Apologies for the delay. At last, the data are in a state to analyse. We ended up with 85 genomes funded by BioPlatforms Australia, of which 80 were Psilocybe subaeruginosa.
The data are assembled and annotated, and the below figure is a way to visualise the relationships among the sampled populations, plus three genomes from GenBank of P. azurescens and P. cyanescens. The most obvious take home at this early stage is P. azurescens and P. cyanescens are likely conspecific with P. subaeruginosa. No surprises here, this was always the hypothesis. But good to see it play out the way we expected.
These data aren't perfect yet and I'm still finalising the SNPs. More information coming, especially on the psilocybin gene cluster, soon!
Most of my time at the moment is toward publishing the analyses of P. cubensis and the story behind their introduction to Australia. We've resolved mating in cubes, which is similar to P. subaeruginosa, but with more red herrings for compatibility. I'll tease this out a tad more soon.
@Feral Beryl Bunyip, I sequenced a genome of one of the mushrooms you sent me. Give me a shout if you have dreams of what should happen with this treat :).
I've been contacted by many Australians interested in volunteering for clinical trials. The jam is I work on the evolution of mushrooms and don't run clinical trials.
Here's an opportunity for those of you who microdose psilocybin and live in Sydney, Australia.
Dr Vince Polito in the School of Psychological Sciences and his team at Macquarie University are looking for individuals who microdose (or are already planning to microdose) using psilocybin or ‘magic mushrooms’.
Participants will visit their lab on two occasions: once after taking a microdose and once after taking a placebo. They will use an MEG scanner to explore what happens in peoples’ brains when they microdose.
Added bonus, they can reward your participation financially!
For more information and to sign up, please visit microdosingstudy.com or email email@example.com
You can find more about Vince Polito’s research here.
You can read more about their study here.
Thank you Ronny, Eva, Jay, Jacob, Nicole, Billy, Sophie, and Caine for taking care of us and all the hospitality at Entheogenesis. Fun on a bun, and fantastic to meet so many of the people who have sent me spores this year.
After my talk, which you can watch here if you attended the conference, I spoke to more than 10 people about their experiences of Wood Lover's Paralysis, which occurs as a side effect when eating Psilocybe subaeruginosa, and temporarily paralyses people during a psilocybin experience.
The grey areas around the cause of WLP are: (i) is there variation among humans (are there more susceptible people), (ii) is it caused by metabolism when mushrooms grow on particular substrates, or (iii) is it caused by secondary metabolites produced by genotypes of P. subaeruginosa?
It felt like the majority of you have experienced WLP and with varying symptoms (from full paralysis including not being able to speak, to paralysis of limbs). We might be able to rule out that some people are immune, even though one member of our community has never experienced WLP after >30 years of practice.
The anecdotal evidence leans toward substrate or genotype. Paralysis occurred in people who had picked from wild areas and cultivated garden beds, and paralysis reoccurred when people ate smaller doses of the same batch of harvested mushrooms (interesting).
In a manuscript coming out soon (it's been reviewed, just stuck in a bottleneck), we show an additional copy of one of the genes that produce an enzyme in the metabolic pathway of psilocybin. PsiH genes convert tryptamine into 4- Hydroxytryptamine, but when you have redundant copies of a gene, they can start to innovate. Redundant genes are not under selection (their previous function is wrapped up by the original copy) and they can explore mutations over generations to take on versatile functions. If the new enzymes produced are not deleterious and confer a slight advantage, they'll stick around in the gene pool.
The first hypothesis to explore is that there are functional copies of the psiH3 gene in the population of P. subaeruginosa, and individuals with those copies produce a Wood Lover's Paralysis phenotype. Those data should be coming to me soon (it is Christmas after all) and we can all share in the excitement.
I collected a couple of Psilocybe cubensis before the season commences because these might have alleles that are suited to fruiting in versatile conditions. Could be interesting to incorporate some of these genetics in future crosses.
The cultures for genomes have grown and I will take samples to AGRF this week. We could expect genome data by Christmas, and with that we'll have a good indication of species diversity in Australia (to answer the question of whether Psilocybe subaeruginosa is more than one taxon).
We're submitting a manuscript on mating in P. subaeruginosa, and if that gets through review, I can share some neato knowledge about the psilocybin gene cluster in wood loving species. More answers on cubes coming soon as well.
Thank you to Kelly from BioPlatforms Australia, who has helped support sequencing of 100 genomes of Psilocybe subaeruginosa collected in 2022. Thank you also to the collectors of P. subaeruginosa: Caine B (and helpers), Snu, Jan T, Dave H (and team from Kosciuszko), Tim S, and anyone who has anonymously sent prints. Our project is just over one year in, with quite a lot of data considering there has been no financial support (until BioPlatforms stepped in). There are over 100 haploid cultures of Psilocybe lodged in the herbarium, and we will have sequenced 140 genomes in less than 18 months. This is an effort from the community interested in Psilocybe, I'm just the bloke at the end of the chain.
The stories on mating, biodiversity, introduction of P. cubensis, and variation at the psilocybin locus are unfolding nicely. I probably won't have finished everything before my contract finishes in November, but I'll keep working on genetics of magic mushrooms as long as I have a computer, and all these data will be made public for the community to blaze ahead. Pictured below, preparation of the 100 cultures for sequencing. Get in touch if you would like to make use of the data, otherwise they'll be public in 2 years maximum (from when I get the raw data).
Here are some new analyses with a longer-term aim to determine how long gold tops have been in Australia. Originally, in the network analyses from past posts, it appeared that populations of gold tops were structured by geography, e.g. mushrooms from Mareeba would not reproduce with mushrooms from Lismore.
On the road to determine the effective population size of Psilocybe cubensis in Australia, it now looks like there is some admixture (sexual reproduction among populations).
The below figure is a journey to determine how we should treat the populations of P. cubensis in Australia. I tested how many groups best fit the data (which is 'K' in the figure). The figure depicts how populations across Queensland and NSW would look if treated as 2–6 different groups. I settled on 6 as the number of groups in the sequenced populations. If we added new locations, no doubt we would see more geographic structure.
The curious result is that populations from Cairns, Gold Coast and Sunshine Coast all group together. They are genetically similar.
This could mean that manure has been moved from southeast Queensland to northern Queensland (or vice versa). Though it is difficult to know for sure. It's also interesting that different mushrooms from the Sunshine Coast are either related to those in Cairns, or form their own segregated population.
Leave it with me, but if you have ideas on why these three locations may not be structured by geography, let's explore them together :). Thanks again to the legends who collected the mushrooms for these analyses!
Here you can visualise diversity of the psilocybin gene cluster in populations of gold tops in NSW and Queensland. We could pretty much say there are four alleles of the psilocybin gene cluster present across the distribution of gold tops. There is near 100% sequence identity across 30,000 base pairs that encode four genes for psilocybin production. The diversity occurs mostly in two genes, PsiK and PsiM. Whether this has an impact on psilocybin phenotype is something I intend to find out through breeding.
I produced this figure for a talk at Splendour in the Grass coming up on the 23rd of July. Come and say hi if you're going to be there.
We potentially have funding to sequence the 120 or so cultures I've made from spore prints sent in from you all in the community. I'll share more when it's official. If you have a population of Psilocybe subaeruginosa that you want included in the study, I'll need those spores in the next couple of weeks. Get in touch if you want to know how your population compares to others in Australia (we have good sampling from Tassie, Victoria, and southeast Queensland).
Below is a new way to visualise the diversity of gold tops in Australia compared to the populations cultivated globally. Note that there is not much diversity in the Golden Teacher strain. Our analyses of this show it has a low effective population size (probably from 50+ years of inbreeding) especially compared to the diversity in our outbreeding population here in Australia. More on this hopefully coming in a publication with the Oz genomes soon.
Here's a taste of what will come from 32 new Psilocybe cubensis genomes freshly assembled. First of all, thank you to Andrew B, Matt W, Bocky and Dan, Rhys L, and all landholders in southeast Queensland for spores. We ended up with over 50 haploid (or so I thought) cultures of Psilocybe cubensis.
Three of the 32 genomes were probably dikaryotic, which is a reflection on how good I think I am at culturing compared to my actual culturing ability. The figure is a network based on 529,027 SNPs. Preliminary interpretation, there is probably structure by geography, the populations are not admixed.
More soon, including some answers about mating! We've resolved reproduction in Psilocybe, now just going through the motions of publishing.
This figure compares basidiospores from P. subaeruginosa collected in SE Queensland (A & C) and Tasmania (B, by Caine B), and of P. cubensis (D). Psilocybe cubensis and P. subaeruginosa are sister taxa (they shared a most recent common ancestor). One might interpret there is not much morphological difference between the populations of P. subaeruginosa separated by a strait and two states.
Queensland Health Seminar coming up. Talks on fungi, toxic plants, stinging trees and confiscated contraband in Brisbane!
Recording available here: https://vimeo.com/713129405/2c456a2298
Recommend watching the talk on Clandestine Dimethyltryptamine (DMT) laboratories encountered in Queensland by Dr Tim Currie.
Our research on Psilocybe