Population genetic diversity and climate/habitat stability
We found higher nuclear and mitochondrial diversity in the Northern, Central and Eastern population, than in Southern populations (Figure 4; Table S8). Linear regression analyses revealed that nuclear genetic diversity was significantly correlated with latitude for nDNA but not with longitude (Table 3). Conversely, we found that mtDNA genetic diversity was not correlated with latitude nor with longitude. Likewise, analyses showed that all nuclear genetic diversity estimates (H E, π) were positively correlated with the three environmental stability estimates (StabilityENV, StabilityHOST and StabilityENV-HOST) from the LGM (~21 Kya) to the present, but mitochondrial genetic diversity estimators (HD, π) were not correlated (Table 3; Figure 4).
Discussion
Nuclear SNPs and mtDNA data revealed significant population structure across the range of C. cactorum . Landscape genomic analyses provided support for the hypothesis that a combination of environmental conditions and habitat suitability, influenced by shifts in host species distributions during the Last Glacial Maximum (LGM), were the main forces shaping population genetic structure of C. cactorum across its native Argentine range. Shifts in the distribution of Opuntiahost species, mediated by climatic changes during the Quaternary, are suggested to have had a direct influence on the distribution of C. cactorum , creating fragmented ranges that led to reduced gene flow among populations, promoting genetic differentiation. Results also supported the habitat stability hypothesis, whereby regions within which suitable environments have remained stable since the LGM to the present harbored more genetic diversity than regions of lower habitat stability. Relatively higher habitat stability within the northern region of the distribution of C. cactorum created refuge conditions promoting the maintenance of higher levels of genetic diversity over time, compared to other areas. The hypothesis that the geographically widespread cultivation of O. ficus-indica facilitated contemporary gene flow among otherwise geographically distant populations was rejected, based on population genomic analyses revealing limited genetic admixture and a hierarchical pattern of population differentiation concordant with geography.