Hybridization, polyploidy, and apomixis have made phylogenetic estimation in Rubus challenging. I used target capture to sequence approximately 1000 low copy nuclear loci and the chloroplast genome for 94 accessions representing the genus Rubus and distributed worldwide. Species phylogenies were estimated using two coalescent based methods, ASTRAL-II and SVDQuartets, and compared to identify eight major groups within this genus. Only two subgenera, Anoplobatus and Orobatus, are monophyletic. Multiple putative allopolyploids, including R. humulifolius, R. ursinus, R. glaucus, R. macraei, and R. caesius, were identified in phylogenetic network analyses. Since the chloroplast genome reflects maternal inheritance, putative progenitor groups for hybrids were identified by comparing nuclear and chloroplast phylogenies.
I estimated divergence times and ancestral ranges using ASTRAL-II generated topologies. The root age was constrained using fossil calibrated divergence times from a recently published phylogeny of Rosaceae. Rubus diversified during the Miocene and likely migrated from North America to Asia and elsewhere multiple times during the Miocene. Ancestral state reconstruction indicated that the Rubus most recent common ancestor (MRCA) was a diploid, unarmed, compound-leaved plant with persistent stipules that were adnate to the petiole. Target capture sequencing facilitated a broad analysis of phylogenetic relationships and evolutionary history in Rubus.