Abstract
Phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees. Here we explore the use of reduced-representation genome sequencing, specifically in the form of restriction-site associated DNA (RAD), for phylogenetic inference and the detection of ancestral hybridization in non-model organisms. As a case study, we investigate Pedicularis section Cyathophora, a systematically recalcitrant clade of flowering plants in the broomrape family (Orobanchaceae). Two methods of phylogenetic inference, maximum likelihood and Bayesian concordance, were applied to data sets that included as many as 40,000 RAD loci. Both methods yielded similar topologies that included two major clades: a “rex-thamnophila” clade, composed of two species and several subspecies with relatively low floral diversity, and geographically widespread distributions at lower elevations, and a “superba” clade, composed of three species characterized by relatively high floral diversity and isolated geographic distributions at higher elevations. Levels of molecular divergence between subspecies in the rex-thamnophila clade are similar to those between species in the superba clade. Using Patterson’s D-statistic test, including a novel extension of the method that enables finer-grained resolution of introgression among multiple candidate taxa by removing the effect of their shared ancestry, we detect significant introgression among nearly all taxa in the rex-thamnophila clade, but not between clades or among taxa within the superba clade. These results suggest an important role for geographic isolation in the emergence of species barriers, by facilitating local adaptation and differentiation in the absence of homogenizing gene flow. [Concordance factors; genotyping-by-sequencing; hybridization; partitioned D-statistic test; Pedicularis; restriction-site associated DNA.]
Highlights
High-throughput sequencing technologies offer much greater potential for efficiently sampling entire genomes of any taxon for phylogenetically informative variation
We investigate the utility of restrictionsite associated DNA sequencing (RADseq) data for resolving recalcitrant phylogenetic relationships in the angiosperm genus Pedicularis (Orobanchaceae, the broomrape family), which consists of about 700 species of hemiparasitic herbs having a center of diversity in the Hengduan Mountains of south-central China (Yang et al 1998)
In comparison to previous studies, which used sequence data sets of at most a few markers, each on the order of 1 kbp in length, the RADseq data set is notable for its size, having more than 40,000 loci and 60,000 potentially informative sites in the largest supermatrix
Summary
High-throughput sequencing technologies offer much greater potential for efficiently sampling entire genomes of any taxon for phylogenetically informative variation. The potential for informative gene tree variation within a single RAD locus is relatively small, but to the extent that restriction sites are conserved across samples, the collective potential of RADseq for detecting many singlenucleotide polymorphisms (SNPs) across the genome is large. For this reason, it has been applied to date almost.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
