Tuber indicum is an ectomycorrhizal ascomycete that produces edible ascocarps. Based on a number of specimens with known exact origin, we investigate the speciation of the Tuber indicum complex in southwest China. Internal transcribed spacer (ITS) and simple sequence repeat (SSR) markers were used in the study. Phylogeography and population genetics analyses were combined to detect 31 wild populations of the T. indicum complex. Two distinct lineages, Tuber cf. indicum and Tuber cf. himalayense, were identified in the T. indicum complex that exhibited significant phylogeographic structures and genetic differentiation. The characteristics of haplotypes distributing along the river demonstrate that the diffusion and modern distribution pattern of species was influenced by river expansion. These findings are critical for the protection of the diversity of truffles in this region.
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