Phylogenomics and evolution of the Lauraceae based on targeted capture data.

The family Lauraceae, a hyper-diverse magnoliid family comprising approximately 63 genera and over 3,000 species, plays a key ecological role in tropical and subtropical forests. Yet deep relationships among its nine tribes remain unresolved, likely due to limited sampling and complex evolutionary processes such as incomplete lineage sorting (ILS) and gene flow. To address these challenges, we generated datasets of 255 single-copy nuclear genes and chloroplast genomes using a newly designed Lauraceae-specific probe set, achieving the most comprehensive genus-level sampling (84%) to date. Phylogenomic analyses reconstructed a robust nuclear tree, which resolved the Neocinnamomeae as sister to the Caryodaphnopsideae and revealed pronounced gene tree conflict and pervasive cytonuclear discordance. To investigate the evolutionary processes underlying these patterns, comprehensive analyses were conducted. The results indicate that conflicting nuclear gene trees reflect the combined effects of ILS, gene tree estimation error, and gene flow, with ILS dominating across the core Lauraceae, whereas cytonuclear discordance is primarily driven by extensive gene flow. Diversification analyses further indicate that episodes of rapid lineage accumulation coincide with major gene flow events, suggesting a potential role of gene flow in the diversification of Lauraceae. Overall, this study provides a robust nuclear phylogenomic framework for Lauraceae and demonstrates that gene flow had profound effects on its evolutionary history, shedding light on the contribution of gene flow to the diversification of hyper-diverse tropical plant lineages.