Recent Population Genetic Divergence in Two Globose Cacti Endemic to the Queretano–Hidalguense Desert, Mexico

Mammillaria parkinsonii and M. perbella are species endemic to the Queretano–Hidalguense Desert (QHD), a potential globose cacti Pleistocene refuge. We tested if the phylogeographic and genetic structures of these species are temporally consistent with the Pleistocene glacial refuge hypothesis. In this case, there would be high haplotype divergence associated with population contraction during the Last Glacial period (115-11.7 kya). Chloroplast DNA sequences and ISSR nuclear markers were used to estimate genetic diversity and structure, haplotype networks, and divergence times. Changes in paleodistribution were modeled using the Ecological Niche Model (MNE). cpDNA and ISSR markers revealed low-to-moderate genetic diversity in M. pakinsonii and M. perbella (π = 0.0004, 0.0044 respectively; HS = 0.362–0.434, 0.293–0.400, respectively) and high population differentiation (GST = 1, 0.722, respectively; ΦST = 0.378, 0.3957, respectively), with no evidence of gene flow (Nm = 0, 0.29, respectively). The estimated divergence times and MNE showed that population divergence began during the Last Glacial in M. perbella and continued into the Holocene for both species. This divergence is associated with population contraction, geographic isolation, and disruption of gene flow. This joint evidence indicated that Pleistocene–Holocene glacial cycles may have driven the recent divergence of these Mammillaria species in the QHD.