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OfflineStrophariaceae
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Re: Description for new Psilocybe species [Re: CureCat]
    #10205457 - 04/21/09 06:16 AM (5 years, 6 months ago)

Quote:

CureCat said:
It's not a question of either or.




Literally took the words right off my fingertips.


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OfflineStrophariaceae
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Re: Description for new Psilocybe species [Re: CureCat]
    #10205468 - 04/21/09 06:23 AM (5 years, 6 months ago)

Quote:

Strophariaceae said:
As I asked before, has anybody (Workman? Guzman?) looked at these microscopically? I'd be happy to do this, BTW, but I don't want to jump all over anybody else's work if its being done.



Yup.  You really need to look at Workman's gallery.  I've linked ya to it a bunch of times.




I mean, microscopy of the SoCal species (more than just the spores, preferably). There's nothing like that at Workman's gallery, or anywhere else I've seen.


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OfflineStrophariaceae
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Re: Description for new Psilocybe species [Re: nightflyer]
    #10205474 - 04/21/09 06:27 AM (5 years, 6 months ago)

Quote:

nightflyer said:
99% of the taxonomic work here on the shroomery
are based on the classical  microscopic characteristics
like Spores, Pleurocystidia etc.




Because almost all Shroomery posters are amateurs (in the best sense), not academics.

A good microscope – $500 on eBay. Anybody priced a sequencer recently?


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Re: Description for new Psilocybe species [Re: Strophariaceae]
    #10205504 - 04/21/09 06:45 AM (5 years, 6 months ago)

Quote:

nightflyer said:
Beautiful. But where are the results?



Scientific Journals mostly.  The actual sequence is not usually published, but the results are referenced and kept on file for future studies.

Quote:

nightflyer said:
I miss posts of RNA sequencing work on the shroomery.



I've posted some.  I don't really see the relevance though, since few people on here know how to use that information or they don't have access to the technology.

Also, when you use sites like Genbank to make sense of your results, it does not automatically enter your sequence into the database.  You'll notice that all those sequences you linked to have corresponding authors and articles.  I really wish the database automatically incorporated sequences, but I can also see some obstacles if that were the case.


Quote:

Strophariaceae said:
I mean, microscopy of the SoCal species (more than just the spores, preferably). There's nothing like that at Workman's gallery, or anywhere else I've seen.




Oooh, okay sorry.  I don't know.  I bet it is on Workman's to do list.  Alan may have looked at it.  PM subbedhunter if you want to look at it.


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InvisibleCureCatM
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Re: Description for new Psilocybe species [Re: Strophariaceae]
    #10205515 - 04/21/09 06:57 AM (5 years, 6 months ago)

Quote:

Strophariaceae said:
Anybody priced a sequencer recently?



Hehehe.  There are one or two outdated models that are collecting dust at that lab, but without all of the other equipment (there is a LOT of other equipment) it is really useless.  Other local labs don't really have use for them, and they are massive and really heavy, so it would cost a lot to send one anywhere.


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Invisiblenightflyer
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Re: Description for new Psilocybe species [Re: CureCat]
    #10205562 - 04/21/09 07:43 AM (5 years, 6 months ago)

Quote:

CureCat said: You'll notice that all those sequences you linked to have corresponding authors and articles.  I really wish the database automatically incorporated sequences, but I can also see some obstacles if that were the case.







That's true. Those are only basic informations.
You have to look at the original papers to get
all informations. At our university, as a member,
you have online access to more than 10'000 journals and it's allowed
to print the content.
That's our site:
http://www.ethbib.ethz.ch/zs_e.html


And let me clear up something else:
I don't know how this is ruled in the USA,
but when you are studying mycology in Europe,
you are NOT a geneticist for sure. If you want to become
a geneticist, you have to study first molecular biology
and then you have to specialize.
The fact that somebody is able to operate
a sequencer and read a sequence does not
mean that he is a geneticist.


--------------------
PSILOCYBE  CYANOFRISCOSA - EUROPE 2009



http://www.shroomery.org/forums/showflat.php/Number/11179100


Edited by nightflyer (04/21/09 07:56 AM)


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InvisibleCureCatM
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Re: Description for new Psilocybe species [Re: nightflyer]
    #10205576 - 04/21/09 07:56 AM (5 years, 6 months ago)

I don't mean that a Mycologist has any official title as a Geneticist.
I mean that Mycologists, Botanists, and Microbiologists do most, if not all of the work on fungal genetics- not just any Geneticists. 

So I guess I'm not sure what you intended in saying that "mycologists and geneticists live on different planets"?
I thought you meant that Mycologists disregard genetics.


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


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Invisiblenightflyer
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Re: Description for new Psilocybe species [Re: CureCat]
    #10205589 - 04/21/09 08:05 AM (5 years, 6 months ago)

I have made the experience, that some mycologists (at least in my country)
have negative sentiments and prejudices against the use of genetics in mushroom
taxonomy. I have no prejudices.


--------------------
PSILOCYBE  CYANOFRISCOSA - EUROPE 2009



http://www.shroomery.org/forums/showflat.php/Number/11179100


Edited by nightflyer (04/21/09 09:32 AM)


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Invisiblenightflyer
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Re: Description for new Psilocybe species [Re: Strophariaceae]
    #10205731 - 04/21/09 09:29 AM (5 years, 6 months ago)

Quote:



As I asked before, has anybody (Workman? Guzman?) looked at these microscopically? I'd be happy to do this, BTW, but I don't want to jump all over anybody else's work if its being done.




Here are the pics from Alan Rockefeller
posted in Subbedhunter's thread:

http://www.shroomery.org/forums/showflat.php/Number/8552924#8552924


--------------------
PSILOCYBE  CYANOFRISCOSA - EUROPE 2009



http://www.shroomery.org/forums/showflat.php/Number/11179100


Edited by nightflyer (04/21/09 10:21 AM)


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InvisibleMr. Mushrooms
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Re: Description for new Psilocybe species [Re: Strophariaceae]
    #10206242 - 04/21/09 12:22 PM (5 years, 6 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


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


Edited by Mr. Mushrooms (04/21/09 12:28 PM)


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OfflineStrophariaceae
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Re: Description for new Psilocybe species [Re: Mr. Mushrooms]
    #10206794 - 04/21/09 02:05 PM (5 years, 6 months ago)

Small but important point – genomics (the use of molecular DNA techniques) is not quite the same as genetics, though of course they overlap. Lots of fields (most of biology by now, really) use genomics, but genetics is a specialty.

Phylogenetics (which is comes from the work "phylogeny" rather than "gene") really isn't genetics per se, either – neither the classical Mendelian kind nor population genetics. In genetics, one looks at markers and traits that are polymorphic within a population or interacting populations. Of course, a few sophisticated folks do both population genetics and phylogenetics as a way of getting a handle on speciation.

Example – Tom Bruns makes heavy use of genomics, but I would not consider him to be a geneticist. (John Taylor might fit that description, though.)


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InvisibleMr. Mushrooms
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Re: Description for new Psilocybe species [Re: Strophariaceae]
    #10207023 - 04/21/09 02:48 PM (5 years, 6 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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InvisibleBlimeyGrimey
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Re: Description for new Psilocybe species [Re: Mr. Mushrooms]
    #10207565 - 04/21/09 04:29 PM (5 years, 6 months ago)

ITS sequences mutate quickly, right?


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InvisibleMr. Mushrooms
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Re: Description for new Psilocybe species [Re: BlimeyGrimey]
    #10207757 - 04/21/09 04:56 PM (5 years, 6 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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InvisibleBlimeyGrimey
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Re: Description for new Psilocybe species [Re: Mr. Mushrooms]
    #10210820 - 04/22/09 12:33 AM (5 years, 6 months ago)

"Sequence comparison of the ITS region is widely used in taxonomy and molecular phylogeny because it a) is (due to the high copy number of rRNA genes) easy to amplify even from small quantities of DNA, and b) has a high degree of variation even between closely related species. This can be explained by the relatively low evolutionary pressure acting on such non-functional sequences"

"The ITS region is now perhaps the most widely sequenced DNA region in fungi. It has typically been most useful for molecular systematics at the species level, and even within species (e.g., to identify geographic races). Because of its higher degree of variation than other genic regions of rDNA (for small- and large-subunit rRNA), variation among individual rDNA repeats can sometimes be observed within both the ITS and IGS regions. In addition to the standard ITS1+ITS4 primers used by most labs, several taxon-specific primers have been described that allow selective amplification of fungal sequences (e.g., see Gardes & Bruns 1993 paper describing amplification of basidiomycete ITS sequences from mycorrhiza samples). ITS region is nowadays being used to know the genetic diversity among different strains of bacteria by sequencing the ITS gene."

Source : Internal transcribed spacer - Wikipedia


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InvisibleMr. Mushrooms
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Re: Description for new Psilocybe species [Re: BlimeyGrimey]
    #10211105 - 04/22/09 01:28 AM (5 years, 6 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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Offlinepsilocybin_qualm
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Re: Description for new Psilocybe species [Re: Mr. Mushrooms]
    #10262282 - 04/30/09 02:33 PM (5 years, 5 months ago)

Any further advancements on this


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OfflineSubbedhunter420
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True name discovered, long process.. i know [Re: Subbedhunter420]
    #14752731 - 07/11/11 07:59 PM (3 years, 3 months ago)

Hello everyone, I apologize for digging up these old threads, but I would like to acknowledge Alteredstates and my own findings of this supposed species to actually be Psilocybe Ovoideocystidiata. I just want to confirm it, and I was not sure if everyone was aware of this update. Thanks to Alan Rockefeller for analyzing our samples.

-thank you, and apologies-
      Subbedhunter420

p.s. I have a wikipedia article about myself now. haha
http://en.wikipedia.org/wiki/User:Subbedhunter420


--------------------
My Subbalteatus Guide (revised edition with new pictures)
http://www.shroomery.org/9608/Subbedhunter420s-Guide-to-Hunting-and-Identifying-Panaeolus-subbalteatus
You should read it.
And check my site out...
http://www.huntmushrooms.com

Sometimes...


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