Aim The history of Agave lechuguilla, a characteristic and dominant plant of the Chihuahuan Desert, was reconstructed in order to determine the importance of the Neogene orogenic uplift and the Quaternary glacial–interglacial climatic changes on the genetic patterns of a native Chihuahuan Desert species. Location Chihuahuan Desert, Mexico and United States. Methods Chloroplast DNA data from A. lechuguilla were analysed to describe levels of genetic diversity and structure and to infer the species’ demographic history, using traditional methods and approximate Bayesian computation (ABC). The time of divergence of the different haplogroups was estimated with a Bayesian approach. In addition, ecological niche modelling was used to identify possible refugia. Results Molecular dating analyses showed that A. lechuguilla originated 4.46 Ma and later differentiated into four haplogroups. The average chloroplast genetic diversity was low (Hd, 0.24), with high levels of genetic differentiation (GST, 0.780). Demographic analysis, niche modelling and ABC indicated a recent expansion from at least five glacial refugia located south of the species’ current distribution. Main conclusion Agave lechuguilla originated in the Neogene, and the glacial–interglacial events of the Pleistocene resulted in the expansion and contraction of its range, playing an important role in its intraspecific diversification. These contraction–expansion events are consistent with biogeographical regions previously identified in the Chihuahuan Desert.

Aim Our aim was to analyse the temporal dynamics of areas of endemism of Bursera species (Burseraceae), a dominant element of the Mexican tropical dry forest, between the Last Glacial Maximum (LGM) and the present day. We aimed to identify stable core sectors that have held permanent populations of endemic species. Location Mexican dry forest. Methods We modelled the geographical distributions of 81 species of Bursera and identified their areas of endemism at the LGM and at present. For each area of endemism, changes in time, species composition and distribution were analysed, and a spatially explicit temporal hypothesis was formulated. Results Three areas of endemism supported by geographically congruent elements were identified: the Central Mexican Pacific Coast, Western Balsas, and Eastern Balsas–Tehuacán/Cuicatlán–Tehuantepec. Within them we identified stable core sectors (refugia). Main conclusions The areas of endemism identified represent distinct evolutionary biotic components of the Mexican dry forest. Their stable core sectors may facilitate phylogeographical predictions at the level of species or species assemblages. The framework adopted allows us to formulate spatially explicit temporal hypotheses about biotic processes, based exclusively on geographical data.

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