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OfflineAlan RockefellerM
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Phylogenetic tree of the Psilocybe cubensis clade, including P. natalensis * 9
    #27501474 - 10/12/21 12:23 AM (2 years, 3 months ago)

Someone sent me a Psilocybe natalensis ITS sequence a few months back, so I had a pretty good idea what P. natalensis was - but it wasn't my sequence so I didn't want to share it.  This week I made a Psilocybe natalensis sequence in my lab, which matches the other P. natalensis sequence I have.  I've also uploaded it to Genbank, the first sequence of this species there.

The strain is Natal Super Strength.

Photos of the collection:  https://mushroomobserver.org/472561

Here is a tree I made which includes P. natalensis and related species, with P. allenii as an outgroup.



The Psilocybe cf. cubensis sequence is interesting - it's quite close to cubensis, and has some noise, but I don't think it's just a bad read of cubensis because it has some of the same nucleotide substitutions that Psilocybe ovoideocystidiata has.  Gaston Guzman collected it in Nepal in October of 2001.  Without studying the collection (it's in XAL) I can't tell if it's a new species or if it's something which hasn't been sequenced yet like Psilocybe pseudoaztecorum.

Other things you can see in this tree are that Penis Envy has the same ITS sequence as regular cubensis, Psilocybe ovoideocystidiata from the east coast is the same as it is on the west coast and Psilocybe thaiaerugineomaculans is the same as Psilocybe thaiduplicatocystidiata.

In case you'd like to experiment with making phylogenetic trees or analyze the natalensis sequence yourself, here's the FASTA file:  http://images.mushroomobserver.org/natalensis.fas


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Invisiblemycorry
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Re: Phylogenetic tree of the Psilocybe cubensis clade, including P. natalensis [Re: Alan Rockefeller]
    #27501823 - 10/12/21 10:25 AM (2 years, 3 months ago)

Great work!

I may be getting my hands on Psilocybe indica and Psilocybe chuxiongensis in the near future, but a lot of traders feed me big claims. Also, with the cool weather here I can finally get some healthy pseudoaztecorum fruit to test.

That tree may get a lot clearer this year


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Invisibleseldom seen
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Re: Phylogenetic tree of the Psilocybe cubensis clade, including P. natalensis [Re: mycorry]
    #27502880 - 10/13/21 08:53 AM (2 years, 3 months ago)

Ahhh saw this just in time for lunch, I fkn love these.


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OfflineAlan RockefellerM
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Re: Phylogenetic tree of the Psilocybe cubensis clade, including P. natalensis [Re: mycorry] * 1
    #27503348 - 10/13/21 04:06 PM (2 years, 3 months ago)

I have Psilocybe indica in line to be sequenced - I imagine what I have is the same as what you would be getting.

Psilocybe chuxiongensis is not circulating as far as I know - fortunately there is a type sequence of that in Genbank so verifying that it is the real deal will be simple and decisive.


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Offlinecrabs
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Re: Phylogenetic tree of the Psilocybe cubensis clade, including P. natalensis [Re: Alan Rockefeller]
    #28242927 - 03/23/23 12:12 PM (10 months, 10 hours ago)

Hey Alan,

Apologies if I'm resurrecting an old thread here but it seems relevant.  Can you explain in layman's terms what this phylogenic tree means specificialy in regard to Allenii's relation to Cubensis? Sharing a common ancestor? How closely related?


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OfflineAlan RockefellerM
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Re: Phylogenetic tree of the Psilocybe cubensis clade, including P. natalensis [Re: crabs] * 4
    #28249165 - 03/27/23 11:42 AM (9 months, 27 days ago)

Quote:

crabs said:
Can you explain in layman's terms what this phylogenic tree means specificialy in regard to Allenii's relation to Cubensis? Sharing a common ancestor? How closely related?




Psilocybe allenii is pretty distantly related to Psilocybe cubensis - it's on the other side of the genus.  In this case I added Psilocybe allenii as an outgroup - adding a sequence that is not part of the group being studied helps put the studied clade into context. 

There are two strategies I use to see how closely related things are.    One is to make a phylogenetic tree with both species and everything in between.    This would show Psilocybe allenii to be pretty far from cubensis, with a whole lot in the middle.

The other is to look up sequences of the same gene of both species in Genbank and compare them in BLAST.  The alignment shows how many differences there are in the sequence - species with more differences are more distantly related.  This gives a numerical output which is sometimes useful.

For example the Psilocybe allenii holotype is https://www.ncbi.nlm.nih.gov/nuccore/NR_119821

If you click the Run BLAST link on the right you get this page.

Clicking the "Align two or more sequences" box and adding AY281023 (a cube ITS sequence) shows you:



I searched for pipe space "| " to highlight the differences.

You can compare the ITS sequence of any other Psilocybe species to see how different they are.    More closely related species are more likely to be able to successfully hybridize, though there is no hard cutoff.  I have heard that cubensis will hybridize with P. natalensis but not with P. ovoideocystidiata, though you might be able to do it with more attempts or with protoplast fusion or snake venom.

Let me know if you have any questions about any of this.


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Offlinecrabs
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Re: Phylogenetic tree of the Psilocybe cubensis clade, including P. natalensis [Re: Alan Rockefeller]
    #28256418 - 03/31/23 03:26 PM (9 months, 23 days ago)

Thanks Alan!  Greatly appreciate the explanation and guidance.


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