Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae-Gillenieae Clade.

Plant biologists have debated the evolutionary origin of the apple tribe (Maleae; Rosaceae) for over a century. The "wide-hybridization hypothesis" posits that the pome-bearing members of Maleae (base chromosome number = 17) resulted from a hybridization and/or allopolyploid event between progenitors of other tribes in the subfamily Amygdaloideae with = 8 and = 9, respectively. An alternative "spiraeoid hypothesis" proposed that the = 17 of Maleae arose via the genome doubling of = 9 ancestors to = 18, and subsequent aneuploidy resulting in = 17. We use publicly available genomic data-448 nuclear genes and complete plastomes-from 27 species representing all major tribes within the Amygdaloideae to investigate evolutionary relationships within the subfamily containing the apple tribe. Specifically, we use network analyses and multi-labeled trees to test the competing wide-hybridization and spiraeoid hypotheses. Hybridization occurred between an ancestor of the tribe Spiraeeae ( = 9) and an ancestor of the clade Sorbarieae ( = 9) + Exochordeae ( = 8) + Kerrieae ( = 9), giving rise to the clade Gillenieae ( = 9) + Maleae ( = 17). The ancestor of the Maleae + Gillenieae arose via hybridization between distantly related tribes in the Amygdaloideae (i.e., supporting the wide hybridization hypothesis). However, some evidence supports an aspect of the spiraeoid hypothesis-the ancestors involved in the hybridization event were likely both = 9, so genome doubling was followed by aneuploidy to result in = 17 observed in Maleae. By synthesizing existing genomic data with novel analyses, we resolve the nearly century-old mystery regarding the origin of the apple tribe. Our results also indicate that nuclear gene tree-species tree conflict and/or cytonuclear conflict are pervasive at several other nodes in subfamily Amygdaloideae of Rosaceae.