Diversity of alleles at mitochondria
We called 1,334 SNPs in mitochondrial contigs using a k-mer approach
(k=31) with kSNP and plotted mitochondrial genotypes in a haplotype
network (Fig. S4). There were 17 mitochondrial genotypes across the 9
populations defined by DAPC analyses and 14 geographic locations
(including P. azurescens and P. cyanescens ), indicating
high mitochondrial diversity. Psilocybe cyanescens had a
near-identical mitochondrial genotype to populations of P.
subaeruginosa in Australia, and P. azurescens clustered among
Australian genotypes differing by as few as two parsimony informative
characters.
High intraspecific diversity of the ITS region in P.
subaeruginosa
We examined whether the ITS region was informative at species rank inP. subaeruginosa , as phylogenetic relationships based on the ITS
region are used as a proxy for species identification. Phylogenetic
relationships were compared across 26 different ITS types, reflective of
ITS sequence diversity within and among populations of P.
subaeruginosa and related taxa identified on GenBank (Fig. 6). We used
a haplotype network to visualise the proportions of individuals that
shared a particular ITS type. Psilocybe subaeruginosa was
paraphyletic in the ITS region with respect to P. allenii ,P. azurescens , P. cyanescens , P. makarorae , andP. weraroa . Based on parsimony informative characters, ITS
sequences of P. allenii , P. azurescens , and P.
cyanescens clustered with samples of P. subaeruginosa from
Australia, whereas P. makarorae and P. weraroa had unique
ITS sequences not sampled from Australia. Psilocybe cubensis ,
sampled from eight ITS-types in 166 individuals, is a sister taxon toP. subaeruginosa (Bradshaw et al., 2022) and most sequences
cluster with cultivars (exemplified by the AlbinoAplus sequence, Fig.
6). These sequences of P. cubensis are representative of
naturalised and cultivated populations rather than diversity in its
centre of origin.