Comparative analysis shows high level of lineage sorting in genomic regions with low recombination in the extended Picea likiangensis species complex

• The study delves into the intricate evolutionary patterns within the extended Picea likiangensis species complex (e-PLSC), uncovering significant incongruity between chloroplast and nuclear trees. • The discordance is attributed to introgression (54.99%) and incomplete lineage sorting (ILS; 33.12%). • Recombination rates played a pivotal role in shaping incomplete lineage sorting and introgression, with regions of high recombination exhibiting elevated levels of both ILS and introgression. • Genes implicated in high-level introgression and ILS are found to be associated with abiotic stress responses, suggesting their role in adaptive evolution. • Our study emphasizes that lower recombination rates result in enhanced precision when capturing authentic species relationships.