Evolutionary framework and tribal circumscription of Amaranthaceae sensu stricto based on a comprehensive phylogenomic analysis.

Abstract

The evolutionary history of Amaranthaceae sensu stricto (s.s.) has been shaped by multiple whole-genome duplications and rapid radiations, producing an ecologically diverse lineage whose internal relationships have long remained unresolved. Earlier studies, constrained by limited genomic resources and sparse taxon sampling, left the relationships of higher-level classification of this economically important lineage incomplete and its reticulate evolutionary history undiscovered. Using a customized bait set targeting 1000 low-copy nuclear loci of Amaranthaceae s.s., we reconstructed a globally sampled phylogeny representing 96% of all recognized genera. This sampling includes many rare and previously inaccessible taxa obtained largely from herbarium collections. Our results reveal the sources of a strongly reticulate and highly polyploid evolutionary history, involving at least two deep hybridization events and up to six ancient whole genome duplications. These processes generated substantial gene tree discordance along the backbone of the phylogeny, clarifying the sources of previous analytical instability. However, the major clades recovered are consistently and strongly supported across phylogenetic inferences. Based on these results, we recognize 11 tribes within Amaranthaceae s.s., including the formal circumscription of the newly identified tribes Allmaniopseae and Wadithamneae. This provides a robust framework for future phylogenetically informed research within Amaranthaceae s.s.