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We have examined the phylogeographical distribution of chloroplast DNA (cpDNA) lineages of Fouquieria columnaris (Kellogg) Kellogg ex Curran (Fouquieriaceae) in the Sonoran Desert, to understand how historical climatic and/or geological changes have influenced genetic patterns in the species. Using two chloroplast intergenic DNA spacers (psbJ-petA and ndhF-rpl32), we found low levels of nucleotide diversity (π = 0.0025) but high levels of haplotype diversity (h = 0.9339). Analysis of 28 haplotypes revealed four lineages, one belonging to the continental massif and three to the peninsula of Baja California. This structure may be explained and dated by three events: (1) formation of the Gulf of California during the late Miocene (7.24 Mya), (2) activity of the Tres Vírgenes volcanic field (1.20 Mya) and (3) opening of the mid-peninsula seaway during the late Pleistocene (1.53 Mya). Furthermore, the cpDNA lineages show evidence for population contraction during the Last Glacial Maximum, with a subsequent population expansion in the Holocene.

Phylogeography and genetic structure of an iconic tree of the Sonoran Desert, the Cirio (Fouquieria columnaris), based on chloroplast DNA