Magic mushrooms are fungi that produce psilocybin, an entheogen with long-term cultural use and a breakthrough compound for treatment of mental health disorders. Fungal populations separated by geography are candidates for allopatric speciation, yet species connectivity typically persists because there is minimal divergence at functional parts of mating compatibility genes. We studied whether connectivity is maintained across populations of a widespread species complex of magic mushrooms that has infiltrated the Northern Hemisphere from a hypothesised centre of origin in Australasia. We analysed 89 genomes of magic mushrooms to examine erosion of species connectivity in disparate populations with support from gene flow, kinship, structure, allelic diversity, and mating compatibility. We used comparative genomics and synteny to test whether the genes that produce psilocybin are under selection in natural populations of magic mushrooms. Despite phenotypic plasticity and intercontinental distribution, sexual compatibility is maintained across geographically isolated populations of magic mushrooms. Psilocybin loci have high allelic diversity and evidence of balancing selection. Australasia is the centre of origin of wood-degrading magic mushrooms and geographically separated populations are fully sexuall compatible, despite minimal gene flow since differentiation from a shared ancestor. Movement of woodchips, mulch, or plants has most likely facilitated invasion of these mushrooms in the Northern Hemisphere.

Fungi that are edible or fermentative were domesticated through selective cultivation of their desired traits. Domestication is often associated with inbreeding or selfing, which may fix traits other than those under selection, and causes an overall decrease in heterozygosity. A hallucinogenic mushroom, Psilocybe cubensis, was domesticated from its niche in livestock dung for production of psilocybin. It has caused accidental poisonings since the 1940s in Australia, which is a population hypothesized to be introduced from an unknown center of origin. We sequenced genomes of 38 isolates from Australia and compared them with 86 genomes of commercially available cultivars to determine (1) whether P. cubensis was introduced to Australia, and (2) how domestication has impacted commercial cultivars. Our analyses of genome-wide SNPs and single-copy orthologs showed that the Australian population is naturalized, having recovered its effective population size after a bottleneck when it was introduced, and it has maintained relatively high genetic diversity based on measures of nucleotide and allelic diversity. In contrast, domesticated cultivars generally have low effective population sizes and hallmarks of selfing and clonal propagation, including low genetic diversity, low heterozygosity, high linkage disequilibrium, and low allelic diversity of mating-compatibility genes. Analyses of kinship show that most cultivars are founded from related populations. Alleles in the psilocybin gene cluster are identical across most cultivars of P. cubensis with low diversity across coding sequence; however, unique allelic diversity in Australia and some cultivars may translate to differences in biosynthesis of psilocybin and its analogs.

It all begins with an idea.