Evolutionary history reveals spatial concentration of threatened evolutionary diversity in Agave across the Americas

Global biodiversity loss threatens not only species survival but also the loss of unique evolutionary history, highlighting the need to understand how macroevolutionary processes shape the evolutionary diversity and its vulnerability to extinction. Radiations of arid-adapted plants provide a useful system to examine how diversification and dispersal generate present-day biodiversity patterns. Here, we reconstruct the evolutionary history of Agave across the Americas using a time-calibrated phylogenomic framework (207 taxa, 286 nuclear genes) and integrate these results with biogeographic inference and Evolutionarily Distinct and Globally Endangered (EDGE) metrics to identify conservation priorities. We find that Agave originated in Aridoamerica during the late Miocene (∼7 Ma), followed by dispersal into Mesoamerica, Central America, and the Caribbean. This history has generated a spatially uneven distribution of evolutionary distinctiveness, with arid ecosystems harboring a disproportionate share of evolutionarily unique and threatened lineages. We identify 70 EDGE taxa, with exceptional conservation priority (the most endangered species were: Agave montium-sancticaroli , A. aurea var. promontorii , and A. albopilosa in EDGE and EDGE2). We identify key regions in Mexico, USA, and Guatemala—such as the Tehuacán–Cuicatlán Valley, Oaxaca, the Chihuahuan Desert and Arizona—that combine high phylogenetic diversity with elevated concentrations of threatened evolutionary history. These patterns reflect the interaction between macroevolutionary dynamics, and ecological specialization, and are further intensified by anthropogenic pressures, as evidenced by the high proportion of Agave species listed under the IUCN Red List. Our results demonstrate that integrating evolutionary history with extinction risk can improve spatial conservation prioritization.