe
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Data from: Host-targeted RAD-Seq reveals genetic changes in the coral Oculina patagonica associated with range expansion along the Spanish Mediterranean coast
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SNP discovery in Cryptomeria japonica var. sinensis using restriction-site associated DNA sequencing (RAD-seq）
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Data from: Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference
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Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches
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Data from: The phylogeographic history of Megistostegium (Malvaceae) in the dry, spiny thickets of southwestern Madagascar using RAD-seq data and ecological niche modeling.
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A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris
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International Brain Laboratory public data
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OpenNeuro
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