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OfflineAlan RockefellerM
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Panaeolus phylogenetic tree * 3
    #14123739 - 03/15/11 07:03 AM (10 years, 3 months ago)

I just made this rough draft phylogenetic tree of Panaeolus using mega5 and information from Genbank.

http://plantobserver.org/Panaeolus.phylogenetic.tree.pdf

FASTA file:

http://plantobserver.org/Panaeolus.fasta

From this I may have learned:

* Panaeolus papilionaceus and P. sphinctrinus are likely the same species
* Panaeolus acuminatus is close to P. olivaceus
* Panaeolus cinctulus is close to Panaeolina foenisecii and the split from Panaeolus to Panaeolina is not supported by genetic evidence as Panaeolina does not seem to form a separate clade outside of Panaeolus.
* Panaeolus semiovatus is only distantly related to the rest of Panaeolus
* Copelandia forms a distinct clade within Panaeolus, and maybe should be a subgenus or section.
* Panaeolus cambodginiensis may be the same as P. cyanescens


If anyone can provide me with more Panaeolus sequences that would be great.  There are only 21 good 28s sequences in Genbank.  And the bottom three are highly questionable.


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OfflineSt. Chibes
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #14123834 - 03/15/11 08:38 AM (10 years, 3 months ago)

Thanks for posting that Alan!
So we should call Panaeolina foeniseciiPanaeolus foenisecii ?

I never did figure out how to use that software to make these trees on my mac. I have everything I need, I just can't figure out how to open the fasta files and run the software...


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Re: Panaeolus phylogenetic tree [Re: St. Chibes]
    #14124198 - 03/15/11 11:02 AM (10 years, 3 months ago)

yeah bravo!


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OfflineTwiztidsage
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Re: Panaeolus phylogenetic tree [Re: AIRDOG]
    #14124471 - 03/15/11 12:36 PM (10 years, 3 months ago)

:popcorn:


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OfflineNeoSporen
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Re: Panaeolus phylogenetic tree [Re: Twiztidsage]
    #14124804 - 03/15/11 03:03 PM (10 years, 3 months ago)

Great work Alan :super: It's nice to see things like this. Helps me understand how different mushrooms may be related. Your work is an inspiration to us all. :cheers:


--------------------
Having lived through an existence close to nature, one accepts the small and simple things as most important in life. Sun, wind, rain and snow. The sounds birds make, smells of fresh wild flowers. Love of all kinds, from friends and family, thy self and our neighbors. Beautiful sunrises to the darkest clouds dancing above in the sky. To forgive, learn, share and express. This is the only thing a man such as myself can ask for. What comes as the result is nothing short of the core of human existence, to truly live free in body and mind.


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OfflineLuckOfTheFryish
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Re: Panaeolus phylogenetic tree [Re: NeoSporen]
    #14124983 - 03/15/11 03:40 PM (10 years, 3 months ago)

Quote:

* Panaeolus papilionaceus and P. sphinctrinus are likely the same species


i agree.

Quote:

* Panaeolus cinctulus is close to Panaeolina foenisecii and the split from Panaeolus to Panaeolina is not supported by genetic evidence as Panaeolina does not seem to form a separate clade outside of Panaeolus.




also agree. i can help you out with this if youd like.


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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #14125248 - 03/15/11 04:33 PM (10 years, 3 months ago)

Interesting stuff.

Quote:

Alan Rockefeller said:
If anyone can provide me with more Panaeolus sequences that would be great.  There are only 21 good 28s sequences in Genbank.  And the bottom three are highly questionable.




Could you elaborate on what you mean?  Collecting more samples to sequence?

Edit:  And are there any sequences on Panaeolopsis yet?


Edited by Byrain (03/15/11 04:33 PM)


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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #14126260 - 03/15/11 07:49 PM (10 years, 3 months ago)

Alan, which inference method did you use to construct this tree?


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OfflineKaiser
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Re: Panaeolus phylogenetic tree [Re: CureCat]
    #14126388 - 03/15/11 08:17 PM (10 years, 3 months ago)

Very interesting thanks for the link.
It doesn't surprise me that Panaeolina foenisecii is close to Panaeolus cinctulus since they look very similar with the only difference being the spore colour (which I guess is the only reason why it is a separate genus).
And I wonder were the genus Panaeolopsis fits in with all this.


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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: Byrain]
    #14126690 - 03/15/11 09:13 PM (10 years, 3 months ago)

Quote:

CureCat said:
Alan, which inference method did you use to construct this tree?




It is a maximum likelihood tree, with the numbers being branch lengths.


Quote:

Byrain said:
And are there any sequences on Panaeolopsis yet?




There will be one very soon.


Quote:

St. Chibes said:
I never did figure out how to use that software to make these trees on my mac.





You don't need any software, you can do it all on the web using the online version of mafft


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OfflineHashishin13
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #14127472 - 03/15/11 11:32 PM (10 years, 3 months ago)

Why are Pan foes on there like 4 times?


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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: Hashishin13]
    #14127486 - 03/15/11 11:35 PM (10 years, 3 months ago)

Four collections were sequenced.


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OfflineSt. Chibes
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #14127522 - 03/15/11 11:42 PM (10 years, 3 months ago)

Quote:

Alan Rockefeller said:
Quote:

St. Chibes said:
I never did figure out how to use that software to make these trees on my mac.




You don't need any software, you can do it all on the web using the online version of mafft





Thanks for the link.


--------------------
:pipesmoke::mushroom2::sun::quagmire:

Check out my Original Instrumental Piece:
Photinus pyralis


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Offlinepsylosymonreturns
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Re: Panaeolus phylogenetic tree [Re: St. Chibes]
    #14127739 - 03/16/11 12:13 AM (10 years, 3 months ago)

nice worky alan. :thumbup:


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OfflineSt. Chibes
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Re: Panaeolus phylogenetic tree [Re: psylosymonreturns]
    #14127776 - 03/16/11 12:21 AM (10 years, 3 months ago)

I think I'm retarded....
I don't get it...


--------------------
:pipesmoke::mushroom2::sun::quagmire:

Check out my Original Instrumental Piece:
Photinus pyralis


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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: St. Chibes]
    #14128053 - 03/16/11 01:07 AM (10 years, 3 months ago)

Rough instructions for making phylogenetic trees with mafft using only a web browser:


1) Get the DNA from Genbank, http://www.ncbi.nlm.nih.gov/nuccore?term=Panaeolus%20large%20subunit
At the bottom right click Send to:, chose file with FASTA format
2) Go to online mafft, start from the FASTA file on your hard drive, open all plots, make sure the lines are red.
If any graphs have blue lines remove the sequence from the file, reverse them with rev_comp, then put them back in.  http://www.bioinformatics.org/sms/rev_comp.html
3) If sequences do not allign well put the best/longest one at the top
4) Click the phylogenetic tree button

Better trees could be made by trimming off unaligned parts and manually verifying that the alignments are sane.


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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #14128727 - 03/16/11 03:25 AM (10 years, 3 months ago)

Here is a tree I made for Rhodocollybia

http://plantobserver.org/rhodocollybia.pdf


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OfflineNeoSporen
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #14128825 - 03/16/11 04:02 AM (10 years, 3 months ago)

Thanks for all the links. I'll have to sit down for a few hours and figure it all out.


--------------------
Having lived through an existence close to nature, one accepts the small and simple things as most important in life. Sun, wind, rain and snow. The sounds birds make, smells of fresh wild flowers. Love of all kinds, from friends and family, thy self and our neighbors. Beautiful sunrises to the darkest clouds dancing above in the sky. To forgive, learn, share and express. This is the only thing a man such as myself can ask for. What comes as the result is nothing short of the core of human existence, to truly live free in body and mind.


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OfflineSt. Chibes
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Re: Panaeolus phylogenetic tree [Re: NeoSporen]
    #14129633 - 03/16/11 11:02 AM (10 years, 3 months ago)

I'm going to attempt again tonight.
Thanks Alan.


--------------------
:pipesmoke::mushroom2::sun::quagmire:

Check out my Original Instrumental Piece:
Photinus pyralis


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Offlinewintersbefore
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller] * 1
    #17809946 - 02/15/13 10:40 PM (8 years, 4 months ago)

:bump:


Quote:

Alan Rockefeller said:
Rough instructions for making phylogenetic trees with mafft using only a web browser:


1) Get the DNA from Genbank, http://www.ncbi.nlm.nih.gov/nuccore?term=Panaeolus%20large%20subunit
At the bottom right click Send to:, chose file with FASTA format
2) Go to online mafft, start from the FASTA file on your hard drive, open all plots, make sure the lines are red.
If any graphs have blue lines remove the sequence from the file, reverse them with rev_comp, then put them back in.  http://www.bioinformatics.org/sms/rev_comp.html
3) If sequences do not allign well put the best/longest one at the top
4) Click the phylogenetic tree button

Better trees could be made by trimming off unaligned parts and manually verifying that the alignments are sane.





Here's what I did, sort of following those directions:
1. First I found BLAST:


2. Then I clicked on the NCBI so I could search for something:


3. Then I started typing the name of the mushroom I wanted to search for:


4. Then I told it to do a Nucleotide blast:


5. It brought up these mushrooms, and I clicked on the first one:


6. Then I told it to do a blast query on that particular sequence so that I could see all of the other sequences in GenBank that were a pretty good match for the one I typed in:



7. Then I selected from those that came up:


8. Then I saved them as a Fasta file:


9. Then I went to THIS WEBSITE and uploaded the file that I just downloaded:

and hit submit


10. Then I clicked on Phylogenetic Tree:


11. It produces this tree:



I think theres problems with this tree because I didn't "root" it? or didn't root it properly? Or I didn't really chose an outgroup, just randomly selected the sequences that came up first... I will try again later by including an outgroup somehow...


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Mushrooms, Mycology and Psychedelics >> Mushroom Hunting and Identification

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