Nuclear phylogenomic analysis of Allium (Amaryllidaceae) species from Kazakhstan reveals incomplete lineage sorting and gene flow

BACKGROUND: The genus Allium L. (Amaryllidaceae J.St.-Hil.) comprises more than 1,000 species distributed primarily across the Northern Hemisphere and represents one of the most taxonomically and economically important lineages of monocots. Despite extensive molecular research based on nuclear and plastid markers, phylogenetic relationships within the genus remain incompletely resolved, largely due to limited locus sampling and pervasive phylogenetic discordance. RESULTS: We implemented a nuclear phylogenomic approach using the Angiosperms353 target-enrichment probe set to investigate evolutionary relationships and sources of gene tree conflict within Allium. A total of 47 accessions representing 43 species were analyzed using 302 loci. Concatenation-based and multispecies coalescent analyses support the division of Allium into three evolutionary lineages but reveal gene-tree discordance, particularly within the third lineage. Subgenera Allium, Cepa, and Polyprason were recovered as non-monophyletic, with several species showing conflicting placements across analytical frameworks. Multiple complementary analyses demonstrate that incomplete lineage sorting (ILS) is a major contributor to this discordance. Phylogenetic network inference and D-statistic tests detected gene flow among several lineages, indicating reticulate evolution contributed to the genus's complex genomic structure. Divergence time estimates place the origin of Allium in the early Eocene (~ 52 Mya), with major diversification in the Miocene. Rapid lineage diversification during this period likely promoted the persistence of ancestral polymorphisms and contributed to widespread phylogenomic conflict. CONCLUSIONS: Our results provide a nuclear phylogenomic framework for Allium and demonstrate that the combined roles of ILS and gene flow have shaped the evolutionary history of one of the largest monocot genera.