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52 results for “RAD-seq”
Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq
<p><span>Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RADADOR, to mitigate the ADO in outgroups by recovering missing loci from previously published transcriptomes in our study of a gymnosperm genus </span><em>Torreya</em><span>. Using the supplemented RAD-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and test hypotheses on diversity anomaly in eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for </span><em>Torreya</em><span>. Using the fossilized-birth-death model and divergence-extinction-cladogenesis method we resolved detailed biogeographic history of </span><em>Torreya</em><span> that suggested a Jurassic origin in the Laurasia and differential speciation and extinction among continents accounting for the modern diversity anomaly biased toward Eastern Asia (EA). The history also supported a vicariance origin of the modern </span><em>Torreya</em><span> from a widespread ancestor in EA and NA in the mid-Eocene, cross-Beringia exchange in the early Paleogene before the vicariant isolation, in contrast to the "Out of NA" pattern common to gymnosperms and in contrast to the "Out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies on </span><em>T. jackii</em><span>, suggesting differential lineage sorting of plastid genomes among </span><em>Torreya</em><span> species or plastid genome capture in </span><em>T. jackii</em><span>.</span></p>
RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" in Journal of Evolutionary Biology
<p>This a data set from the paper RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" to be published in Journal of Evolutionary Biology</p>
VCF File containing genotype calls for 136 Populus alba x Populus tremula hybrids obtained through both RAD-seq and GBS
<p>VCF file used to compare genotype calls obtained through RAD-seq and GBS for 126 common garden seedlings of Populus tremula and Populus alba hybrids. See Bresadola et al. (2019) for more details.</p>
Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq
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Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs
<p><i><span>Background</span></i></p> <p><span>The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in <i>de-novo</i> genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (<i>Penaeus monodon</i>) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq).</span></p> <p><i><span>Results</span></i></p> <p><span>Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7,542 high-quality SNPs were retained. From these, 4,236 high-quality genome-wide loci were selected for bates-probe development and 4,194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 </span>± 14.7 to 93.0% ± 3.5%<span>), </span>increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7<span>), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches.</span></p> <p><i><span>Conclusion</span></i></p> <p><span>Importantly, this assay equips the <em>P. monodon</em> industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as <em>P. monodon</em> breeding programs transition to undertaking genomic selection.</span></p>
VCF File containg replicate RAD-seq genotype calls for four Populs alba x Populus tremula hybrids.
<p>VCF file used to estimate RAD-seq genotyping errors in Bresadola et al. (2019).</p>
RAD-seq generated single nucleotide polymorphisms resolve patterns of genetic diversity and structure of the freshwater mussel Ptychobranchus fasciolaris in glaciated and unglaciated regions of North America
<p>Included are the initial unfiltered SNP output from the STACKS pipeline, and the final filtered SNP dataset in VCF format used to do analysis in the manuscript titled "<span>RAD-seq generated single nucleotide polymorphisms resolve patterns of genetic diversity and structure of the freshwater mussel <em>Ptychobranchus fasciolaris </em>in glaciated and unglaciated regions of North America" which was submitted to <em>Hydrobiologia </em>in September 2024.</span></p>
Data from: Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling
Nyssa sylvatica complex consists of several woody taxa occurring in eastern North America. These taxa were recognized as two or three species including three or four varieties by different authors. Due to high morphological similarities and complexity of morphological variation, classification and delineation of taxa in the group have been difficult and controversial. Here we employ data from RAD-seq to elucidate the genetic structure and phylogenetic relationships within the group. Using the genetic evidence, we evaluate previous classifications and delineate species. We also employ Species Distribution Modeling (SDM) to evaluate impacts of climatic changes on the ranges of the taxa and to gain insights into the relevant refugia in eastern North America. Results from Molecular Variance Analysis (AMOVA), STRUCTURE, phylogenetic analyses using Maximum likelihood, Bayesian Inference, and Splittree methods of RAD-seq data strongly support a two-clade pattern, largely separating samples of N. sylvatica from those of N. biflora-N. ursina mix. Divergence time analysis with BEAST suggests the two clades diverged in the mid Miocene. The ancestor of the present trees of N. sylvatica was suggested to be in the Pliocene and that of N. biflora-N. ursina mix in the end of the Miocene. Results from SDM predicted a smaller range in the southern part of the species present range of each clade during the Last Glacial Maximum (LGM). A northward expansion of the ranges during interglacial period and a northward shift of the ranges in the future under a model of global warming were also predicted. Our results support the recognition of two species in the complex, N. sylvatica and N. biflora, following the phylogenetic species concept. We found no genetic evidence supporting recognitions of intraspecific taxa. However, we propose subsp. ursina and subsp. biflora within N. biflora due to their distinction in habits, distributions, and habitats. Our results further support movements of trees in eastern North America in response to climatic changes. Finally, our study demonstrates that RAD-seq data and a combination of population genomics and SDM are valuable in resolving relationship and biogeographic history of closely related species that are taxonomically difficult.
Data from: Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling
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Data from: Substantial differences in bias between single-digest and double-digest RAD-seq libraries: a case study
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Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs
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RAD-seq data from: Evidence of local adaptation despite strong drift in a Neotropical patchily distributed bromeliad
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Supplementary data for Cariou et al (2020, Molecular Ecology Resources, "How consistent is RAD-seq divergence with DNA-barcode based clustering in insects?")
<p>This dataset accompanies a paper by Cariou et al, to be published in Molecular Ecology Resources, where we assessed in 92 insect species if the genetic clustering of specimens into species like units, on the basis of mitochondrial DNA, was consistent with genome wide divergence, as estimated by RAD-seq data. The present repository includes: (1) a detailed description of the bioinformatic analysis indicating which programs were used, together with parameter values, (2) the raw RAD-seq data following demultiplexing, (3) the consensus sequences of all RAD loci for all specimens, and (4) large tables indicating genetic distances at all RAD loci for all species.</p>
SNP discovery in Cryptomeria japonica var. sinensis using restriction-site associated DNA sequencing (RAD-seq)
<p>Our study is the first to explore the genetic composition of ancient <i>Cryptomeria</i> trees across distribution range in China. <i>Background and Objectives:</i> <i>Cryptomeria japonica </i>var. <i>sinensis</i> is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike <i>Cryptomeria</i> in Japan, genetic Chinese<i> Cryptomeria </i>has seldom been studied, although there is ample evidence of its great ecological and economic value. <i>Materials and Methods:</i> Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese <i>Cryptomeria</i> through ddRAD-seq technology. <i>Results:</i> The results reveal lower genetic variation but higher genetic differentiation (<i>Ho</i>=0.143, <i>F<sub>ST</sub></i>=0.1204) than Japanese <i>Cryptomeria </i>(<i>Ho</i>=0.245, <i>F<sub>ST</sub></i>=0.0455). The 86% within-population variation is based on analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. STRUCTURE analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. Demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese <i>Cryptomeria</i> had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species' unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.</p>
RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees
<p>A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus <i>Diospyros</i> in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene <i>Diospyros</i> species, generated genome-wide SNP data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene <i>Diospyros</i> species diverged millions of years ago and are largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization also occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now co-exist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role introgression may have played in adaptation and diversification of Mascarene <i>Diospyros,</i> and its relevance for conservation.</p>
Data from: Host-targeted RAD-Seq reveals genetic changes in the coral Oculina patagonica associated with range expansion along the Spanish Mediterranean coast
Many organisms are expanding their ranges in response to changing environmental conditions. Understanding the patterns of genetic diversity and adaptation along an expansion front is crucial to assessing a species' long-term success. While next-generation sequencing techniques can reveal these changes in fine detail, ascribing them to a particular species can be difficult for organisms that live in close association with symbionts. Using a novel modified restriction-site associated DNA sequencing (RAD-Seq) protocol to target coral DNA, we collected 595 coral-specific single nucleotide polymorphisms (SNPs) from 189 colonies of the invasive coral Oculina patagonica from the Spanish Mediterranean coast, including established core populations and two expansion fronts. Surprisingly, populations from the recent northern expansion are genetically distinct from the westward expansion and core populations, and also harbor greater genetic diversity. We found that temperature may have driven adaptation along the northern expansion, as genome scans for selection found three candidate loci associated with temperature in the north but none in the west. We found no genomic signature of selection associated with artificial substrate, which has been proposed for explaining the rapid spread of O. patagonica. This suggests that this coral is simply an opportunistic colonizer of free space made available by coastal habitat modifications. Our results suggest that unique genetic variation, possibly due to limited dispersal across the Ibiza Channel, an influx of individuals from different depths, and/or adaptation to cooler temperatures along the northern expansion front may have facilitated the northward range expansion of O. patagonica in the western Mediterranean.
Data from: Identifying patterns of dispersal, connectivity, and selection in the sea scallop, Placopecten magellanicus, using RAD-seq derived SNPs
Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used Restriction-site Associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. Based on 245 individuals sampled range-wide at 12 locations from Newfoundland to the Mid-Atlantic Bight we identified and genotyped 7163 Single Nucleotide Polymorphisms; 112 (1.6%) were identified as outliers potentially under directional selection. Bayesian clustering revealed a discontinuity between northern and southern samples and latitudinal clines in allele frequencies were observed in 42.9% of the outlier loci and in 24.6% of neutral loci. Dispersal estimates derived using these clines and estimates of linkage disequilibrium imply limited dispersal; 373.1 ± 407.0 km (mean ± SD) for outlier loci and 641.0 ± 544.6 km (mean ± SD) for neutral loci. Our analysis suggests restricted dispersal compared to the species range (>2000 km) and that dispersal and effective connectivity differ. These observations support the hypothesis that limited effective dispersal structures scallop populations along eastern North America. These findings can help refine the appropriate scale of management and conservation in this commercially valuable species.
Data from: Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals.
Discrepancies between morphology-based taxonomy and phylogenetic systematics are common in Scleractinian corals. In Pocillopora corals, nine recently identified genetic lineages disagree fundamentally with the 17 recognized Pocillopora species, including 5 major Indo-Pacific reef-builders. Pocillopora corals hybridize in the Tropical Eastern Pacific, so it is possible that some of the disagreement between the genetics and taxonomy may be due to introgressive hybridization. Here we used 6769 genome-wide SNPs from Restriction-site Associated DNA sequencing (RAD-Seq) to conduct phylogenomic comparisons among three common, Indo-Pacific Pocillopora species - P.'damicornis, P. eydouxi and P. elegans - within and between populations in the Tropical Eastern Pacific (TEP) and the Central Pacific. Genome-wide RAD-Seq comparisons of Central and TEP Pocillopora confirm that the morphospecies P.'damicornis, P. eydouxi and P. elegans are not monophyletic, but instead fall into three distinct genetic groups. However, hybrid samples shared fixed alleles with their respective parental species and, even without strict monophyly, P. damicornis share a common set of 33 species- specific alleles across the Pacific. RAD-Seq data confirm the pattern of one-way introgressive hybridization among TEP Pocillopora, suggesting that introgression may play a role in generating shared, polyphyletic lineages among currently recognized Pocillopora species. Levels of population differentiation within genetic lineages indicate significantly higher levels of population differentiation in the Tropical Eastern Pacific than in the Central West Pacific.
Data from: RAD-seq reveals genetic structure of the F2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression
Background: Hybridization of species with porous genomes can eventually lead to introgression via repeated backcrossing. The potential for introgression between species is reflected by the extent of segregation distortion in later generation hybrids. Here we studied a population of hybrids between Salix purpurea and S. helvetica that has emerged within the last 30 years on a glacier forefield in the European Alps due to secondary contact of the parental species. We used 5,758 biallelic SNPs produced by RAD sequencing with the aim to ascertain the predominance of backcrosses (F1 hybrid x parent) or F2 hybrids (F1 hybrid x F1 hybrid) among hybrid offspring. Further, the SNPs were used to study segregation distortion in the second hybrid generation. Results: The analyses in STRUCTURE and NewHybrids revealed that the population consisted of parents and F1 hybrids, whereas hybrid offspring consisted mainly of backcrosses to either parental species, but also some F2 hybrids. Although there was a clear genetic differentiation between S. purpurea and S. helvetica (FST = 0.24), there was no significant segregation distortion in the backcrosses or the F2 hybrids. Plant height of the backcrosses resembled the respective parental species, whereas F2 hybrids were more similar to the subalpine S. helvetica. Conclusions: The co-occurrence of the parental species and the hybrids on the glacier forefield, the high frequency of backcrossing, and the low resistance to gene flow via backcrossing make a scenario of introgression in this young hybrid population highly likely, potentially leading to the transfer of adaptive traits. We further suggest that this willow hybrid population may serve as a model for the evolutionary processes initiated by recent global warming.
Data from: Attack of the PCR clones: rates of clonality have little effect on RAD-seq genotype calls
Interpretation of high-throughput sequence data requires an understanding of how decisions made during bioinformatic data processing can influence results. One source of bias that is often cited is PCR clones (or PCR duplicates). PCR clones are common in restriction site associated sequencing (RAD-seq) datasets, which are increasingly being used for molecular ecology. To determine the influence PCR clones and the bioinformatic handling of clones have on genotyping, we evaluate four RAD-seq datasets. Datasets were compared before and after clones were removed to estimate the number of clones present in RAD-seq data, quantify how often the presence of clones in a dataset cause genotype calls to change compared to when clones were removed, investigate the mechanisms that lead to genotype call changes, and test if clones bias heterozygosity estimates. Our RAD-seq datasets contained 30 – 60% PCR clones, but 95% of RAD-tags had five or fewer clones. Relatively few genotypes changed once clones were removed (5-10%), and the vast majority of these changes (98%) were associated with genotypes switching from a called to no-call state or vice versa. PCR clones had a larger influence on genotype calls in individuals with low read depth but appeared to influence genotype calls at all loci similarly. Removal of PCR clones reduced the number of called genotypes by 2% but had almost no influence on estimates of heterozygosity. As such, while steps should be taken to limit PCR clones during library preparation, PCR clones are likely not a substantial source of bias for most RAD-seq studies.
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