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InvisibleMr. Mushrooms
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Re: New Psilocybe species [Re: koraks]
    #9176981 - 11/03/08 11:03 AM (15 years, 2 months ago)

Quote:

koraks said:
Quote:

BlimeyGrimey said:

So anyone can write up the paper? Is a certain degree (PhD) needed?



For scientific journals, a degree is not necessary, but it's usually pretty difficult to get accepted if you don't know your way around scientific publishing. I'm not in biology or exact sciences, so I couldn't help you with this, I'm afraid. Perhaps Senor_Hongos, Alan_Rockefeller or Workman could be of help, if they have time to spare?




That's correct, Koraks.  I don't know about now but back in the day you could even name species if you could write the description in Latin and knew the ins and outs of peer-review publishing.

I appreciate the recommendation but I'm afraid my time is already allotted for several projects to some very patient Shroomerites.  Alan and Workman are more than qualified (as if that needed to be said).  If I had a project I needed help on both of those men are at the top of a very short list.

:thumbup:


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InvisibleMr. Mushrooms
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Re: New Psilocybe species [Re: Subbedhunter420]
    #9198337 - 11/06/08 09:08 PM (15 years, 2 months ago)

Quote:

Subbedhunter420 said:
Ok.

Alteredstates and I have decided for the moment on

"Psilocybe Meridianus"

Which means "Southern" and "of the noon". Cuz its always sunny here.:grin:




Very nice.  :thumbup:  I was waiting for it.  I am naming a mushroom I found too.  Look for it in my new thread. :wink:


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InvisibleMr. Mushrooms
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Re: Description for new Psilocybe species [Re: Strophariaceae]
    #10204522 - 04/20/09 10:45 PM (14 years, 9 months ago)

Quote:

Strophariaceae said:


BTW, does anybody actually have any myco contacts in Japan?




Shroomery member, kablamo moved there last month and requests have been made.

Good luck.


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InvisibleMr. Mushrooms
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Re: Description for new Psilocybe species [Re: Strophariaceae]
    #10204905 - 04/21/09 12:05 AM (14 years, 9 months ago)

Quote:

Strophariaceae said:
(In fact, I'd go so far as to say that when dealing with closely-related species, microscopy will provide a lot more info more quickly than simple molecular methods will � I think you'd probably need a really large multi-gene sample to resolve Psilocybe in the same section definitively.) Based on my reading of Guzman's monograph and my own knowledge of the northern Cal population, a quick look at the pleurocystidia would tell you whether you're dealing with something closer to the Northern Cal species or closer to P. meridionalis.




While you're at it, you might explain the so-far-unexplained here.  Which genes are chosen for sequencing and why?  I think a lot of us are waiting for entire genome data but that seems a long ways away.  For now, a solid answer to my question would be quite informative.

And you're welcome for the link.


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InvisibleMr. Mushrooms
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Re: Description for new Psilocybe species [Re: Strophariaceae]
    #10206242 - 04/21/09 10:22 AM (14 years, 9 months ago)

Quote:

Also, keep in mind that the biological species concept developed for vertebrates doesn't necessarily apply to fungi. If you did mating-compatible monokaryon crosses and the two barrage out each other, then yes, you have different species.

The reverse, however, isn't true. If the two do mate, they may still not really be the same species. There are species that are separated by continental distances and millions of years of evolutionary time, but put mating strains together on a plate and they'll cross.

Closely related fungi are notorious for this – Czech mycologist Jan Brovika reports full mating compatibility between P. cyanescens and P. azurescens, for example.




What are you suggesting here, phylogenetic species concept?  What has been the reigning paradigm within mycology?  To my understanding Brovika's research implies a complex rather than a fully marked species delineation.

You're welcome, again, for the link.  We've sorely needed a contact from Japan for some time now. 

Quote:

I'm not entirely sure of the rationale behind which genes are chosen, but I know the gold standard seems to be a mixture of genes like ITS and LSU that are neutral in regards to natural selection (change is entirely a product of genetic drift) and protein-coding genes, which might be responding to environmental selection.





The rationale is precisely the information I am looking for.  If you know of resources or a direction I might take please post it.  I'm sure you know they have been using 16s rRNA in prokaryotes because they are conserved.  However this is under reevaluation due to suspected HGT.  As a result the phylogenetic tree might be remade, again.  I wouldn't want that to happen within mycology.

Quote:

Another reason one would want to sample from multiple genes is to cancel out the effects of potential horizontal gene transfer. Horizontal gene transfer is rare in higher eukaryotes, but it does happen. Hence, there are certain genes that will place oomycete species smack in the middle of the ascomycetes. A larger sampling of the genome shows them to be very distantly related within Eukaryota. It has been shown, however, that the oomycetes have acquired certain fungal genes, and this, along with convergent natural selection, is a factor in making this algal-derived group so fungus-like.




This was a point I made in some evolution thread(s) cactu made.  A wealth of information, however, in my view, philosophically flawed.  Fungal HGT seems suspect to me.  What kind of transference are we talking here, transformation, transduction, what?  Moreover, this is precisely why I would wait until entire genomes were sequenced before I embarked on the remaking of fungal taxonomy, including new names.

Quote:

Also, choice of genes has to do with what level of taxonomy you're dealing with. The molecular clock for some genes is very slow, while in others its very rapid. When you're looking at a broad phylogeny, say, the Eukaryota as a whole, you're going to want to use slowly evolving genes. If you're looking at closely-related species, like say the different species of Psilocybe section Stuntzae, then you want to sample from some rapidly evolving genes. If you're doing within-species population genetics work, then you want to sample from genes that are polymorphic within the species, and look at them in terms of classical Mendelian gene frequencies.




Kudos for the lesson in phylogenetic interpretation.  I feel I should point out the obvious at this point.  We're doing more here than having a conversation.  We're creating a database (or at least that's my motive).  As you know the Shroomery is the most popular website/message board for mushrooms on the Internet.  As such, we have a grave responsibility to disseminate correct information which is, and will become, a valuable resource for many amateur students of mycology.  It's a way to "get the word out."

Having said that I think it's important to explain my view.  I'm not a fan of phylogeny or cladistics because they require too much interpretation and extrapolation of the facts.  I'm an empiricist.  I want to check morphology, macro and micro, chemical reactions and use genetic sequencing for direct data as compared against the specimens and groups found within those paradigms.  These markers are ironclad and immovable.  They do not require a historical reconstruction of putative events that will never have the certitude of a morphological form combined with an entire genome's sequence.

The fossil record and the genes of fungus are sparse.  Reconstructing their taxonomy on that basis seems like a fool's game, however affiliated with academia it may be.

Cheers,
MM


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Edited by Mr. Mushrooms (04/21/09 10:28 AM)


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InvisibleMr. Mushrooms
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Re: Description for new Psilocybe species [Re: Strophariaceae]
    #10207023 - 04/21/09 12:48 PM (14 years, 9 months ago)

Salient and specific.  Nevertheless, what we can hold in our hand or produce from a sequencer is static.  The interpretation of the data is something else.

Again, this is the rationale is precisely the information I am looking for.  If you know of resources or a direction I might take please post it.  Does this mean you do not know of a resource where I might glean the reasoning behind ITS or LSU?  That information would be invaluable from a taxonomic point of view.

Thank you for the explication.


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InvisibleMr. Mushrooms
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Re: Description for new Psilocybe species [Re: BlimeyGrimey]
    #10207757 - 04/21/09 02:56 PM (14 years, 9 months ago)

Well, given the fact that Guzman's daughter, and others like Else, are using them as they are, it would be axiomatic to think so.  However, I have no idea whether they are or aren't.  That is another reason for my request.


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InvisibleMr. Mushrooms
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Re: Description for new Psilocybe species [Re: BlimeyGrimey]
    #10211105 - 04/21/09 11:28 PM (14 years, 9 months ago)

Thanks.  If the variation rate is that high there must be a delineation as to what constitutes the species level.  Perhaps Gardes & Bruns paper will provide a clue.


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