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AimWe investigate the influence of late Neogene orogenic activity and Pleistocene glacial-interglacial cycles on intraspecific divergence and demographic history in the gymnosperm shrub Ephedra compacta. We test refugia hypotheses to explain geographical patterns of genetic diversity and phylogeographic structure in a warm North American desert that reaches inter-tropical latitudes.

LocationChihuahuan Desert, Mexican Plateau, Sierra Madre Oriental, Tehuacan Valley.

MethodsGeographical patterns of genetic diversity were estimated using chloroplast DNA sequences of 191 individuals from 24 populations. AMOVA and SAMOVA analyses were used to assess population and phylogeographic structure, respectively. Approximate Bayesian computation (ABC) was implemented to test phylogeograhic scenarios of population divergence and demographic expansion. Ecological niche modelling (ENM) was performed to predict the potential distribution of E. compacta during the late Pleistocene and to estimate historical habitat stability. Refugia hypotheses were tested by estimating the linear associations between habitat stability, latitude and parameters of genetic diversity.

ResultsHigh levels of population and phylogeographic structure were observed with six geographical groups explaining most of the variation. The best-supported phylogeographic scenario assumed population divergence and demographic expansion during the Pleistocene. ENM predictions showed historical changes in the potential distribution of E. compacta, with a broader geographical extent in the present. Habitat stability was positively associated with population genetic diversity.

Main conclusionsThe intraspecific population divergence and demographic expansion in E. compacta is probably associated with the glacial-interglacial cycles of the Pleistocene. Our ENM predictions also support a scenario of habitat contraction and expansion during this time period. The phylogeographic history of E. compacta is predicted by climate refugia dynamics in which specific areas, primarily in the Mexican Plateau harbour the highest levels of habitat stability and genetic diversity.