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InvisibleByrain

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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20695217 - 10/12/14 11:02 PM (9 years, 3 months ago)

I wonder where Panaeolus guttulatus would fit into this...

Quote:

5 Gill edge (pocket-lens) with yellowish dropiets by
sticky secretes of cheilocystidia (fig. 3 f); spores with
oildrops; sulphidia absent    . .  .  .        P. sect. Guttulati
Only species:    Panaeolus guttulatus (29)




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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: Byrain]
    #20695250 - 10/12/14 11:15 PM (9 years, 3 months ago)

Quote:

Byrain said:
I wonder where Panaeolus guttulatus would fit into this...





Me too.  Luckily, someone in Europe is mailing me some this week.


If anyone else has Panaeolus, Panaeolina or Copelandia collections, I would like to add them to this tree.


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InvisibleByrain

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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20695263 - 10/12/14 11:20 PM (9 years, 3 months ago)

Cool!  Do they have photos and/or microscopy?  When and where do you want more collections?


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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: Byrain]
    #20695269 - 10/12/14 11:22 PM (9 years, 3 months ago)

Quote:

Byrain said:
Cool!  Do they have photos and/or microscopy?  When and where do you want more collections?





He promised P. guttulatus and P. olivaceus and unspecified others, he didn't say if he had photos or microscopy. 

You can drop the collections in the mail any time in October or November.


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Offlineheelsplitter
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20695482 - 10/13/14 12:56 AM (9 years, 3 months ago)

Quote:

It doesn't say that at all.  Look at the numbers - they are super important!  Copelandia is 1.2 units away from Psilocybe semilanceata, and the closest Panaeolus is 2.5 units away.  You need to add up all the numbers in the branches to see how far away from P. semilanceata each branch is.  That's a huge difference, and shows that Copelandia is much closer to Psilocybe than anything in Panaeolus.



That's a pretty good reason for splitting off Copelandia. My issue with splitting off Copelandia was just that Panaeolus would be monophyletic whether or not it was included. A subgenus basal to the rest of a genus and a separate genus for that subgenus would still be the same clade, so the Linnean rank it's given doesn't really change anything. Uncertainty in the monophyly of that genus does.

Quote:

If either of these papers were correct, when I do a BLAST search on Panaeolus or Copelandia species, I would expect to see those genera start showing up after I scroll down past the Panaeolus/Copelandias.  I don't.  What I see is a bunch of Panaeolus/Copelandia, then Psilocybes start to show up.  That indicates that Psilocybe is closest, and when I chose a Psilocybe outgroup the tree looked great because the sequence wasn't so distant that everything else was almost identical by comparison.



That's pretty exciting! Do other members of Hymenogastraceae start showing up after Psilocybe?

Quote:

Panaeolae has already been named. You could name that clade "Panaeolaceae" to give it a family-level, but that clade would be synonymous with Panaeolae, and Panaeolae is synonymous with Panaeolus unless you split Copelandia from it. Cool results overall though, especially with the clades of Panaeolus.




Quote:

Copelandia should be split off, and Panaeolaceae sounds like a great family name to put those two genera in.



I checked and Panaeolaceae has already been named according to mycobank. Mycobank lists it as "invalid" but doesn't give a reason. I'm thinking that it's probably because Panaeolaceae is a junior synonym of Panaeoleae (Panaeolae was a typo on my part). Panaeoloideae is also a junior synonym of Panaeoleae. Panaeolaceae looks nicer, but it's the same thing as Panaeoleae.I don't know what rank Panaeoleae is supposed to have, but whether that rank is above or below family, Panaeoleae and Panaeolaceae still refer to the same clade.

I have some Copelandia specimens that I've been planning to send you for a while but haven't gotten around to yet due to being busy with school work. I'll send those out pretty soon and add some Panaeolus (cf. cinctulus and cf. foenisecii) specimens too.


Edited by heelsplitter (10/13/14 12:52 PM)


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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: heelsplitter]
    #20695497 - 10/13/14 01:02 AM (9 years, 3 months ago)

Quote:

heelsplitter said:
That's pretty exciting! Do other members of Hymenogastraceae start showing up after Psilocybe?




Yes, there's quite a bit of Galerina and Flammula showing up as well.  Try NCBI blast on a few Panaeolus and Copelandia and see what you think.


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Invisibled0urd3n
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #20890328 - 11/25/14 06:48 PM (9 years, 2 months ago)

Hey I was going to send you that blueing Flammulina at some point do you still want Panaeolus species for the tree? I could throw in a cinctulus if it is helpful.

I also wanted to ask is there any updates on whether is Panaeolus foenisecii again or still Panaeolina? Want to call it by the proper name I remember you saying they might or did change it back. Maybe that was an old thread.


--------------------


Edited by d0urd3n (11/25/14 06:49 PM)


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OfflineHashfinger
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Re: Panaeolus phylogenetic tree [Re: d0urd3n]
    #20890415 - 11/25/14 07:02 PM (9 years, 2 months ago)

I believe I still have P. fimicola collection somewhere. Its about two years old. Is it still any value to your research?


--------------------
Species List (Georgia): Psilocybe caerulescens/weilii, Psilocybe atlantis/galindoi, Psilocybe cubensis, Psilocybe ovoideocystidiata, Psilocybe caerulipes, Psilocybe semilanceata, Psilocybe fagicola, Copelandia cyanescens, Panaeolus cinctulus, Panaeolus fimicola, Panaeolus olivaceus, Gymnopilus luteofolius, Gymnopilus aeruginosus, Gymnopilus junonius, Pluteus salicinus

(Ohio): Psilocybe ovoideocystidiata, Psilocybe caerulipes, Pluteus cyanopus, Pluteus salicinus sensu lato..., Panaeolus cinctulus, Gymnopilus luteus, Gymnopilus luteofolius, Gymnopilus junonius, Gymnopilus aeruginosus


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OfflineAlan RockefellerM
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Re: Panaeolus phylogenetic tree [Re: d0urd3n]
    #20891451 - 11/25/14 11:26 PM (9 years, 2 months ago)

Quote:

d0urd3n said:
Hey I was going to send you that blueing Flammulina at some point do you still want Panaeolus species for the tree? I could throw in a cinctulus if it is helpful.




Yes, I am interested in the P. cinctulus group.

Quote:

I also wanted to ask is there any updates on whether is Panaeolus foenisecii again or still Panaeolina? Want to call it by the proper name I remember you saying they might or did change it back. Maybe that was an old thread.





I think Panaeolus foenisecii is the best name for it, but I would like to check the LSU sequences as well since that locus is better for determining genus level differences.


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Offlineheelsplitter
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Re: Panaeolus phylogenetic tree [Re: Alan Rockefeller]
    #22452045 - 10/30/15 01:59 AM (8 years, 3 months ago)
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Quote:

Alan Rockefeller said:
Quote:

Yours show Copelandia as basal to Panaeolus/the rest of Panaeolus; as close to Psilocybe as the rest of Panaeolus is.




It doesn't say that at all.  Look at the numbers - they are super important!  Copelandia is 1.2 units away from Psilocybe semilanceata, and the closest Panaeolus is 2.5 units away.  You need to add up all the numbers in the branches to see how far away from P. semilanceata each branch is.  That's a huge difference, and shows that Copelandia is much closer to Psilocybe than anything in Panaeolus.

The numbers are calculated from the number of base pair differences.




This just means that Panaeolus species are more divergent from the common ancestor of Panaeolus, Copelandia and Psilocybe than Copelandia species are AFAIK. Copelandia isn't more closely related to Psilocybe since Copelandia and Panaeolus share a more recent common ancestor, which the cladogram shows.

Quote:

Alan Rockefeller said:
Quote:

While Panaeolus might not be closely related to Psathyrellaceae (which your cladogram doesn't show), that's not particularly informative when other cladograms have found:




I read the Moncalvo paper and tried all of the things he said were close as outgroups.  All of them flattened the tree to a level where it was nearly useless because none of them were actually close.  Once I deleted the stuff he claimed were close, the tree became useful.

Following the Matheny paper, I added a bunch of Inocybe and Tubaria species, and the same thing happened, but even worse.

I also tried adding various species from the Psathyrellaceae, same result.  None of the stuff that was supposed to be in the same family was at all close.

I have no idea how those guys got these results, but in my time looking at the data I haven't seen anything to suggest that either is even close to being correct.

If either of these papers were correct, when I do a BLAST search on Panaeolus or Copelandia species, I would expect to see those genera start showing up after I scroll down past the Panaeolus/Copelandias.  I don't.  What I see is a bunch of Panaeolus/Copelandia, then Psilocybes start to show up.  That indicates that Psilocybe is closest, and when I chose a Psilocybe outgroup the tree looked great because the sequence wasn't so distant that everything else was almost identical by comparison.




The issue there is just that you're comparing ITS results to some (not super great) multilocus analyses. Dentinger et al. (2015) (see the link) proved that Moncalvo's and Matheny's analyses weren't very accurate, but an ITS tree is likely to be even less accurate. 

Quote:

Alan Rockefeller said:

Yes, there's quite a bit of Galerina and Flammula showing up as well.  Try NCBI blast on a few Panaeolus and Copelandia and see what you think.




I ran BLAST on a couple of these a while back and didn't get around to posting about it until now. I mostly got Psilocybe, Alnicola, Naucoria and Galerina showing up. That would place Panaeolus in Hymenogastraceae or just somewhere in the "stropharioid clade", but the ITS region alone isn't super great for determining intergeneric relationships. It would be pretty sweet if someone sequenced the whole genome of a Panaeolus species so that it could be compared with Dentinger et al. (2015) (link attached, it's pretty exciting stuff) so its position could be resolved, but they also didn't include Hymenogaster citrinus, so that would have to be done too. I know it's possible to make a meta-tree somehow that would just use Dentinger et al.'s analysis as a framework to compare one locus or a couple loci from a Panaeolus species to, but it seems really intimidating and difficult.


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InvisibleJoust
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Re: Panaeolus phylogenetic tree [Re: heelsplitter]
    #22452271 - 10/30/15 05:15 AM (8 years, 3 months ago)

Quote:

The issue there is just that you're comparing ITS results to some (not super great) multilocus analyses. Dentinger et al. (2015) (see the link) proved that Moncalvo's and Matheny's analyses weren't very accurate, but an ITS tree is likely to be even less accurate. 




Ive found this to be true in my studies as well.


--------------------
~~~~~~***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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