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maynardjameskeenan
The white stipes



Registered: 11/11/10
Posts: 16,391
Loc: 'Merica
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Re: Are these pan cintulus's??? [Re: Byrain]
#20058803 - 05/29/14 10:37 PM (9 years, 9 months ago) |
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Wouldn't that be like calling a Catfish a feline because they have whiskers?
-------------------- May you be filled with loving kindness. May you be well. May you be peaceful and at ease. May you be happy. AMU Q&A
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maynardjameskeenan
The white stipes



Registered: 11/11/10
Posts: 16,391
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Re: Are these pan cintulus's??? [Re: nomendubium]
#20058823 - 05/29/14 10:42 PM (9 years, 9 months ago) |
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Quote:
nomendubium said: I don't see Panaeolus cinctulus on that tree? Challenge accepted
If you follow that link of Alan's I posted it has direction on putting a tree together, it's not hard at all to make one.
-------------------- May you be filled with loving kindness. May you be well. May you be peaceful and at ease. May you be happy. AMU Q&A
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Byrain

Registered: 01/07/10
Posts: 9,664
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Quote:
maynardjameskeenan said: Wouldn't that be like calling a Catfish a feline because they have whiskers?
Not really, we already understand the differences in relationship between catfish and felines. If you want to make it better, I suggest you put the time into learning how to use your microscope to the best of its ability and contributing to the ongoing Panaeolus studies. Accepted science changes all the time.
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maynardjameskeenan
The white stipes



Registered: 11/11/10
Posts: 16,391
Loc: 'Merica
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Re: Are these pan cintulus's??? [Re: Byrain]
#20058911 - 05/29/14 11:00 PM (9 years, 9 months ago) |
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You're right, I should.
-------------------- May you be filled with loving kindness. May you be well. May you be peaceful and at ease. May you be happy. AMU Q&A
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Peteza34
Myco-enthusiast



Registered: 09/13/12
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nomendubium



Registered: 05/16/14
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Re: Are these pan cintulus's??? [Re: Peteza34]
#20060275 - 05/30/14 09:11 AM (9 years, 8 months ago) |
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ok. I'm new to genbank and DNA sequencing. Seems like a steep learning curve, but I WILL learn it and love it  Problem number 1 In Alans tree. The strangely positioned "Paneaolus subbalteatus" AB104674.2 If you click on the pubmed entry 12808251 This is a DNA sequence of a Powdered mushroom! from 2003 I might add. At the time of publication they probably didn't have a lot of sequences to compare to and elected to call it Panaeolus subbalteatus because that species was the closest thing yet sequenced at the time. Now 12 years later it is clear that the correct identity for the entry would have been/is Panaeolina foenisecii
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Byrain

Registered: 01/07/10
Posts: 9,664
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Re: Are these pan cintulus's??? [Re: nomendubium]
#20060290 - 05/30/14 09:18 AM (9 years, 8 months ago) |
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That is the problem with relying on the names listed in genebank without actually examining the corresponding collection. I wonder where Panaeolina castaneifolia would fit in there and where all the Panaeolina collections were collected...
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nomendubium



Registered: 05/16/14
Posts: 500
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Re: Are these pan cintulus's??? [Re: Byrain]
#20060379 - 05/30/14 09:53 AM (9 years, 8 months ago) |
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also, here is a copy of the publication NOTE the sample P. subbalteatus was collected in 1983! Therefor was 20 years old when it was sequenced https://www.jstage.jst.go.jp/article/cpb/51/6/51_6_710/_pdf
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nomendubium



Registered: 05/16/14
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Re: Are these pan cintulus's??? [Re: nomendubium]
#20060437 - 05/30/14 10:14 AM (9 years, 8 months ago) |
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lets see! the foes on the same branch with the sub are DQ071696.2 Germany AF041537.1 USA AY207266.1 Germany then there is the one on the branch with the P. semiovatus, DQ071765.1 Germany I should say that is the location of the submission, it is not clear where the collection was made because I can't see Mycological research, vol. 111. If anyone has access to it or can find it for free (I'm not paying $31) link please!
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nomendubium



Registered: 05/16/14
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Re: Are these pan cintulus's??? [Re: nomendubium]
#20060473 - 05/30/14 10:23 AM (9 years, 8 months ago) |
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furthermore DQ071696.2 (on the branch with the rest of the foes) is 100% coverage/100% ident to DQ071765.1 (on the branch with semiovatus)...so I don't know why it's on the wrong branch, but it obviously is. And there you have it boys and girls, Panaeolina foenisecii on it's own branch
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Byrain

Registered: 01/07/10
Posts: 9,664
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Re: Are these pan cintulus's??? [Re: nomendubium]
#20060523 - 05/30/14 10:35 AM (9 years, 8 months ago) |
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This is where I wish everyone of those collections had a corresponding MO observation # complete with detailed pictures and micro... It feels like having your hands tied behind your back when trying to get the necessary details on these collections as you seen with the $30 price tag for the article...
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maynardjameskeenan
The white stipes



Registered: 11/11/10
Posts: 16,391
Loc: 'Merica
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Re: Are these pan cintulus's??? [Re: Byrain]
#20061385 - 05/30/14 02:52 PM (9 years, 8 months ago) |
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Are you making sure to compare the same regions of the sequences?
-------------------- May you be filled with loving kindness. May you be well. May you be peaceful and at ease. May you be happy. AMU Q&A
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nomendubium



Registered: 05/16/14
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they were both full sequences, ie the 100% query coverage. Like I've previously said, genetic comparing is still new to me. It seems like if they are 100% match they must be comparing the same regions...? For the two, I hyperlinked them, so if you click on one and hit blast the next one on the list is the other one. 100% & 100%. I'm interested in Alan telling us how he got them into two different branches on his tree
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maynardjameskeenan
The white stipes



Registered: 11/11/10
Posts: 16,391
Loc: 'Merica
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Re: Are these pan cintulus's??? [Re: nomendubium]
#20061490 - 05/30/14 03:16 PM (9 years, 8 months ago) |
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I remember Alan saying that you want to compare ITS (internal transcribe spacers), I'll doing some digging, it's been awhile since I've playing around with it. You might want to send him a PM because he might not read this thread. wintersbefore has also done a lot of work with Panaeolus DNA- I think shes a professional mycologist although I haven't seen her post anything in awhile, she would be a good person to answer your questions.
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Alan Rockefeller
Mycologist

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Re: Are these pan cintulus's??? [Re: Byrain]
#20129043 - 06/14/14 12:47 PM (9 years, 8 months ago) |
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Log in to view attachment
Quote:
nomendubium said: ok. I'm new to genbank and DNA sequencing. Seems like a steep learning curve, but I WILL learn it and love it  Problem number 1 In Alans tree. The strangely positioned "Paneaolus subbalteatus" AB104674.2 If you click on the pubmed entry 12808251 This is a DNA sequence of a Powdered mushroom! from 2003 I might add. At the time of publication they probably didn't have a lot of sequences to compare to and elected to call it Panaeolus subbalteatus because that species was the closest thing yet sequenced at the time. Now 12 years later it is clear that the correct identity for the entry would have been/is Panaeolina foenisecii 
Where in that paper does it say the Panaeolus subbalteatus was powdered? I can't find it.
If I BLAST AB104674.2, it appears as though the closest match is Panaeolus papilionaceus, is there a reason you think that Panaeolus foenisecii is more likely? I guess being on the same branch of the tree is a good reason...but it's still 9 base pairs different, and looking at the alignment it doesn't look like sequencer errors. I think that the sequence in question is not Panaeolus foenisecii but a closely related species.
I just made a new Panaeolus tree, this time using the ITS region. This is a maximum liklihood tree using the Tamura 3 parameter model w/ 500 rounds of bootstrapping, gamma distributed rates among sites and the gap treatment set to partial deletion.
Sequences were gathered from genbank based on the name of the sequence, and one sequence that I generated from Mexican material is included. This pretty much follows the recommendations in http://mbe.oxfordjournals.org/content/early/2013/03/13/molbev.mst012.full, except I didn't use BLAST to get the sequences.
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maynardjameskeenan
The white stipes



Registered: 11/11/10
Posts: 16,391
Loc: 'Merica
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Quote:
Alan Rockefeller said:
I just made a new Panaeolus tree, this time using the ITS region.
Can I see it?
-------------------- May you be filled with loving kindness. May you be well. May you be peaceful and at ease. May you be happy. AMU Q&A
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Alan Rockefeller
Mycologist

Registered: 03/10/07
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Yes, it is attached to the post above.
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maynardjameskeenan
The white stipes



Registered: 11/11/10
Posts: 16,391
Loc: 'Merica
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I see it now...
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nomendubium



Registered: 05/16/14
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the first line of the PubMed entry, linked above, Quote:
"Magic mushrooms" (MMs) are psychoactive fungi containing the and Psychotropics Control Law in Japan. Because there are many kinds of MMs and they are often sold even as dry powders in local markets, it is very difficult to identify the original species of the MMs by morphological observation.
It doesn't specifically say they were powdered, but it is the subject of the arcticle. Furthermore, according to their analysis, Panaeolus sphinctrinus(aka Panaeolus papilionaceus) is more psyco-active than their specimen of proported Panaeolus subbalteatus. That surely seems dubious, no?
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