Home | Community | Message Board


This site includes paid links. Please support our sponsors.


Welcome to the Shroomery Message Board! You are experiencing a small sample of what the site has to offer. Please login or register to post messages and view our exclusive members-only content. You'll gain access to additional forums, file attachments, board customizations, encrypted private messages, and much more!

Shop: Left Coast Kratom Buy Kratom Extract   PhytoExtractum Kratom Powder for Sale   Mushroom-Hut Substrate Bags   North Spore North Spore Mushroom Grow Kits & Cultivation Supplies

Jump to first unread post Pages: 1
OfflinePscientist
KushKaptain
Male


Folding@home Statistics
Registered: 11/13/09
Posts: 2,679
Loc: Sirius X1
Last seen: 29 minutes, 40 seconds
Re: Psilocybe sierrae aka P. subfimetaria [Re: BlimeyGrimey] * 1
    #28636541 - 01/27/24 07:49 AM (11 hours, 32 minutes ago)

As someone who studies and interprets molecular sequenceswith some regularity, I was excited to see this thread and would love to share my thoughts.


Firstly, I will start by saying that interpreting molecular sequences can be a bit challenging. I will also mention that my experience comes from non-fungal sequences, so my thoughts originate in that context.

It is possible that this is a new species (P. sierrae) and that the ITS barcode has not diverged enough to distinguish these two species from each other. However, in this case I would say that seems unlikely. The best way to truly know is full genome sequencing and comparison with other P. stuntzii species. There are examples of defined animal species (through morphology or other means) that are not resolvable at molecular barcode loci, which adds to the difficulty to interpret these data. Additionally, the degree of sampling plays a huge factor here, if species are poorly sampled, and represented in genetic databases, the ability to make meaningful conclusions about taxonomic identity are limited as well, because the full range of genetic diversity is not represented for the species that are likely candidates.

Making inferences from a single molecular sequence is also difficult, and generally discouraged in the molecular taxonomy literature. The rates of change at these barcode loci can be influenced by many things such as the time since speciation between this organism that was sequenced, and its last common ancestor with P. stuntzii (if it is a novel species). It can also be influenced by mutation rates in the species as well. 

I suppose an experimental way to know if this is a novel species (I would imagine) are mating tests between the mycelia (not sure if these are done in this field). At least in non-fungal species the defining barrier for a species is generally the inability to produce viable interspecies hybrids. I know mycelia can have +/- mating types in some psilocybe species, so I am not sure if this sort of test can be used to evaluate interspecies hybrid fruits and sporulation capacity. The way I would like most to evaluate a true novel species would be this experiment in combination with whole genome sequences.


Now, interpreting the BLAST results for this ITS1 sequence:

The immediate interpretation definitely suggests that this sequence is most like P. stuntzii when using GenBank. If these two sequences are from different species (hypothesis), they must not have speciated long ago, or the rates of mutation are quite slow, and as a result mutations have not accumulated in ITS. The best way to know is to perform an integrative taxonomic approach which involves leveraging morphological data, with the molecular data (which it sounds like was done in this thread by others).

Now, I will point out some other observations about this sequence:

If we consider all of the intraspecific variation that is observed in P. stuntzii at this ITS sequence (by looking at all the ITS BLAST hits for this sequence from P. stuntzii) we can see that there are sequences with up to 98.9% similarity across the entire ITS sequence (OR167896), and even less when not considering the full query sequence (98.1%, KC669295). I will also point out that there are not many samples for this species, so the intraspecific variation at the ITS locus is likely not well captured here.

Despite that, these stuntzii records are pretty similar to the query sequence, but I will also draw your attention to the fact that there are ITS sequence from other species with a high degree of similarity to this sequence as well. For example, record MH856273 from P. semilanceata is 97.2% similar across the entire sequence. This level of difference would make me confident that at least this sequence seems most like P. stuntzii and can be resolved from P. semlianceata at this barcode locus. However, the interpretation is confounded by the fact that there is a P. baeocystis record OQ318237 that is 98.2% similar to the sample sequence, although a smaller alignment is considered in that case (93.5% of the query sequence). Additionally, P. angulospora seems to be closely related as well (97.4% identical across 93.5% of the sequence.

To me it seems that using the ITS1 sequence alone, it is hard to distinguish between P. stuntzii, P. semilanceata, P. angulospora, and P. baeocystis at least to a high degree of certainty.

The sequence certainly looks more like P. stuntzii to me, but I wouldn't be confident in the ID based on this sequence alone. Secondly, if you place the sequence into other species identification engines that can accept ITS sequence, it suggests there are a few species that are close matches including P. stuntzii, P. semilanceata, P. fasciata, P. hispanica, and P. strictipes, and it seems they actually cannot be resolved either. It suggests the best match to actually be P. semlianceata. What's more, P. strictipes seems to not be represented in GenBank, so when looking at these sequences, multiple database searches might be best.

In general, I would say that personally I would not confidently ID this species based on ITS sequence alone. The ID would have to be made based in other distinguishing morphological features as well (spore features, gill features etc.), and if possible other molecular data (ideally whole genome).

Those are my thoughts, happy to answer questions or clarify if need be.


--------------------
Any information posted on this website from this account is hypothetical and only to be used for legal purposes. :super:


Extras: Unfilter Print Post Top
OfflinePscientist
KushKaptain
Male


Folding@home Statistics
Registered: 11/13/09
Posts: 2,679
Loc: Sirius X1
Last seen: 29 minutes, 40 seconds
Re: Psilocybe sierrae aka P. subfimetaria [Re: BlimeyGrimey]
    #28637096 - 01/27/24 03:59 PM (3 hours, 22 minutes ago)

Quote:

BlimeyGrimey said:
Thank you for that rundown!

I'm not 100% convinced that even breeding studies would definitively identify multiple species as being synonymous. There seems to be evidence that species such as P. azurescens and cyanescens will breed and I believe most species within the same sect will probably breed, even if they don't do it often or readily.

Now I remember why I tend to stick to the hunting and cultivation of mushrooms instead of the taxonomy.





Interesting, thanks for sharing.

These species can breed, and generate fruits that have spores that are themselves viable? That is quite fascinating.


If that is the case, I wonder what the accepted definition of a species is for fungi then. It could be a morphological classification that may (or may not) be different from the classifications that would be determined using molecular data, or through experiment.


edit: upon looking I can't find azurescens ITS in Genbank, so I cannot evaluate ITS similarity with cyanescens, but it would be interesting.


--------------------
Any information posted on this website from this account is hypothetical and only to be used for legal purposes. :super:


Edited by Pscientist (01/27/24 04:07 PM)


Extras: Unfilter Print Post Top
Jump to top Pages: 1

Shop: Left Coast Kratom Buy Kratom Extract   PhytoExtractum Kratom Powder for Sale   Mushroom-Hut Substrate Bags   North Spore North Spore Mushroom Grow Kits & Cultivation Supplies


Similar ThreadsPosterViewsRepliesLast post
* Genetic Relationship of Psilocybe Species... fastfred 5,153 11 10/19/14 11:52 PM
by Alan Rockefeller
* RogerRabbit gets P. cubensis "Red Boy" aka Redspore!!!
( 1 2 3 all )
fastfred 16,172 49 04/18/11 01:41 PM
by RogerRabbit
* Psilocybe zapotecorum WorkmanV 4,417 3 06/22/05 04:56 AM
by scatmanrav
* Psilocybe semilanceata help please.
( 1 2 all )
Paid 9,155 30 06/09/03 10:48 AM
by comario2
* Selection of "Psilocybe atlantis"
( 1 2 all )
WorkmanV 8,831 33 08/23/05 08:21 AM
by blackout
* Presence of Phenylethylamine in Hallucinogenic Psilocybe Mus Hermes_br 3,158 18 03/31/05 06:09 PM
by hjalmar
* Several Psilocybe cyanescens questions LordByron 7,202 16 01/04/08 09:28 PM
by LordByron
* Psilocybe hispanica
( 1 2 3 4 5 6 all )
WorkmanV 23,547 112 11/05/23 12:38 PM
by smalltalk_canceled

Extra information
You cannot start new topics / You cannot reply to topics
HTML is disabled / BBCode is enabled
Moderator: RogerRabbit, Pastywhyte, bodhisatta
21,176 topic views. 0 members, 5 guests and 1 web crawlers are browsing this forum.
[ Show Images Only | Sort by Score | Print Topic ]
Search this thread:

Copyright 1997-2024 Mind Media. Some rights reserved.

Generated in 0.025 seconds spending 0.007 seconds on 17 queries.