Malus (Rosaceae) systematics and diversification: insights from a RAD-seq phylogeny

Malus (Rosaceae) - the apples - are a genus of 25 to 55 flowering tree species renowned for their taxonomic complexity. Hybridization, apomixis, and polyploidy work together to confound both species circumscription and phylogenetic inference in the genus. We present the most comprehensive phylogenetic sampling of species and infraspecies to date, using analysis of RAD-seq data to (1) identify major clades within the genus, (2) propose a revised infrageneric classification, and (3) place previously unsampled taxa into that classification. In addition, we (4) review nomenclature and taxonomy for numerous taxa still incompletely understood based on work to date, and typify infrageneric names to standardize their use.