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Dataset results
8 results for “Hyb-Seq”
Rare and widespread: Integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma
<p class="MsoCommentText">Premise</p> <p class="MsoCommentText">Genera that are widespread but have a geographically discontinuous distribution and are represented by few species are intriguing. Did they achieve their disjunct distribution recently, or is it ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale floristic pattern in which closely related species appear co-distributed in isolated regions over the edges of Africa and nearby archipelagos. Genus <i>Camptoloma</i> (Scrophulariaceae) is the most notable example, comprising three species isolated from each other at the ends of the African continent: <i>C. canariense </i>in the west, endemic to the Canary Islands; <i>C. lyperiiflorum </i>in the east, endemic to the Horn of Africa - Southern Arabia; and <i>C. rotundifolia</i>, restricted to Southern Africa.</p> <p class="MsoCommentText">Methods</p> <p class="MsoCommentText">Here, we employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of <i>Camptoloma</i> within Scrophulariaceae, using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian MCMC approaches. Population history was estimated with phylogeographic structured coalescent methods.</p> <p class="MsoCommentText">Key Results</p> <p class="MsoCommentText">Our results support <i>C. rotundifolia</i> as sister to the disjunct clade formed by <i>C. canariense</i> and <i>C. lyperiiflorum.</i> Stem divergence was dated in the Late Miocene, while the origin of extant diversification within the genus was inferred as Early Pliocene.</p> <p class="MsoCommentText">Conclusions</p> <p>We show that the current disjunct distribution of <i>Camptoloma </i>across Africa was likely the result of fragmentation and extinction/population bottlenecking events associated to historical aridification cycles, consistent with the "climatic refugia" hypothesis.</p>
Morus Hyb-Seq data for: Phylogeny and biogeography of Morus (Moraceae)
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Rare and widespread: Integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma
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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>
Developing Asparagaceae1726: an Asparagaceae-specific probe set targeting 1,726 loci for Hyb-Seq and phylogenomics in the family
<p>Dataset associated with the release of Asparagaceae1726: a Hyb-Seq probe set targeting 1726 conserved, low-copy nuclear genes specifically for phylogenomics in the angiosperm family Asparagaceae. Phylogenomic analysis of this number of genes could aid the often-challenging delineation of taxa and resolution of relationships within Asparagaceae.</p> <p>Asparagaceae1726 is a first attempt at establishing a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family.</p>
Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches
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Data from: 346 target gene sequences from Vitaceae for Hyb-Seq
<p>The Vitaceae (the grape family) consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop -- the grape <i>Vitis vinifera</i>. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbon-like trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.</p>
Data from: 346 target gene sequences from Vitaceae for Hyb-Seq
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