Population genetics of Zamia decumbens (Zamiaceae, Cycadales), an endangered cycad from the Maya Mountains of Belize

We utilized 10 microsatellite loci to examine the genetic diversity, genetic structure, and demographic history of Zamia decumbens Calonje, Meerman, M.P. Griff. & Hoese, an endangered cycad species occurring in small populations on karst topography within the Maya Mountains of Belize. Four populations in two distinct habitats were sampled: three inside dolines (one at a cave entrance and two at the bottom of sinkholes) and one on a rocky hilltop. Genetic variation in the species reflects the demographic history of the sampled populations which appears closely linked to the karstification of the limestone bedrock on which it occurs rather than being structured geographically or by habitat type. Contemporary gene flow between populations is low, with the cave population facilitating most of the genetic connectivity in the region as a source of migrants to other populations. Coalescent‐based modeling revealed that the two sinkhole populations were established first, and the hilltop and cave populations were more recently founded from a common ancestral population. All populations were in Hardy–Weinberg equilibrium and moderately heterozygous, yet signatures for recent bottleneck events were recovered for the doline populations. Furthermore, a high inbreeding coefficient and high average pairwise relatedness were found for the hilltop population, the latter possibly the result of recent illegal harvesting activities.