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Truffles have evolved from epigeous (aboveground) ancestors in nearly every major lineage of fleshy fungi. Because accelerated rates of morphological evolution accompany the transition to the truffle form, closely related epigeous ancestors remain unknown for most truffle lineages. This is the case for the quintessential truffle genus  Tuber , which includes species with socio-economic importance and esteemed culinary attributes. Ecologically,  Tuber  spp. form obligate mycorrhizal symbioses with diverse species of plant hosts including pines, oaks, poplars, orchids, and commercially important trees such as hazelnut and pecan. Unfortunately, limited geographic sampling and inconclusive phylogenetic relationships have obscured our understanding of their origin, biogeography, and diversification. To address this problem, we present a global sampling of  Tuberaceae  based on DNA sequence data from four loci for phylogenetic inference and molecular dating. Our well-resolved  Tuberaceae  phylogeny shows high levels of regional and continental endemism. We also identify a previously unknown epigeous member of the  Tuberaceae  – the South American cup-fungus  Nothojafnea thaxteri  (E.K. Cash) Gamundí. Phylogenetic resolution was further improved through the inclusion of a previously unrecognized Southern hemisphere sister group of the  Tuberaceae . This morphologically diverse assemblage of species includes truffle (e.g.  Gymnohydnotrya  spp.) and non-truffle forms that are endemic to Australia and South America. Southern hemisphere taxa appear to have diverged more recently than the Northern hemisphere lineages. Our analysis of the  Tuberaceae  suggests that  Tuber  evolved from an epigeous ancestor. Molecular dating estimates  Tuberaceae  divergence in the late Jurassic (∼156 million years ago), with subsequent radiations in the Cretaceous and Paleogene. Intra-continental diversification, limited long-distance dispersal, and ecological adaptations help to explain patterns of truffle evolution and biodiversity.

Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage