Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches

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 Hamamelis (the witch-hazels) and Castanea (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 trimm...