Analyses of SNPs and genes clustered wood-degrading magic
mushrooms from the northern hemisphere among Australian populations
We included 86 haplotypes from at least 28 separate mushrooms in
Australia, with some haplotypes collected as populations and not
associated with a single pileus. Our sampling covered 12 sites in
eastern Australia (Fig. 2A) and included two reference genomes ofP. azurescens and one of P. cyanescens from the USA. kSNP
called 1,580,296 SNPs, and we tested for population structure based on
ancestry of 6,757 LD-corrected SNPs, which was a subset that excluded
all sites that contained indels or missing data (Figs 2B, 2C). Mixed
ancestry within sites and among known siblings appeared in DAPC analyses
beyond K=7 (Fig. 2C). DAPC analyses showed populations were admixed in
geographic locations. Psilocybe azurescens and P.
cyanescens clustered with P. subaeruginosa in 2D plots (Fig 2B)
and had recent shared ancestry with Australian populations (Fig. 2C).
We visualised relationships among genomes of P. subaeruginosawith SplitsTree neighbour networks based on 1,555,848 LD-corrected SNPs,
including indels (Fig. 2D), and 194 aligned protein coding genes (76,076
amino acids, Fig. S1) identified by OrthoFinder. Relationships recovered
by SNPs and genes were congruent. Psilocybe azurescens andP. cyanescens clustered among Australian populations.
Most individuals in populations from Bunya, Clifton Hill, Ellendale,
kunanyi, Ravensbourne, and Shelley were sampled as siblings that could
be linked to the same pileus (Fig. 2D). We used the AJK statistic (Yang
et al., 2010) to investigate the relatedness of haplotypes within
populations (Fig. S2). The observed relatedness suggests that haplotypes
in clusters observed in Figure 2D are as related as known siblings even
if they were not from the same pileus. These close relationships are
supported by likelihoods of the AJK statistic ≥0.91, which is the lowest
likelihood for known siblings sampled from Ellendale, Tasmania.
Groups defined by DAPC and supported by network analyses of SNPs and
genes show that P. subaeruginosa is structured by geography in
Australia. Relationships among groups reflect geographic boundaries, for
example, samples east of the Great Dividing Range (which divides the
eastern coast of Australia), namely Khancoban, Shelley, Clifton Hill,
and Geelong, differed from populations west of the range in South
Australia, Tasmania, and central Victoria. Full sib haplotypes sampled
from one spore print from Clifton Hill (Fig. 2D e) were completely
intermixed with sibling haplotypes (based on genetic distance and the
AJK statistic) of other fruiting bodies from planted garden beds in both
Clifton Hill and Geelong. A possible explanation for this is that a
parental, dikaryotic genotype has spread long distances via woodchips
and mulch in Victoria, facilitated by the perennial nature of P.
subaeruginosa mycelium. Geographic areas with mixed ancestry based on
DAPC (Fig. 2C) and genetic distance (Fig. 2D), namely Clifton Hill and
Shelley, indicate that pilei were sampled from fruiting mycelia of
different genotypes at the same location.