Scientists (Pawel Kosentka et al) complied and produced genetic and chemical data that showed muscarine and psilocybin containing mushrooms are both mutually exclusive and that the loss of muscarine production (observed 10-13x) comes before the gaining of psilocybin production (observed 2x transitions) in a large sample of European and North American species.
[edited 10/9/2020 Provided explanation for Approve & Reject; added more caveats; SEO]
Hypotheses and Takeaways
The authors of this work propose two hypothesis they intended to test for: 1) Possession of muscarine is an ancestral trait of the Inocybaceae family; and 2) Psilocybin-containing taxa form a monophyletic group. To do so they chose to compile decades of qualitative data (from the 80's to the early 2000's) on the detection of muscarine and psilocybin in the Inocybaceae family and compile that data with their own produced genetic and chemical data.
The supplemental data was in the form of liquid chromatography tandem mass spectrometry (LC-MS/MS), which in conjunction with standard solutions, allows for robust identification and even quantification. While the general intent of this paper was to qualify the presence and absence of muscarine, not quantify, the methods presented by the researchers are fully capable of producing reliable quantifiable data (Fig 1). The data depicts orders of magnitude differences in concentrations (observed area counts divided by sample wight) within the thirty samples tested. As an outside observer, I believe, this reinforces the idea that muscarine production is a gradual loss over time and not a sudden one.
Insight into Compound and Biological Effects
Muscarine, a choline-like alkaloid binds to acetylcholine receptors
- Symptoms include profuse sweating, lacrimation (crying), and bradycardia (reduced heart rate)
- Typically observed quickly within two hours after consumption
- Observed largely in the mushroom (basidiomata) of species of Inocybe sampled from North America and Europe [1–10]
Psilocybin, a tryptamine alkaloid that acts on serotonin 5-HT2A/C receptor sites
- Symptoms include hallucinations  and indigestion
- First observed in Inocybe in the 1980s [1,12,13]
- There are multiple analogs to Psilocybin: norbaeocystin, baeocystin and psilocin; all of which tend to co-occur with psilocybin
- Aeruginascin, an indole alkaloid and trimethylammonium analogue of psilocybin, has been observed in the European species I. aeruginascens  which has also been shown to lack muscarine 
Conclusions and Caveats
Muscarine Analysis via LC–MS/MS looked at thirty species of Inocybaceae sampled primarily outside Europe, then tied that data set to an assembled (~500 species of Inocybe, Auritella, and Tubariomyces) sequence list focused on the nuclear DNA of the large ribosomal sub-unit RNA (LSU/ITS) to produce the most taxonomically inclusive data-set for the family observed up until 2013 (the date of publication). From this the researchers reconstructed a chronogram (Fig. 2) for the family to examine patterns of muscarine and psilocybin evolution within a geological time frame.
Based on these data, muscarine and psilocybin were observed to be both mutually exclusive compounds in species of Inocybaceae and it would appear the loss of muscarine is a prerequisite to a gain of psilocybin in species of Inocybaceae. There were two lineages that were observed to no only lose muscarine production, but gain psilocybin production on separate occasions (Sup Fig 1).
The researchers do note a few caveats on their data, and bring them forward for peer review. The first of which is that
there was immense difficulty in parsing the data from decades of different works. Various methods were performed that "could be expected to provide varying levels of confidence in the reported relative amounts of muscarine". Similarly, some data was reported in a qualitative manner (+/-), while others presented in a quantitative manner (%); for conservation of data, they researchers opted to "(refine) all of the data into a +/− system and (resolve) conflicting results by majority-rule". They also noted that their data produced what they called "taxonomic quandaries", one species (I. flocculosa) was identified in the literature under three different names; while another species (I. rimosa) have been, since initial potency research, shown to breakdown into a more intricate species complex. Due to this the researchers "only coded positive the most reliably identified sample (from northern Europe)". They put it best: "Lastly, in the literature we uncovered a clear geographic bias for taxa sampled from Europe and North America only."
They also stress that the phylogenetic results presented should serve as a “springboard from which to target additional or crucial taxa”, but not an unquestionable foundation to teach. This is in part due to the fact that the genetic results are dependent on a single target gene for phylogenetic analysis. While the LSU/ITS does have it's limitations, the researchers observe that “the LSU/ITS dataset is the most taxonomically densely [sic] sampled phylogeny of the family to date” and will likely form the backbone of whatever future phylogeny arise in this space.
Accept or Reject Proposed Hypotheses?
Reasons to Accept
Reasons to Reject
1) Possession of muscarine is an ancestral trait of the Inocybaceae family
2) Psilocybin-containing taxa form a monophyletic group
Reviewing the data and the conclusions put forth it can be stated that none of the hypotheses proposed could be accepted. The reason for the rejection can be tied to the following issues (emphasis and parentheticals mine):
1) "Although not an ancestral (trait) for the (Inocybacea) family as a whole, muscarine is a shared derived trait for an inclusive clade containing three of the seven major lineages of Inocybacea (the Inocybe, Nothocybe, and Pseudomsperma clades), the common ancestor of which might have may have evolved (about sixty) million years ago."
2)"The chronogram also informs us of a minimum of two independent transitions to a psilocybin-containing state, both of which occurred relatively recently during the Miocene between (ten) and (twenty) million years ago, once in a lineage containing I. tricolor, I. haemacta, and I. corydalina and its allies; and independently in I. aeruginascens."
References (from article)
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