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4 results for “RAD phylogenomics”
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>
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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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>
Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches
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