Using genome-wide diversity and population structure to define management units in the cirio (Fouquieria columnaris), an emblematic tree of the Sonoran Desert

An important research goal for plant species of conservation concern is to identify and spatially delimit genetically distinct populations and understand their degree of connectivity. Here, we evaluated structure, diversity, and genetic connectivity using neutral genetic markers in cirio ( Fouquieria columnaris ), a unique succulent tree restricted to the northwestern Sonoran Desert in Mexico. Using genome-wide sequencing, 1,137 biallelic single nucleotide polymorphisms (SNPs) were identified in 55 individuals from 7 sites (6 on the Baja California Peninsula, 1 in coastal Sonora), belonging to populations that were previously shown to constitute distinct lineages according to chloroplast DNA. There was relatively minor cytonuclear discordance, which was attributed to the northernmost peninsular site; when that site was removed, there was concordance between chloroplast and nuclear DNA matrices. We recognize four genetic groups as demographically independent units. Pairwise comparisons of nuclear genetic differentiation between localities (Jost’s D) ranged from 0.035 to 0.008. We detected positive inbreeding values and diversity patterns associated with historical bottlenecks and habitat fragmentation. There was asymmetric gene flow from the small Sonoran mainland population to the much larger northern peninsular population, an unexpected result that may be influenced by pollinators. The most strongly differentiated populations based on SNPs were Sierra Bacha on the Sonoran coast with the southernmost peninsular site, Tres Vírgenes. Within the Peninsula there was a statistically significant pattern of isolation by distance. Our findings provide a detailed view of the genetic structure and connectivity of this emblematic tree that may help guide conservation actions.