Data from: Genomic diversity and structure of a Neotropical microendemic fig tree

<p>Genetic diversity is a key component of evolution and unraveling factors that promote genetic differentiation in space and time is a central question in evolutionary biology. One of the most diverse and ecologically important tree genera in tropical forests worldwide is <em>Ficus (Moraceae)</em>. It has been suggested that, given the great dispersal capacity of pollinating fig wasps (Chalcidoidea; Agaonidae), the spatial genetic structure, particularly in monoecious fig species, should be weak. However, no studies have addressed the factors that determine the genetic structure of <em>Ficus</em> species in regions of high geological, geographic, and climatic complexity, such as the Mexican Transition Zone. Using nuclear single nucleotide polymorphisms (5,311 SNPs) derived from low-coverage whole genomes and 17 populations, we analyzed the population genomics of <em>Ficus</em> <em>pringlei</em> to characterize neutral and adaptive genetic variation and structure and its association with geographic barriers such as the Trans-Mexican Volcanic Belt, environmental heterogeneity, and wind connectivity. From genomic data of 71 individuals, high genetic diversity, and the identification of three genomic lineages were recorded (North, South, and Churumuco). The results suggest that genetic variation is primarily determined by climatic heterogeneity. <em>Ficus</em> <em>pringlei</em> populations from the north and south of the Trans-Mexican Volcanic Belt also exhibited minimal genetic differentiation (F_ST= 0.021), indicating that this mountain range may not act as an insurmountable barrier to gene flow. Wind connectivity is also highlighted in structuring putative adaptive genetic variation, underscoring the intricate complexity of the various factors influencing genetic variation in the species. This study provides information on the possible mechanisms underlying the genetic variation of endemic species of the tropical dry forest of Western Mexico, such as <em>F</em>. <em>pringlei</em>.</p>