Resolving the Magnolia pacifica complex (Magnoliaceae): a coalescent-based approach reveals five distinct evolutionary lineages

Background and aims – Species delimitation using multilocus coalescent-based methods has provided new insights into evolutionary processes and species boundaries. In this study, we applied a multilocus, multispecies coalescent framework to investigate species limits and estimate divergence times within the Magnolia pacifica complex, a group of endemic species from western and north-western Mexico traditionally classified based on morphological and ecological traits without explicit statistical evaluation. Material and methods – We obtained sequences of three chloroplast intergenic spacers ( trnT-trnL , rpl32-trnL , trnH-psbA ) and three nuclear genes (LFY, PHYA, AGT1) from 67 individuals representing all six described species and the closely related Magnolia iltisiana . Phylogenetic reconstructions were performed using Bayesian inference and maximum likelihood. Divergence times were estimated using the RelTime-ML algorithm. Species delimitation was conducted under the multispecies coalescent model using Bayesian Phylogenetics and Phylogeography (BPP) with algorithms A10 and A11. Key results – Our analyses confirm the monophyly of the M. pacifica complex within Magnolia sect. Magnolia and integrate M. iltisiana into the complex. Divergence of the complex was dated to 1.27 million years ago. Species delimitation analyses revealed five separately evolving lineages: M. pacifica (including M. talpana ), M. iltisiana , M. pugana (including M. granbarrancae ), M. tarahumara , and M. vallartensis , and we formally synonymize M. talpana under M. pacifica and M. granbarrancae under M. pugana . Conclusion – Pronounced morphological divergence has, in some cases, occurred within genetically cohesive lineages, highlighting a pattern of incipient differentiation. Our delimitation effectively resolves the M. pacifica species complex, providing a robust phylogenetic hypothesis and a refined taxonomic framework for understanding the diversification of Mexican magnolias and for guiding conservation priorities.