Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Phylogenomic evidence from an increasing number of studies has
demonstrated that different data sets and analytical approaches often
reconstruct strongly supported but conflicting relationships. In this
study, 785 single-copy nuclear genes and 75 complete plastomes were used
to infer the phylogenetic relationships and estimate the historical
biogeography of the apple genus Malus sensu lato, an
economically important lineage disjunctly distributed in the Northern
Hemisphere and involved in known and suspected hybridization and
allopolyploidy events. The nuclear phylogeny recovered the monophyly
of Malus s.l. (including Docynia); however, the
genus was supported to be biphyletic in the plastid phylogeny. An ancient
chloroplast capture event in the Eocene in western North America best
explains the cytonuclear discordance. Our conflict analysis demonstrated
that ILS, hybridization, and allopolyploidy could explain the widespread
nuclear gene tree discordance. One deep hybridization event (Malus
doumeri) and one recent event (Malus coronaria) were detected
in Malus s.l. Furthermore, our historical biogeographic
analysis integrating living and fossil data supported a widespread East
Asian-western North American origin of Malus s.l. in the
Eocene, followed by several extinction and dispersal events in the
Northern Hemisphere. We also propose a general workflow for assessing
phylogenomic discordance and biogeographic analysis using deep genome
skimming datasets.