AbstractAim To investigate the impact of Quaternary climate cycles on the coastal Atacama Desert flora by assessing phylogeographical patterns of the desert
shrub Nolana crassulifolia (Solanaceae) and its congener Nolana incana. Location The latitudinal aridity gradient from the southern margin of the coastal Atacama Desert
to the mediterranean semi‐arid region of Chile (25–33° S). Methods Two cpDNA regions were sequenced for 130 individuals in 15 populations of these two closely related
species, covering their entire distribution range (1000 km) along the arid to semi‐arid Chilean coast. We explored haplotype relationships in a statistical parsimony network, and assessed population genetic diversity, population differentiation and phylogeographical structure.
In addition, we conducted demographic analyses and spatial analysis of genetic variation, identified barriers to gene flow with Monmonier's algorithm, and used Bayesian phylogenetic reconstruction to estimate divergence dates between lineages. Results We found a total of 14 haplotypes – four of them shared by both species – and high levels of genetic differentiation among populations, but no past distribution breaks that could account for major vicariant events. Genetic diversity
decreased continuously from north to south, with loss of haplotypes and a greater number of monomorphic populations in the southern range. Landscape analysis revealed greater genetic differentiation in the northernmost populations of both species. Main conclusions The documented north–south gradient of declining genetic diversity, the origin and location of ancestral haplotypes in northern sites, and the loss of haplotypes from southern populations all support the hypothesis of post‐glacial
range expansion of Nolana southwards during arid/warmer cycles in the Atacama. The higher genetic diversity and greater differentiation of northern populations of both Nolana species support the hypothesis that populations survived in northern arid sites during wetter/colder
episodes of the glacial cycles. We suggest that Quaternary arid phases in the Atacama promoted southward expansion of the coastal desert vegetation.