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Invisiblefastfred
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Genetic Relationship of Psilocybe Species...
    #5667933 - 05/24/06 09:06 AM (17 years, 10 months ago)

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.

The "unknowns" are all P. Cubensis.


-FF

edit: Changed pic and added 3 more trees!



Edited by fastfred (05/24/06 12:56 PM)

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Offlinebeforetimetook
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Re: Genetic Relationship of Psilocybe and Panaeolus Species... [Re: fastfred]
    #5668357 - 05/24/06 11:28 AM (17 years, 10 months ago)

still looks like jive to a fool


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ain't no place I'd rather be

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Invisiblemycogirl
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Re: Genetic Relationship of Psilocybe and Panaeolus Species... [Re: beforetimetook]
    #5671019 - 05/25/06 12:14 AM (17 years, 10 months ago)

Very interesting. Phylogenetic trees are interesting because when comparing separate sequences, you can have very different results.

Also that bootstrap based on algorithms from the ITS-1 locus, seems strange. Why are two P. cubensis species so far apart? I wonder what the ITS-1 locus codes for.


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Invisiblefastfred
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Re: Genetic Relationship of Psilocybe and Panaeolus Species... [Re: mycogirl]
    #5705644 - 06/02/06 09:48 PM (17 years, 9 months ago)

Phylogenetic trees can be difficult to interpret sometimes. Some of the branches could have been arranged a little better I think.

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.

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

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.

Here is a diagram of some of these regions...



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It drinks the alcohol and abstains from the weed or else it gets the hose again. -Chemy

The difference between the substances doesn't matter. This is a war on consciousness, on our right to the very essence of what we are. With no control over that, we have no need to speak of freedom or a free society. -fireseed

"If we are going to have a war on marijuana, the least we can do is pull the sick and the dying off the battlefield." -Neal Levine (MPP)

I find the whole "my drug should be legal but yours should be illegal" mindset disgusting and hypocritical. It's what George Bush and company do when they drink a cocktail and debate the best way to imprison marijuana users. -Diploid

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Invisiblemycogirl
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Re: Genetic Relationship of Psilocybe and Panaeolus Species... [Re: fastfred]
    #5705854 - 06/02/06 10:48 PM (17 years, 9 months ago)

Thanks for the diagrams, It looks like they chose a coding region and a non coding region for the different phylogenetic trees.

It looks to me like the LSU analysis puts both the p. cubensis together, but that ITS-1 analysis puts the two so far apart. Do you know why that is?


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Invisiblefastfred
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Re: Genetic Relationship of Psilocybe and Panaeolus Species... [Re: mycogirl] * 1
    #5706441 - 06/03/06 01:23 AM (17 years, 9 months ago)

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.

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. The LSU is much larger, it's 1116 bp. When I was looking at the sequence data I also noticed that most of the PC sequences in GenBank are just partial sequences. That could be part of the problem.

I was looking at GenBank and compiled a few figures... There are 15 published sequences for PC. Below is a summary.

#,Region,[#bp]
3 ITS-1 [196, 236, 234 bp]
1 ITS-2 [163 bp]
5 LSU(25S-28S) [(3)971, (2)1116 bp]
2 18S [41 bp]
3 5.8S [156, 37 bp]
1 28S(Part of LSU) [104 bp]

I was trying to look up the sequences in question to see if I could find an answer. I had assumed that the numbers following the species were accession numbers, but they're not. I have no idea what they are. The numbers from the first tree ARE accession numbers, but the numbers in the others are not. I think the numbers are in the papers, but I didn't have the ambition to look them up.

I was going to mention that anyone who has a desire to study the subject further could do some good work for the community. The first tree has accession numbers and you can also search GenBank by species or keyword. Someone with some spare time on their hands could use ClustalW (VectorNTI is even better if you have access to it) to analyze the sequences and compare them with other species. All you have to do is play with GenBank for awhile to get all the sequences you're interested in, then enter them in ClustalW, and then construct some phylogenetic trees. It's not very hard to do. It would be nice to have someone do this with a variety of species to construct some larger trees.

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.

Web version of ClustalW
http://www.ebi.ac.uk/clustalw/

GenBank
http://www.ncbi.nlm.nih.gov/Genbank/

GenBank PC sequence search
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&term=psilocybe+cubensis


-FF


--------------------
It drinks the alcohol and abstains from the weed or else it gets the hose again. -Chemy

The difference between the substances doesn't matter. This is a war on consciousness, on our right to the very essence of what we are. With no control over that, we have no need to speak of freedom or a free society. -fireseed

"If we are going to have a war on marijuana, the least we can do is pull the sick and the dying off the battlefield." -Neal Levine (MPP)

I find the whole "my drug should be legal but yours should be illegal" mindset disgusting and hypocritical. It's what George Bush and company do when they drink a cocktail and debate the best way to imprison marijuana users. -Diploid

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InvisibleEonTan
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Re: Genetic Relationship of Psilocybe and Panaeolus Species... [Re: fastfred]
    #5707109 - 06/03/06 11:08 AM (17 years, 9 months ago)

Have you tried mating a subcubensis with a cubensis? Becuase we KNOW that the redspore mates with non redspore strains, so they are the same species. DO we KNOW about the cubensis/subcubensis compatability?

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Invisiblefastfred
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Re: Genetic Relationship of Psilocybe and Panaeolus Species... [Re: EonTan]
    #5707531 - 06/03/06 01:47 PM (17 years, 9 months ago)

I think the burden of proof lies on the person claiming to have discovered a new species.

Since the claimed differences are very small, and the only published sequence is identical with P. cubensis (in a highly variable region I might add)...
I think that he was initially given the benefit of the doubt, but now the ball is back in his court to offer more evidence that it truly deserves to be classified as different species.


-FF


--------------------
It drinks the alcohol and abstains from the weed or else it gets the hose again. -Chemy

The difference between the substances doesn't matter. This is a war on consciousness, on our right to the very essence of what we are. With no control over that, we have no need to speak of freedom or a free society. -fireseed

"If we are going to have a war on marijuana, the least we can do is pull the sick and the dying off the battlefield." -Neal Levine (MPP)

I find the whole "my drug should be legal but yours should be illegal" mindset disgusting and hypocritical. It's what George Bush and company do when they drink a cocktail and debate the best way to imprison marijuana users. -Diploid

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InvisibleZen Peddler
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Re: Genetic Relationship of Psilocybe and Panaeolus Species... [Re: fastfred]
    #5740740 - 06/12/06 04:33 AM (17 years, 9 months ago)

interesting that the species that this sequencing suggest are most closely related to cubensis are mushrooms that are nearly all lignious and are VERY different to Ps.cubensis - I couldnt get the picture to come up - were any non-active coprophilus species sequenced as i would have assumed these would be much closer to cubensis than the Ps.cyanescens cluster (Ps.cyanescens, Ps.subaeruginosa, Ps.subaeruginescens). Semilanceata again is a very different mushroom to all of these - more a grassloving species like mexicanna.
Pluteus from this site did rNA and Dna sequencing of the Ps.cyanescens family - and the last i heard he had made some 'very interesting' findings...
I guess you already aware that the only person still claiming Ps.australiana is an independent entity from Ps.subaeruginosa is Guzman - there are 4 studies that have demonstrated synonmy using isozyme protein analysis, Rna sequencing and just microscopic examinations of cystidia shape (which are identical).


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OfflineChemiker
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Re: Genetic Relationship of Psilocybe Species... [Re: fastfred]
    #6365735 - 12/13/06 11:33 AM (17 years, 3 months ago)

I really think a citation is in everyone's best interest:

Nugent, K G. and Saville, B J. Forensic analysis of hallucinogenic fungi: a DNA-based approach. Forensic Science International. 140, pp. 147 - 157. (2004)

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OfflineAlan RockefellerM
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Re: Genetic Relationship of Psilocybe Species... [Re: fastfred] * 1
    #20727098 - 10/19/14 11:29 PM (9 years, 5 months ago)

Quote:

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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OfflineAlan RockefellerM
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Re: Genetic Relationship of Psilocybe and Panaeolus Species... [Re: fastfred] * 1
    #20727184 - 10/19/14 11:52 PM (9 years, 5 months ago)

Quote:

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.


 
Quote:

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.




 
Quote:

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.

Quote:

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.



Quote:

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.

Quote:

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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