Abstract: Thamnocalamus, a bamboo genus endemic to the Himalaya, comprises four to six species with a complex taxonomic history. Distinguishing Thamnocalamus from Fargesia based on vegetative characteristics is particularly challenging, as previous studies frequently resulted in misclassifications of species between the two genera. Leveraging subgenome-scale syntenic nuclear genes and genomic distance-based k-mer analyses through deep genome skimming, we dissected the complex phylogenetic relationships within Thamnocalamus to facilitate subsequent taxonomic revision. Our study presents: (1) an updated phylogeny improved in resolution and sampling density, (2) characterization of the evolutionary process underlying gene tree incongruence, and (3) enumeration of four Chinese Thamnocalamus species with a diagnostic morphological key. Based on a robust phylogenetic framework and morphological comparisons, we propose a new combination, T. damuniu, and further investigate potential hybridization among Thamnocalamus species. Consequently, Thamnocalamus crassinodus and T. unispiculatus were inferred to be of hybrid origin but with differential inheritance probability proportions, together with incomplete lineage sorting, which likely contributes to the gene tree incongruence and non-monophyly of T. crassinodus in k-mer-based analysis. As many poorly known bamboo species were described solely from vegetative specimens, we emphasize the necessity of integrating molecular evidence into taxonomic decisions and describing new species within the taxonomically challenging Bambusoideae, calling for reassessment of species with uncertain generic status integrating nuclear genomic data of multiple individuals per species, and detailed morphological comparisons.

Key words: conflicting gene trees, deep genome skimming, Himalaya, new recombination, Thamnocalaminae