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InvisibleJoust
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20062655 - 05/30/14 08:57 PM (9 years, 9 months ago)

Great job Alan, doing some real research now!


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~~~~~~***Psilocybin Mushrooms***~~~~~~
_________A Practical Guide To Psilocybin Mushrooms_________

:sporedrop:                      "Think about the species, not your scale". -NeoSporen                      :sporedrop:

"Mr. Joust, I see you don't actually partake in the psilocin, but it looks like it may partake in you!" -Gojira


       

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Offlinenomendubium
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Re: Panaeolus phylogenetic tree [Re: Joust]
    #20062866 - 05/30/14 09:59 PM (9 years, 9 months ago)

ok. I'll agree with that. The other 2 specimens I found labelled Panaeolus subbalteatus don't even make the list. I'm not trying to critisize you, I'm improving the tree. I think it being labelled subbalteatus when it is clearly not causes a misleading conclusion about the position of Panaeolina on the tree. Taking that into consideration along with this post and the next one which show that there is 100% match between the Pan foe on the branch with the semiovatus and that Panaeolus foenisecii in the other branch of the tree (with the other foes) then Paneaolina would make it's own little branch. That would
A) Make a lot of sense
B) Allow us to move forward in the science of understanding the relationship of the species


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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: nomendubium]
    #20129724 - 06/14/14 03:33 PM (9 years, 9 months ago)
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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.

I have a tree calculating right now for the rpb1 region, however there aren't many sequences in genbank for that locus, and I don't have the primers to generate my own yet.

The ITS tree is attached to this post as a PDF.

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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20129967 - 06/14/14 04:33 PM (9 years, 9 months ago)
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Here is another tree I just made, this one is with the rpb1 gene.  There weren't too many RPB1 sequences in Genbank, however what there is does seem to work pretty well to make a tree that comes out the way I think things evolved.  Since there weren't too many Panaeolus species, I included some Psilocybes as well.  The Psilocybe sequences are Vicky's, so I have high confidence that they are properly identified.

I used Pholiota flammans as an outgroup and made a maximum likelihood tree using the Kimura two parameter model, gamma distributed rates among sites, and gaps treated with the partial deletion algorithm.  I used the free Mega6 software to do the analysis, following the protocol outlined in Hall 2013.

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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20149493 - 06/18/14 12:05 PM (9 years, 9 months ago)

3 days and 20 hours. 2 downloads. Either no one is the least bit interested in your tree or there is some other reason no one wants to look at it. Why don't you go ahead and just post the tree? If you were a noob, I could understand making a pdf, but you are not, so just post the tree and I'll go ahead and peer review it for you  :thisisheavyman:


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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: nomendubium]
    #20149576 - 06/18/14 12:37 PM (9 years, 9 months ago)


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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20149617 - 06/18/14 12:51 PM (9 years, 9 months ago)

:smile: I meant the Panaeolus tree


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Invisiblemaynardjameskeenan
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Re: Panaeolus phylogenetic tree [Re: nomendubium]
    #20149672 - 06/18/14 01:08 PM (9 years, 9 months ago)

I must have been one of the two people who downloaded it...
I think he might have posted the links and another thread as well.
I hope you don't mind me posting this Alan


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Offlineknarkkorven
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Re: Panaeolus phylogenetic tree [Re: maynardjameskeenan]
    #20153344 - 06/19/14 03:52 AM (9 years, 9 months ago)

Interesting that campanulatus, sphinctrinus, papilionaceus, retirugis are not more closer, since they are considered to be the same species...

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InvisibleByrain

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Re: Panaeolus phylogenetic tree [Re: knarkkorven]
    #20154215 - 06/19/14 09:31 AM (9 years, 9 months ago)

That is why you can't completely count on the names associated with DNA sequences unless you can also examine the associated collection.

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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: knarkkorven]
    #20156003 - 06/19/14 04:21 PM (9 years, 9 months ago)

Quote:

knarkkorven said:
Interesting that campanulatus, sphinctrinus, papilionaceus, retirugis are not more closer, since they are considered to be the same species...





I think they are close enough to be the same species, if you discount the couple obviously mislabeled ones.

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Offlineknarkkorven
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20156381 - 06/19/14 05:57 PM (9 years, 9 months ago)

Yeah, I guess there's a lot of mislabeled mushrooms in the database.
It would be interesting to see a tree with only correct ID's.

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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: knarkkorven]
    #20157728 - 06/20/14 12:25 AM (9 years, 9 months ago)

Quote:

knarkkorven said:
Yeah, I guess there's a lot of mislabeled mushrooms in the database.
It would be interesting to see a tree with only correct ID's.





The most important part of making a phylogenetic tree is selecting which other species to include.  This is usually done by looking at who made the sequence, and deciding if they really knew what they were talking about when they ID'd it.

You could also get the samples and ID them microscopically, but that takes a lot of time.

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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20680650 - 10/09/14 04:28 PM (9 years, 5 months ago)

Here is a new Panaeolus phylogenetic tree that I made today using ITS sequences from genbank and to answer the question "Should Panaeolina foenisecii be included in Panaeolus sensu stricto?" It appears as though Maire errored when he moved Panaeolus foenisecii into Panaeolina in 1933, and we should be using the older name Panaeolus foenisecii.




The tree was built with the website phylogeny.fr, which allows you to do phylogenetic analysis from your web browser without installing any software.

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Invisiblemaynardjameskeenan
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20680686 - 10/09/14 04:36 PM (9 years, 5 months ago)

Why is Panaeolus rickenii in two separate locations? Misidentification?


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May you be filled with loving kindness.
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Offlineknarkkorven
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20680764 - 10/09/14 04:53 PM (9 years, 5 months ago)

It would be nice if collections of Panaeolus papilionaceus / spinchtrinus / campanulatus / etc. could be analyzed when found at the same time and place, I think confusion and misidentifications could have caused a lot of mixed samples in the collections, perhaps even leading to the false misconception of these being all the same species.

I mean, DNA-samples based on mushrooms with visual differences, like this (ignore the cinctulus at the left):

Edited by knarkkorven (10/09/14 05:08 PM)

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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: knarkkorven]
    #20680774 - 10/09/14 04:56 PM (9 years, 5 months ago)

I think that you are right that there are a multiple species hiding under the name Panaeolus papilionaceus.

Whether any of those other species are the type collections of Panaeolus sphinctrinus, P. retirugus or P. campanulatus is the question that needs to be answered.

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OfflineMrcloudy
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Re: Panaeolus phylogenetic tree [Re: knarkkorven]
    #20680800 - 10/09/14 05:03 PM (9 years, 5 months ago)

Quote:

knarkkorven said:
I think confusion and miss identifications could have caused a lot of mixed samples in the collections, perhaps even leading to the false misconception of these being all the same species.






The same problem is widespread in Ganoderma as well.


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10 different Ganoderma species from across the USA

AMU

MrCloudys guide to North American GanodermaUpdated A rough guide to North American Ganoderma species, with an emphasis on the laccate species.

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Invisiblemaynardjameskeenan
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20680821 - 10/09/14 05:06 PM (9 years, 5 months ago)

It might be an idea to start from scratch and make your own collections, not give them name but assign them numbers so the testing results stay objective. Where do the samples for this phylogenetic come from?


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May you be filled with loving kindness.
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May you be peaceful and at ease.
May you be happy.



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Offlineknarkkorven
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Re: Panaeolus phylogenetic tree [Re: maynardjameskeenan]
    #20680851 - 10/09/14 05:15 PM (9 years, 5 months ago)

I noticed that I wrote almost the same thing 3 months back, but this is a thing that keep nagging me when I'm out picking mushrooms... the color difference (one is more brown, the other gray) and the gray young grays have the saw tooth edge. This is the most apparent signs I have noticed about these two. Maybe I should collect some samples if anyone anytime is interested in writing a paper about it or something in the future... :wink:

Here's another couple of photos:


and the two groups to the left here:

Edited by knarkkorven (10/09/14 05:19 PM)

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