Hybridization is a frequent and important force in plant evolution. Next-generation
sequencing (NGS) methods offer new possibilities for clade resolution and ambitious
sampling of gene genealogies, yet difficulty remains in detecting deep reticulation
events using currently available methods. We reconstructed the phylogeny of diploid
representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient
hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through
hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through
a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa
plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated
assembly algorithm. These data were analyzed with diverse phylogenetic methods, including
concatenation, coalescence-based species tree estimation, Bayesian concordance analysis,
and network reconstructions, to provide insights into the evolutionary relationships
of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were
examined through a Bayesian posterior predictive approach (JML) and coalescent simulations.
Two major clades were found, Hippeastrinae and Traubiinae, as previously reported.
Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized
by different chromosome numbers: (1) Tocantinia and Hippeastrum with 2n=22, and (2)
Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n=12, 14, and 18. Strong
cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with
at least six hybridization events is proposed to reconcile nuclear and plastid signals,
along a backbone that may also have been affected by incomplete lineage sorting at
the base of each major subclade.