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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,271
Last seen: 10 hours, 55 seconds
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Re: Genetic Relationship of Psilocybe Species... [Re: fastfred] 1
#20727098 - 10/19/14 11:29 PM (9 years, 3 months ago) |
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fastfred said: Here is a phylogenetic tree of several Psilocybe and Panaeolus species (and others) constructed by sequencing LSU rRNA region (and/or ITS).
There has been a lot of discussion about relationships of these species as of late. Hopefully this will be very interesting to some of you.
Those trees are all fucked up and show very little useful information. I suggest you remake them using the sequences that are now available on genbank. Almost all of the conclusions are wrong.
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Alan Rockefeller
Mycologist

Registered: 03/10/07
Posts: 48,271
Last seen: 10 hours, 55 seconds
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Re: Genetic Relationship of Psilocybe and Panaeolus Species... [Re: fastfred] 1
#20727184 - 10/19/14 11:52 PM (9 years, 3 months ago) |
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fastfred said: It's hard to say why different P. cubensis samples get placed in different branches. Perhaps there is more genetic diversity than one would expect. Or perhaps using such a short and unconserved region of rDNA results in a greater than desired element of randomness. It should be noted that the ITS region is significantly more variable than the SSU and LSU regions. Any region variable enough to give good resolution at the species level is going to produce some artifacts though.
Probably because some of them were not P. cubensis.
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Despite some differences among the trees, they seem to show that P. cubensis is most closely related to: P. montana P. semilanceata P. australiana P. subaeruginosa P. subaeruginascens P. cyanescens Pa. sphintrinus
Psilocybe cubensis is not closely related to any of those species. P. cubensis is closely related to P. ovoideocystidiata, P. subcubensis and P. chuxiongensis.
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As to what the ITS region codes for... I don't think it codes for anything. I'm no expert, but I don't think it produces any sort of gene product.
I agree with that. If it coded for anything, it wouldn't be useful for species level differentiation.
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fastfred said: It's hard to say. I would guess that it's just an artifact. On the other hand it could be a bad sample, problems with the sequencing, etc.. The ITS sequences could be either too similar amongst the samples or too different for making a good phylogenetic tree. One thing I just noticed is that there are 3 ITS-1 sequences in GenBank... Two are complete and the third is only a partial sequence. That could account for the discrepancy. It's pretty sloppy if they let a partial sequence cause a difference like that, but I'm sure it happens.
That is too small. When I see sequences of that length, I just delete them. If the people who made the sequences knew what they were doing, they would be around 700 base pairs.
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ITS-1 is only 234-236 bp long, so it's a very small region. It's become one of the most, if not the most, popular region to sequence in fungi for molecular systematics
Its1f/its4b primers give around 750 base pairs.
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I checked the P. cubensis and P. subcubensis sequences and they are identical. So it looks like the "subcubensis" is another example of someone trying to inflate a tiny phenotypical difference into "the discovery of a new species". Ha! It's worse than the professor hyping the redspore.
My analysis shows they are a little bit different, but more sequences with spore size measurements are needed.
Here is my most recent Psilocybe ITS tree:
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