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 (M..., Taxon sampling, library preparation, and deep genome skimming sequencing
Taxon sampling is designed to resolve the phylogenetic placements and relationships of major clades within Malus s.l. For the convenience of discussion, we followed the widely accepted taxonomic system proposed by Phipps et al. (1990), in which they recognized five sections. Due to the great economic importance of Malus, numerous hybrid cultivars have been used as crops and ornamentals, which have hybridized either within one section or between sections, and this made it difficult to infer the phylogenetic relationships between cultivated and wild species. Hence, we excluded the widely recognized artificial hybrid species in Malus, e.g., M. × asiatica Nakai, M. × astracanica hort. ex Dum.Cours., M. × cerasifera Spach, M. × dawsoniana Rehder, M. × domestica (= M. pumila Mill.), M. × floribunda Siebold ex Van Houtte, M. × halliana, M. × micromalus, M. × heterophylla Spach, M. × magdeburgensis Schoch ex Rehder, M. × p...,