Parallel ddRAD and genome skimming analyses reveal a radiative and reticulate evolutionary history of the temperate bamboos

Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology, molecular) or genetic markers (e.g., nuclear, organelle) often yield inconsistent results. The tribe Arundinarieae i.e., the temperate bamboos, is a clade of tetraploid originated 22 million years ago and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome-skimming for 147 taxa. We first assess the feasibility of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and rapidly radiated lineages, optimize clustering thresholds and analysis workflow for orthology identification. Reference-based ddRAD data assembly approaches perform well and yield strongly supported relationships that are generally concordant with morphology-based taxonomy....