Phylotranscriptomic Analyses Uncover the Evolutionary History and Asymmetric Diversification Patterns of the Wheat Tribe

Syst. Biol. 0(0):1–17, 2026

Lina Sha, Hao Yan, Cao Deng, Fan Yang, Zehou Liu, Jun Li, Yue Zhang, Yiran Cheng,Dandan Wu,Yi Wang,Hou-Yang Kang,Haiqin Zhang, Genlou Sun, Yuhu Shen,Yonghong Zhou, Wuyun Yang , Xing Fan.

Abstract

The wheat tribe Triticeae, widely known for its economic importance, is a species-diverse and polyploid-rich group in Poaceae. However, despite decades of intensive efforts, the phylogenetic relationships, genome origins, and diversification dynamics of Triticeae species remain uncertain. Here, we infer the phylogenetic and diversification patterns of Triticeae using 1546 nuclear genes from 164 transcriptomes/genomes that represent ∼83% of the recognized genera. Our phylogeny provides robust and well-supported estimates of the relationships among diploids and polyploids, which will be indispensable for studying biodiversity and breeding innovative germplasms. Diversification dynamic analysis suggests that Triticeae has undergone continuous evolutionary diversification to varying degrees since its origin during the Miocene, with acceleration in the St-ortholog lineages, indicating asymmetric diversification patterns among the homoeologous lineages in the St-genome-containing polyploid radiation. Multiple factors, including extinct donors and nonreciprocal recombination, complicated the origin of the B and G genomes of wheat and the Y and Xm genomes of wheatgrass. Asymmetric polyploidization and mixed-ploidy introgression might have constituted an evolutionary impetus, driving rapid radiation and hyperdiversity of the St-genome-containing polyploid species in Triticeae. Our results provide new insights into the evolutionary origins of Triticeae that could promote the study of other rapidly radiated lineages in terms of polyploid origin and diversification processes. [Diversification rate; hybridization; polyploid; radiation; Triticeae.]