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InvisibleAnastomosisJihad
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Taxonomical Significance of Microscopic Characters.
    #7909122 - 01/21/08 10:57 AM (16 years, 11 days ago)

Why are the size and shape of spores, basidia, and cystidia so important taxonomically?

Most would not split collections of similar mushrooms into two species merely because one fruit body was a little bit bigger than the other, or because one had a short thick stem and another a long skinny stem. But species level splits are frequently justified by a few microns difference in spore size. Why is spore size so important?

Likewise, nobody would assert that three men were of different species simply because one has thin blond hair, another thick black hair, and a third no hair at all. Yet species level splits are frequently justified by morphological differences in cystidia, which appear to serve no physiological function. Why are the presence, absence, and form of sterile cells important taxonomically?


A further question concerns species concepts. What species concept are you guys working with?


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OfflineAlan RockefellerM
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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7909337 - 01/21/08 12:01 PM (16 years, 11 days ago)

If I invented the whole thing, I would set it up so the macroscopic characteristics get you to the species, then you could use microscopic characteristics to find out which subspecies you have.


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Offlinexmush
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Re: Taxonomical Significance of Microscopic Characters. [Re: Alan Rockefeller]
    #7909421 - 01/21/08 12:23 PM (16 years, 11 days ago)

Another reason is that spore sizes are consistent within a species. There is not that much of a difference between the spore sizes of different individuals within a species. Macroscopic characteristics are not so consistent. Your three different looking men would produce sperm cells that are indistinguishable from each other with regards to size etc.

That being said, I think mushroom taxonomy is a huge clusterfuck.


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OfflineEvets
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Re: Taxonomical Significance of Microscopic Characters. [Re: xmush]
    #7909547 - 01/21/08 01:06 PM (16 years, 11 days ago)

keep in mind that your hypothetical is flawed.
You say species.. but.... hair...can be grouped by class and more so by family...i.e. mammals in this situation. So mammals in a sense aren't defined by hair. Surely a cow w/ black hair is different then a human w/ black hair.


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OfflineToxicManM
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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7909689 - 01/21/08 01:45 PM (16 years, 11 days ago)

xmush is right, that spore size is pretty consistent with a species. I know that in a seminar I did with Bryce Kendrick on molds we identified everything based on the conidia (even without the mold itself).

Alan, I'm sympathetic to that view, but I'm not sure everything could be told apart macroscopically. The vast majority of things could be, but I'm sure you can think of a few examples of species that cannot be distinguished without a microscope.

Happy mushrooming!


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InvisibleCureCat
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Re: Taxonomical Significance of Microscopic Characters. [Re: Alan Rockefeller]
    #7910094 - 01/21/08 03:28 PM (16 years, 11 days ago)

Quote:

Alan Rockefeller said:
If I invented the whole thing, I would set it up so the macroscopic characteristics get you to the species, then you could use microscopic characteristics to find out which subspecies you have.



That goes directly against phylogenetic cladistics.....


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OfflineAlan RockefellerM
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Re: Taxonomical Significance of Microscopic Characters. [Re: CureCat]
    #7912148 - 01/21/08 09:06 PM (16 years, 11 days ago)

> That goes directly against phylogenetic cladistics.....

I don't think it would go against that very often.

It mostly goes against people who are abusing phylogenetic cladistics as an excuse to split when they should be lumping.


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OfflineStrophariaceae
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Re: Taxonomical Significance of Microscopic Characters. [Re: Alan Rockefeller]
    #7912894 - 01/21/08 11:11 PM (16 years, 11 days ago)

Read this as "we should prioritize macro characters, because that's what us regular mushroom collectors use for identification".

Yeah, whatever.


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InvisibleGGreatOne234
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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7913176 - 01/22/08 12:04 AM (16 years, 10 days ago)

I do not have a Phd in Mycology and I did not invent Taxonomy or find every species of mushroom in my area. I did not invent the microscope either. I probably could not tell a person why a orange is the color orange, or say that I invented orange trees. Advocado trees... no I did not invent those either, unfortunately, someone else discovered how to grow them before me (and i was pissed). The Theory of Relativity.. no, I think someone else might have thought that one up besides me. I guess everyone is not that elite of a scientist as Albert Einstein. Then again, there is the shroomery... where many brilliant professors are single handedly changing the way professionals and doctors classify every known bit of information in the universe and beyond. Because up to this point, none of the research was valid until i read this topic. Now I understand the new theories that are encompassing the minds of doctors in Mycology today. I do not drink anymore but.. I think that a glass of champagne is in order, we now have the code for identifying every living organism on the planet down to subspecies.


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Re: Taxonomical Significance of Microscopic Characters. [Re: Alan Rockefeller]
    #7913185 - 01/22/08 12:06 AM (16 years, 10 days ago)

Alan, that would be a very odd species concept. I don't think it would be very functional, what with species variation. How would you draw the line with macroscopic variations, to distinguish one "species" from another??

And as you know, just because it looks the same, doesn't mean they share the same evolutionary heritage. Convergent evolution and all. And then there are some odd-ball species which just don't look like they fit in their genus, until you look at them under the 'scope.


>It mostly goes against people who are abusing phylogenetic
>cladistics as an excuse to split when they should be lumping.

I really disagree. I think it is in stark contrast with the concept of phylogenetics- not just those who "abuse" it. I'm definitely not a splitter, and I don't think I'd be called a lumper either, and I have some real reservations in granting precedence to macroscopic features over microscropic features.


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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7913189 - 01/22/08 12:08 AM (16 years, 10 days ago)

Something that's being left out of this discussion is ecological information (greatly underused by almost everybody these days). I think as mycological taxonomy progresses that ecological associations will become much more important for accurate identification.

Happy mushrooming!


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Offlinexmush
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Re: Taxonomical Significance of Microscopic Characters. [Re: GGreatOne234]
    #7913556 - 01/22/08 02:00 AM (16 years, 10 days ago)

:rofl::lol:


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Re: Taxonomical Significance of Microscopic Characters. [Re: xmush]
    #7913672 - 01/22/08 03:38 AM (16 years, 10 days ago)

^^^
GGO... I have no idea what you're talking about, hehe.


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OfflineAlan RockefellerM
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Re: Taxonomical Significance of Microscopic Characters. [Re: CureCat]
    #7914118 - 01/22/08 10:44 AM (16 years, 10 days ago)

> I really disagree. I think it is in stark contrast with the concept of phylogenetics- not just those who "abuse" it. I'm definitely not a splitter, and I don't think I'd be called a lumper either, and I have some real reservations in granting precedence to macroscopic features over microscropic features.

I guess its about time for you to get a microscope so you can finally figure out what all the mushrooms you find really are.


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InvisibleAnastomosisJihad
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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7914151 - 01/22/08 10:52 AM (16 years, 10 days ago)

This is all very interesting, and I would love to have a conversation about the inadequacies of phylogenetics, but my question remains unanswered.

Why are the presence or absence / shape and size of cystidia taxonomically important.


I know some microscopic features are very important for determining lineages (cell wall construction for instance), and that two fruit bodies can look very similar macroscopically, but under a microscope one can see they are put together in very different ways. Certainly, some micro-morphological characters reveal an organism's evolutionary strategies and help trace descent.

Cystidia, however, appear to serve no function at all, and therefore should be immune to natural selection. Why consider them as more taxonomically significant than hair color?

As for spore size: to say that spore size is consistent within a species, and then to make a species level split based solely on difference in spore size is just begging the question. How do we know that spore size is consistent within a species and not variable by population, like many other features?


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InvisibleCureCat
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Re: Taxonomical Significance of Microscopic Characters. [Re: Alan Rockefeller]
    #7914721 - 01/22/08 01:36 PM (16 years, 10 days ago)

Quote:

Alan Rockefeller said:
I guess its about time for you to get a microscope so you can finally figure out what all the mushrooms you find really are.



Working on it.  I like to make informed decisions about these things.  Hopefully in the next month or two.

Certainly, there are plenty of times I've come to a cross roads and gone "Fuck....  okay, I'll just put Ramaria sp. 'cause there's no way in hell I'm gonna be able to key it out macroscopically, and with any certainty".  I'd usually rather leave the species unknown, than take a blind stab. 
I know at places like Fungus Fairs, most people tend to put their best guess and figure "Eh, it's close enough, no one will care... and if they do, they can change it".

So yeah, I've gotten my feet wet and am quite eager to jump in.  Just got to get some basic materials and figure out what the hell i'm gonna get.
Thanks for letting me tool around on yours.  :wink:
It certainly has some cool features, and is pretty comfortable design (though the chairs are always too short or the tables too high and i have to sit on my feet to reach the oculars, heh).


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InvisibleCureCat
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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7914794 - 01/22/08 01:57 PM (16 years, 10 days ago)

Quote:

AnastomosisJihad said:
As for spore size: to say that spore size is consistent within a species, and then to make a species level split based solely on difference in spore size is just begging the question. How do we know that spore size is consistent within a species and not variable by population, like many other features?



Good question.  I think it has a lot to do with your species concept.  It's kinda tricky.  I am still not sure how i would define species, so I try and follow the leads of the pros, and ask questions and listen to each argument for or against a split, to decide which seems sensible based on what I already know.

Another method used to compare with microscopic variation is sequencing of course, and comparing base pairs with suspected relatives.  Then there are actual mating tests which can be done, but I think a lot of mycologists shy away from this due to the hands on nature (rather than using a device of some sort), the length of time invested, and the number of different strain cultures required.  Then interpreting the results is a whole other mess.
There are other methods, those are the ones that are coming to mind at the moment.

So, based on consistencies seen among different methods, you can begin to sort one species or population from another.  Lets say the results are mixed- some results suggest a separate species, while others conflict that conclusion.  Then the taxonomists and geneticists get to duke it out, and argue their points.  :wink:

My explanation is lacking detail, but perhaps you get the idea.  I think I do.  :crazy:


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InvisibleGGreatOne234
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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7915294 - 01/22/08 03:49 PM (16 years, 10 days ago)

AnastomosisJihad,

From the book How To Identify Mushrooms To Genus III: Microscopic Features, page 2:

"Every macroscopic feature used to describe a basidiocarp has a set of microscopic features which can be correlated with it; for example, the pileus surface of a viscid to glutinous species of Cortinarius is represented by a particular kind of pileipellis called an ixotrichodermium; or the dark brownish color of certain Naucoria species is because of a pigment which incrusts the hyphal wall; or the marginate gill-edge of Leptonia serrulata is the macroscopic expression of the cheilocystidia being filled with a vacuolar pigment. When such correlations are made and understood, the student interested in the study of the fleshy fungi will have acquired the basic, fundamental knowledge prerequisite to all other studies in this fascinating field.".

does that kind of answer your question or have you already read that book?

I personally think that David Largent, David Johnson and Roy Watling did a good job with the book, but it seems clearly obvious that a shroomerite is going to soon be re-writing the International Code of Botanical Nomenclature in such a way that zero riddles or problems will ever arise again in identifying anything. Until then I would trust the actual professionals who followed and branched off in the footsteps of people like Elias Fries.


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InvisibleGGreatOne234
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Re: Taxonomical Significance of Microscopic Characters. [Re: GGreatOne234]
    #7915339 - 01/22/08 03:58 PM (16 years, 10 days ago)

also, i bet that Elias was not a jerk.


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OfflineToxicManM
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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7915458 - 01/22/08 04:23 PM (16 years, 10 days ago)

Cystidia of course do perform functions in the mushrooms, otherwise they wouldn't be there. One example I know of is that in many species of Coprinus there are cystidia to hold the gills apart far enough so that spores being ejected from their basidia don't just run into the opposite gill face and stick there.

There are lots of cystidia out there that we have no idea what function they may serve, but our lack of knowledge is hardly reason to suspect that they serve no function.

Happy mushrooming!


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Re: Taxonomical Significance of Microscopic Characters. [Re: GGreatOne234]
    #7915928 - 01/22/08 05:35 PM (16 years, 10 days ago)


"Every macroscopic feature used to describe a basidiocarp has a set of microscopic features which can be correlated with it;


That is the question, named species that overlap the macroscopic characteristics of other named species are suspect if this true.

Species that change their macroscopic characteristics when transplanted and look exactly like closely related native species are suspect.

One of the problems with professionals is they are not looking at single colonies to see how they change in different habitats and on different substrates, and this is one thing that amateurs can do given the time and inclination.

Professionals can make mistakes.


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OfflineStrophariaceae
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Re: Taxonomical Significance of Microscopic Characters. [Re: GGreatOne234]
    #7919468 - 01/23/08 11:28 AM (16 years, 9 days ago)

Quote:

GGreatOne234 said:
also, i bet that Elias was not a jerk.




Elias Fries was never called an asshole.


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OfflineStrophariaceae
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Re: Taxonomical Significance of Microscopic Characters. [Re: ToxicMan]
    #7919747 - 01/23/08 12:47 PM (16 years, 9 days ago)

GreatOne and ToxicMan -

Thanks for making a few of the arguments I was going to make – took the words right out of my mouth, or off of my fingers as the case may be.

One thing I'd disagree with, slightly:

Quote:

Cystidia of course do perform functions in the mushrooms, otherwise they wouldn't be there.




We don't know enough about cystidia to know if they're actually functional or not. There's also the possibility they could be some kind of vestigial structure, like an appendix or wisdom teeth.

Basically, an character will tend to remain in a population if its positively adaptive or if its adaptively neutral.

My hunch, though, is that cystidia are adaptive and that they have something to do with maintaining the critical moisture environment around the basidia that's necessary for spore release. (For how moisture is related to spore release, I'll refer to a Mycena News article I wrote a few years back, Why Do Mushrooms Look Like Mushrooms?) Also, cystidia may serve a protective function vis-a-vis small fungivores like insects; in fact, the "glandular dots" on Suillus, which are caulocystidia filled with an irritating compound (that actually can cause contact dermatitis in some people, including myself), are almost certainly protective in nature.


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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7920049 - 01/23/08 02:16 PM (16 years, 9 days ago)

Well I will tell you why Strophariaceae. Here in Idaho the potatoes grow quite delicious. And I just love it here in Idaho. But the apple trees here in Washington state are quite good also, and I will never leave this place. Even though China makes 98% of the apple juice for the country the fruits are still some of my favorite and that is why I call it home. Things get stranger as you head down south. The inbetween state is nuts for nuts and coffee and grapes but they just cannot settle on which one to specialize in. All of the bannanas are in California as we all know. Quite a lot of bannanas down there.. :smile:

And by the way, Anno OK'd the hunting forums newest category for "Microscopy", but it is for microscopic features of fungi not fruits and vegetables.


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Offlinexmush
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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7920054 - 01/23/08 02:17 PM (16 years, 9 days ago)

Good points Strophariacae, about adaptive neutrality and everything else. If they were adaptively neutral, then one would expect them to be lost or kept at random. The fact that so many fungi retain this structure might argue against adaptive neutrality.

Although the appendix and wisdom teeth are perhaps not the best examples of vestigal structures. At the risk of going off topic... The appendix appears to be a great source of microflora in the event that the rest of the gut microflora is altered in a negative way. And wisdom teeth are hardly vestigal, and their removal should be considered one of the great swindles of our time. Less than 10% of people who don't have their teeth removed will ever have a problem such as a tooth root abscess. Conincidentally enough, this is about the same rate of appendicitis in the population. So removing everyones' wisdom teeth is like if we prophylactically removed everyone's appendix. From a public health standpoint, wisdom tooth removal leads to a net loss of public health as a result of complications etc.

Now, to segue that back to the topic at hand. I would tend to agree with ToxicMan, and your last paragraph. Cystidia likely serve some function, and we don't know exactly what that (or those) function(s) are. You raise some interesting possibilities though.


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Re: Taxonomical Significance of Microscopic Characters. [Re: xmush]
    #7920128 - 01/23/08 02:45 PM (16 years, 9 days ago)

Quote:

xmush said:
Although the appendix and wisdom teeth are perhaps not the best examples of vestigal structures. At the risk of going off topic... The appendix appears to be a great source of microflora in the event that the rest of the gut microflora is altered in a negative way. And wisdom teeth are hardly vestigal, and their removal should be considered one of the great swindles of our time. Less than 10% of people who don't have their teeth removed will ever have a problem such as a tooth root abscess. Conincidentally enough, this is about the same rate of appendicitis in the population. So removing everyones' wisdom teeth is like if we prophylactically removed everyone's appendix. From a public health standpoint, wisdom tooth removal leads to a net loss of public health as a result of complications etc.




Human anatomy and physiology isn't my strong point. And I totally agree with you about "prophylactic" removal of wisdom teeth. Talk about a needless, expensive, and traumatic medical procedure.


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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7920164 - 01/23/08 02:55 PM (16 years, 9 days ago)

I'm in public health, so I always jump in with these sorts of off topic nuggets of info. But I think that some of these lessons to highlight the idea that anatomical features are rarely truly vestigal, we are just ignorant of their function. The same thing has happened regarding tonsil removal, and I'm sure there are many other examples. And I really do like the idea of adaptively neutral things persisting. But then we're dealing with a random process so we can statistically quantify the likelihood of these structures being present in X number of species given randomness. In other words, having these structures in every species of mushroom would be like flipping a coin and having it come up heads every time. This could happen completely at random, but it is unlikely (and of course this isn't really like a coin flip since we're waiting for genetic mutations to happen that would remove these structures entirely -- it's probably more like some crazy 12-sided die, but you get the point).


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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7920522 - 01/23/08 04:41 PM (16 years, 9 days ago)

Quote:

AnastomosisJihad said:
This is all very interesting, and I would love to have a conversation about the inadequacies of phylogenetics, but my question remains unanswered.




And why do you think phylogenetics is "inadequate"? The reasons given in your rather out-of-context quote of Lynn Margulis and Carl Sagan perhaps?

Quote:


Why are the presence or absence / shape and size of cystidia taxonomically important.

I know some microscopic features are very important for determining lineages (cell wall construction for instance), and that two fruit bodies can look very similar macroscopically, but under a microscope one can see they are put together in very different ways. Certainly, some micro-morphological characters reveal an organism's evolutionary strategies and help trace descent.

Cystidia, however, appear to serve no function at all, and therefore should be immune to natural selection. Why consider them as more taxonomically significant than hair color?




First, the assumption that cystidia serve "no function at all" and are "immune to natural selection" is huge assumption on your part. You don't know this, nor does anybody at this point. (For that matter, how do you know hair color is not a product of selection? I refer you to Cavalli-Sforza's hypothesis that differences in hair and eye color may have been the by-product of sexual selection - article here.)

Secondly, I think you have some very profound misunderstandings of both evolution and taxonomy. First, even if trait is not the subject of natural selection, that does not mean it falls into some kind of evolutionary stasis. Mutation can continue to occur, introducing variance to that trait, and even if that mutation remains adaptationally neutral, it is still subject to change in frequency in populations due to genetic drift. Over time, many not-particularly-meaningful traits become fixed in a population or entire species. And these "neutral" traits are most certainly taxonomically significant if they represent a consistent difference between species (or other taxonomic units). In fact, at the level of DNA, neutral, non-expressing DNA sequences like ITS are often preferred for phylogenetic study, since mutations in these sequences occur in a random manner who's rate of change is, statistically speaking, rather stable, as opposed to genes that are subject to natural selection, who's genetic distance may be exaggerated or decreased depending on the degree of selection acting on those genes.

Quote:

As for spore size: to say that spore size is consistent within a species, and then to make a species level split based solely on difference in spore size is just begging the question. How do we know that spore size is consistent within a species and not variable by population, like many other features?




How is this known? Its known because taxonomists who put together world monographs of various genera (or sections of genera), have actually compiled spore statistics of differing populations of a species. The range of spore sizes between populations is variable, but not hugely so, and certainly not nearly so variable as the range of sizes and forms that a single species of mushroom can take on macroscopically.

Generally speaking, and this pattern is true across all organisms, is that anatomical and cellular traits tend to be conserved longer and exhibit less radical change over evolutionary time than does the larger morphology of an organism. The larger morphology is also more susceptible to the effects of convergent evolution based on similar selective pressures. One only need look at a coyote versus a porpoise versus a shark. A coyote and a porpoise look very different, but on the level of cells and fine anatomy are really quite similar. A porpoise in its larger appearance might superficially look more like a shark than a coyote, but look at virtually anything about its anatomy, and you'd know right away its a closer to a coyote than it is a shark. The same holds true for mushrooms.

That isn't to say that that micromorphology always "trumps" macromorphology, after all, Psilocybe azurescens was separated from Psilocybe cyanescens almost entirely by macro characteristics. Similarly, Guzman came up some years ago with what turned out to be a very flawed morphologically-based phylogeny of Psilocybe based on the assumption that spore shape was somehow a more "primary" characteristic, hence forcing him into a classification scheme that had the presence of psilocin and psilocybin (and, hence, bluing) as having evolved multiple times in Psilocybe. (These days, the best molecular trees demonstrate pretty solidly that actives form one group, inactives aother, and further that the actives and inactives aren't even immediately related, and that the actives form a sister group to Galerina in a newly erected family called the Hymenogastraceae - publication here.)


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OfflineStrophariaceae
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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7920592 - 01/23/08 04:51 PM (16 years, 9 days ago)

Quote:

AnastomosisJihad said:
A further question concerns species concepts. What species concept are you guys working with?




What species concept is at work – in practice, the working concept is clearly a "morphological species concept", that is, if it looks different (on a macro or micro level) and those differences are consistent between populations, then the two populations are different species. In many DNA studies, a "phylogenetic species concept" is at work, meaning if there's as much as a single base-pair difference in the gene or genes you're looking at, that's a species-level difference. These species concepts are, of course, problematic.

One of the big problems with coming up with a better concept of fungal species is that not only is identifying what is a true "species" require more work than simply describing and differentiating between the macro- and micromorphologies and gene sequences of different collections, there's also no entirely clear definition of fungal "species". The biological species concept – that if organisms from two populations can breed and produce fertile offspring, they're the same species – doesn't always work well with fungi because fungi often retain interfertility well after they've gone on different evolutionary "tracks". This idea is based on the idea that, in some genera such as Armillaria, closely related species that nonetheless are separated by continental distances and are thought to have been out of contact with each other for many millions of years, nonetheless remain interfertile. (Even though they may lack interfertility with other relatives even in the same locality.)

Hence, with fungi, you can say one aspect of the evolutionary species concept is true – if the two can't interbreed, they are definitely not the same species. However, the reverse is not necessarily true – two populations that still have the ability to interbreed might nonetheless evolutionarily divergent, and hence properly called different species.

But what relevance this all has on your "micro traits aren't really important" argument is rather unclear.


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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7920939 - 01/23/08 05:58 PM (16 years, 9 days ago)

Quote:

AnastomosisJihad said:

This is all very interesting, and I would love to have a conversation about the inadequacies of phylogenetics, but my question remains unanswered.




And why do you think phylogenetics is "inadequate"? The reasons given in your rather out-of-context quote of Lynn Margulis and Carl Sagan perhaps?



Thanks for replying. I just got back from the library with How to Identify Mushrooms to Genus III, and I need to read it before addressing your post further.

But to answer your question about cladistics; The primary flaw in most cladistic analysis is a failure to account for horizontal gene transfer, cross-phyla hybridization, and speciation by endosymbiosis.

The whole modern synthesis paradigm, and systematics based upon it, is becoming obsolete in light of HGT.


Let's not turn this into a pissing contest if we don't have to. I know it's hard to keep an open mind when you are an expert, but genetics is a new and evolving science. The quote from my signature was from Lynn Margulis' and Dorion Sagan's Acquiring Genomes - A Theory of the Origins of Species.




Thanks again for your replies. I'll get back to this after a little reading.


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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7921344 - 01/23/08 07:26 PM (16 years, 9 days ago)

Good review of Acquiring Genomes, Margulis & Sagan


One page book review of Margulis' and Sagan's Amazon link


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OfflineStrophariaceae
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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7921887 - 01/23/08 09:09 PM (16 years, 9 days ago)

Quote:

AnastomosisJihad said:
But to answer your question about cladistics; The primary flaw in most cladistic analysis is a failure to account for horizontal gene transfer, cross-phyla hybridization, and speciation by endosymbiosis.

The whole modern synthesis paradigm, and systematics based upon it, is becoming obsolete in light of HGT.




I thought that's what you were going to invoke. I think you're way off base here – your idea that HGT is making phylogenetic systematics "obsolete" is utter nonsense.

Yes, horizontal gene transfer is a real phenomenon and one that's not uncommon among prokaryotes and the earliest lineages of eukaryotes. However, the extent to which HGT occurs in those organisms compared to "normal" vertical gene transfer and to what extent that confounds phylogenetic lineages is controversial.

And when it comes to higher eukaryotes, all the evidence I've seen is that horizontal gene transfer is relatively rare and very limited in extent – typically a few genes and most often occurring when an organism contains an endosymbiont of some kind or is an endosymbiont itself.

I've even heard one hypothesis that the reason amanitin was so widespread in so many separate mushroom lineages was a result of some kind of lateral gene transfer, though I've never seen any experimental evidence for this beyond this speculation.

But really, there's no evidence whatsoever that horizontal gene transfer is so extensive among higher eukaryotes that any given eukaryote species could not be said to have one overwhelmingly dominant ancestral lineage. Hence, phylogenetic systematics remains a basically accurate model, even if there are eukaryotes that have picked up the odd gene from a species that was not its main direct ancestor.

I refer you to two papers:


Keeling PJ, et al. 2005. The tree of eukaryotes. Trends in Ecology and Evolution 20(12):670–676.

(Specifically, the section "Lateral gene transfer and the tree of eukaryotes".)

Longer article, but at least have a look at the abstract:

Andersson JO. 2005. Lateral gene transfer in eukaryotes. Cellular and Molecular Life Sciences 62:1182–1197.

Quote:


Let's not turn this into a pissing contest if we don't have to. I know it's hard to keep an open mind when you are an expert, but genetics is a new and evolving science. The quote from my signature was from Lynn Margulis' and Dorion Sagan's Acquiring Genomes - A Theory of the Origins of Species.




Dorian Sagan – excuse me. Lynn Margulis, of course, is somebody who's work I'm aware of and I think she's a top-notch biologist. However, like Thomas Kuhn, she also happens to be somebody who's hugely misunderstood by self-styled iconoclastic thinkers, often lacking grounding in a larger body of scientific theory.

And speaking of pissing contests, let's not turn this pissing contest about who's being more "open minded". I've seen that played as a trump card more than a few times, and its a poor substitute for having a broad understanding of the subject which you are arguing your opinion on.


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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7922083 - 01/23/08 09:51 PM (16 years, 9 days ago)

Your bottom link does not work.

And I did not say microscopic features are unimportant taxonomically, so don't strawman me. Nor did I quote Margulis out of context. I asked why they are important, because the answer is not so obvious to me.

Your modified tree of life from the first link has been replaced by the
Ring of Life. Nature 431, 152-155 (9 September 2004) | doi:10.1038/nature02848; Received 29 January 2004; Accepted 15 July 2004


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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7922200 - 01/23/08 10:13 PM (16 years, 9 days ago)

The bottom link needs to be downloaded using the download link on the page I linked to. Here's a direct link to the abstract, though:

http://www.ncbi.nlm.nih.gov/pubmed/15761667

Also, here's a full-text link to the "Ring of Life" article you mentioned:

http://shiva.msu.montana.edu/courses/mb437_537_2005_fall/docs/Rivera.2004.pdf

I certainly don't think this "ring of life" model has "replaced" "tree of life"-style phylogenies.


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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7922322 - 01/23/08 10:35 PM (16 years, 9 days ago)

I like this Tree model. :smile:



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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7922747 - 01/24/08 12:05 AM (16 years, 8 days ago)

>I certainly don't think this "ring of life" model has "replaced" "tree
>of life"-style phylogenies.

Exactly what I was going to say.

The idea is to incorporate new theories, and from what I read in AJ's link, they are suggesting a new way of interpreting or presenting evolutionary relationships. They are not "replacing".

I had this same incessant argument once with a friend once over Linnaean and Phylogenetic hierarchies.
Or as he would put it, "Linnaeus vs. PhyloCode".
His expertise was not genetics nor taxonomy. He was a political genius in some regards, but he kept arguing with me, saying that the PhyloCode would replace Linnaean taxonomy.
I insisted that the phylogenetics was and will be further integrated into the Linnaean model, as is the way of taxonomic reclassification, and he kept insisting that the current names were arbitrary. I tried explaining phylogeny and nomenclature, but he insisted on a simplified understanding of the issues.
He said I was wrong and that in years to come, I would see all of the current classification discarded, and replaced by the PhyloCode (which of course, he had no understanding of).

That's kind of what I'm seeing here. In order to understand the significance of microscopic features, you may need a fuller perspective of the details...


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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7925698 - 01/24/08 06:40 PM (16 years, 8 days ago)

Strophariaceae - Cladistics, with its nested hierarchies, single common ancestor, and neatly branching strait lines is becoming obsolete. Phylogentetics in the broad sense of attempting to trace an organism's lineage will of course remain a viable science. Some people erroneously equate cladistics and phylogenetics, so I should have been more clear. We can discuss evolutionary anastomosis further if you like, but let's do it in another thread, so that we can keep this thread about taxonomy and microscopic characters.


---------

OK, I finished reading How to Identify Mushrooms to Genus III, and I have a better understanding of what cystidia are, but I'm still uncertain as to why they are more significant taxonomically, within a genus, than other features like cap color.

Amanita muscaria has white, yellow, orange, and red varieties. But macroscopically identical populations of Psilocybes have been split into numerous species based on microscopic characters alone. Why call the macroscopically different Amanitas varieties and the microscopically different Psilocybes species. I think this is a fair question.


Quote:


What species concept is at work – in practice, the working concept is clearly a "morphological species concept", that is, if it looks different (on a macro or micro level) and those differences are consistent between populations, then the two populations are different species.





I like the morphological species concept, but no two of anything are exactly similar morphologically. How do you determine the difference between a species and a variety? Has nothing advanced in this area since Linnaeus noted the problem over 250 years ago?


Is 'species' just a conventional concept?


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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7926945 - 01/24/08 09:42 PM (16 years, 8 days ago)

In mycology traditionally, species have been separated on the basis of compatibility between spores. Spores only have have the full set of chromosomes (much as a sperm or ovum), and germinate to form an asexual mold. If two compatible molds of the same species meet, they form a single organism, typically forming clamp connections so that nuclei can travel from cell to cell and complete the full set. If the molds are incompatible, a zone forms between them where each secretes toxins to repel the other. So if spores from 2 specimens are germinated in petri dishes and they are found to be compatible with each other, they are taken to be the same species.

Happy mushrooming!


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Re: Taxonomical Significance of Microscopic Characters. [Re: ToxicMan]
    #7927270 - 01/24/08 10:35 PM (16 years, 8 days ago)

> So if spores from 2 specimens are germinated in petri dishes and they are found to be compatible with each other, they are taken to be the same species.

That is certainly one way to do it.

I have never tested it myself, it is hard to get just one spore.

I wonder how often that method fails by showing two different species to be incompatible, or by two monokaryotic hyphae of different species finding some way to get along.

I think that everyone should come up with their own species concept and use that. Everyone defines "species" in a different way, it will never be consistent from one mycologist to another, and we shouldn't expect that it ever will be.


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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7930481 - 01/25/08 03:45 PM (16 years, 7 days ago)

Quote:

AnastomosisJihad said:
Strophariaceae - Cladistics, with its nested hierarchies, single common ancestor, and neatly branching strait lines is becoming obsolete.




Well, you repeat this like a mantra, but without some facts to back it up, that's an assertion, not an argument. Why is this true? Because Lynn Margulis said so?

I argue the simple fact that horizontal gene transfer is simply not extensive enough in higher eukaryotes to erase basic common ancestry from a single lineage, and hence, the phylogenetic and cladistic taxonomy that derives from that.

Now, if you have facts to counter this, I'd love to hear them. However, repeating the same old assertions without some kind of facts to back them up does not bring you any closer to the truth of the matter. In fact, the repetition simply gets rather boring after awhile.


Quote:

OK, I finished reading How to Identify Mushrooms to Genus III, and I have a better understanding of what cystidia are, but I'm still uncertain as to why they are more significant taxonomically, within a genus, than other features like cap color.

Amanita muscaria has white, yellow, orange, and red varieties. But macroscopically identical populations of Psilocybes have been split into numerous species based on microscopic characters alone. Why call the macroscopically different Amanitas varieties and the microscopically different Psilocybes species. I think this is a fair question.




The question doesn't really make sense, because you're comparing what characters are being used to make distinctions between species in two entirely different taxa.

Either macro or micro characters can be used to separate species as long as those characters are actually consistent between populations, that is, they always occur in one population but never in the other. Obviously, whether that's a species-level difference or not depends on your species concept. Since the working concept is typically a morphological one, non-overlapping differences in micro or macro characters typically separate species.

Quote:

Quote:


What species concept is at work – in practice, the working concept is clearly a "morphological species concept", that is, if it looks different (on a macro or micro level) and those differences are consistent between populations, then the two populations are different species.




I like the morphological species concept, but no two of anything are exactly similar morphologically. How do you determine the difference between a species and a variety? Has nothing advanced in this area since Linnaeus noted the problem over 250 years ago?




Well, the morphological species concept isn't a "real" species concept, but simply a working assumption on the part of mycologists who don't have the knowledge or resources to determine what actual species-level differences are.

As for varieties, most modern taxonomists have dropped the idea of "varieties" or "subspecies", though obviously, subspecies and varietal names remain until they are validly republished as a species name. The idea of subspecies or variety is kept for the very specialized case of a population that still maintains some gene flow with the larger species but nonetheless has distinct character traits. (And situations like that are rarely understood with any degree of accuracy.) If there isn't gene flow between populations, than those populations are really different species, even if the morphological differences aren't large.


Edited by Strophariaceae (01/25/08 03:49 PM)


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Re: Taxonomical Significance of Microscopic Characters. [Re: ToxicMan]
    #7940633 - 01/27/08 02:47 PM (16 years, 5 days ago)

Quote:

ToxicMan said:
In mycology traditionally, species have been separated on the basis of compatibility between spores. Spores only have have the full set of chromosomes (much as a sperm or ovum), and germinate to form an asexual mold. If two compatible molds of the same species meet, they form a single organism, typically forming clamp connections so that nuclei can travel from cell to cell and complete the full set. If the molds are incompatible, a zone forms between them where each secretes toxins to repel the other. So if spores from 2 specimens are germinated in petri dishes and they are found to be compatible with each other, they are taken to be the same species.






^^^^^This is clearly a "biological species concept".

Quote:

Strophariaceae said:
The biological species concept – that if organisms from two populations can breed and produce fertile offspring, they're the same species – doesn't always work well with fungi because fungi often retain interfertility well after they've gone on different evolutionary "tracks". This idea is based on the idea that, in some genera such as Armillaria, closely related species that nonetheless are separated by continental distances and are thought to have been out of contact with each other for many millions of years, nonetheless remain interfertile. (Even though they may lack interfertility with other relatives even in the same locality.)




So you are saying that certain populations of Honey Mushrooms are different species, even though they can interbreed and produce viable off spring?

If two species can be interfertile, then how do you fit their offspring into a cladogram?


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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7940661 - 01/27/08 02:50 PM (16 years, 5 days ago)

AnastomosisJihad, if the universe was somehow put on pause for 1000 years and i was the only one able to to do anything, and i spent the time reading every single known college text book and scientific journal that was ever published, i still would not have even scratched the surface of what is really happening.


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Re: Taxonomical Significance of Microscopic Characters. [Re: GGreatOne234]
    #7940906 - 01/27/08 03:32 PM (16 years, 5 days ago)

I'm a little more optimistic.  :smile:


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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7941036 - 01/27/08 03:54 PM (16 years, 5 days ago)

Quote:

Well, the morphological species concept isn't a "real" species concept, but simply a working assumption on the part of mycologists who don't have the knowledge or resources to determine what actual species-level differences are.





If you think about it, the morphological species concept is inescapable. Even if there are essential species, and even if a perfect description of every species fell from the sky, we would still find ourselves relying on morphological characters (macro, micro, and molecular) to determine the species of any given specimen. The morphological species concept is the epistemic counterpart to any ontology of species.


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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7941079 - 01/27/08 04:04 PM (16 years, 5 days ago)

ok, why is there lightning? not just from a science book about why they think it happens, but why does lightning really happen?

why is a tomatoe red?

why are most reishi mushrooms so brilliantly colored? what is the real reason.

why did i decide to wear brown sneakers today?

here is a good one for the optimistic, why are there psychoactive compounds in some mushrooms? why do they stain blue? do you really think anyone could ever find the real answer.

why did einstein just discover how to blow up a sub-microscopic atomic bomb, instead of how to explode the whole universe?

kind of off topic i guess, but those are some honest questions that i urge you to answer for me. i do not believe that it is possible for a human to answer them. but, maybe you are the exception to the possibilities to what humans can understand. yes, i am quite pessimistic about it, because i personally believe that humans are the dumbest organisms on the planet.


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Re: Taxonomical Significance of Microscopic Characters. [Re: GGreatOne234]
    #7941778 - 01/27/08 06:18 PM (16 years, 5 days ago)

Why are tomatoes red?

Quote:

Tomatoes are "RED" because it contains a carrotenoid known as "Lycopene". Lycopene is a terpene assembled from 8 isoprene units. The color of lycopene is due to its many conjugated carbon double bonds. Each double bond reduces the energy required for electrons to transition to higher energy states, allowing the molecule to absorb visible light of progressively longer wavelengths. Lycopene absorbs most of the visible spectrum, so it appears red.



http://answers.yahoo.com/question/index?qid=20061001083616AAAbgi9

Your other questions are too easy. Try google.  :tongue:


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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7941905 - 01/27/08 06:36 PM (16 years, 5 days ago)

alright smartass :smile: i figured you would rebutle with something like that.

ok, why is "lycopene" found in tomatoes? why not a different "carrotenoid" or whatever that makes them Blue like a blueberry? or why do tomatoes have carrotenoid at all? why was it put there? if carrotenoid is found on other planets, is it the same exact thing?

why are tomatoe stalks and leaves the shape they are? over millions of years, why did the leaves turn out that shape? -no need to google search morphology of plants. why would the leaves not be similar in shape to Cannabis or Oregano? do tomatoe-like plants grow on the closest Earth-like planet to us also? if so, what do they look like?

and, what time is it right now on Mars? is it January 27th, 2008 on Mars right now? how about one of those planets in the andromeda galaxy, let's say in the dead center nucleus or core of one of those planets, is it January 27th 2008 there too?

does Ganoderma lucidum grow from hardwoods on planets 80,000,000 light years away from our solar system? or is it slightly different, or non existent any where else but Earth?

my appologize to stropharia for going off topic here


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Re: Taxonomical Significance of Microscopic Characters. [Re: AnastomosisJihad]
    #7949865 - 01/29/08 10:30 AM (16 years, 3 days ago)

Quote:

AnastomosisJihad said:
Quote:

Strophariaceae said:
The biological species concept – that if organisms from two populations can breed and produce fertile offspring, they're the same species – doesn't always work well with fungi because fungi often retain interfertility well after they've gone on different evolutionary "tracks". This idea is based on the idea that, in some genera such as Armillaria, closely related species that nonetheless are separated by continental distances and are thought to have been out of contact with each other for many millions of years, nonetheless remain interfertile. (Even though they may lack interfertility with other relatives even in the same locality.)




So you are saying that certain populations of Honey Mushrooms are different species, even though they can interbreed and produce viable off spring?

If two species can be interfertile, then how do you fit their offspring into a cladogram?




There's a big difference between saying two species can be interfertile and two species are interfertile. If the two closely-related species are separated by continental differences, its safe to say that, barring reintroduction of one species to the same area as the other, the two populations are separate and evolutionarily distinct. (Oh, and the old idea that atmospheric spore dispersal spread spores so widely that species and population migration is common is an idea that's been pretty thoroughly debunked. Only a few spores ever make it even a few miles from the sporocarp they came from. Of course, these days, there are all kinds of human-mediated species introductions all over the place, but that's something that's extremely recent on an evolutionary time scale.)

How would that fit on a cladogram? Why would one even try to fit a known hybrid on a cladogram?


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Re: Taxonomical Significance of Microscopic Characters. [Re: Strophariaceae]
    #7951607 - 01/29/08 05:42 PM (16 years, 3 days ago)

Quote:

Of course, these days, there are all kinds of human-mediated species introductions all over the place, but that's something that's extremely recent on an evolutionary time scale.)




Human mediated species introductions, though recent in timescales required for Darwinian evolution, predate the art of taxonomy by tens of thousands of years. It seems likely to me that some of the 'natural species' described in early taxonomies are actually naturalized hybrids, resulting from crosses of indigenous populations with seeds and spores carried by migrating populations of humans. Homo sapiens were ubiquitous before taxonomy began in earnest.

Quote:

The old idea that atmospheric spore dispersal spread spores so widely that species and population migration is common is an idea that's been pretty thoroughly debunked. Only a few spores ever make it even a few miles from the sporocarp they came from.




I have been in patches of Honey Mushrooms that stretched for miles and produced hundreds of thousands of fruit bodies. Populations of that size produce astronomical numbers of spores. Most of them land within a few inches of the fruit body, but some get carried by the wind. Hurricanes, tornadoes, and simple thermal columns can lift surface air  to altitudes of tens of thousands of feet. I think "debunked" might to too strong a claim. Even if no direct evidence of long range spore dispersal has been found, the wind is certainly capable of carrying dust a long way. Particulate pollution from Russian industry frequently makes its way into North America, so there is little reason to suspect a few mushroom spores might not also follow the same vector. 

Animal vectors are also something to consider. A flock of migrating birds that stops to rest in a massive patch of mushrooms will certainly carry some spores with them when the move on.

Large populations of mushrooms are also frequently accompanied by large populations of fungus gnats, so there is another vector for spore dispersal.



Quote:

How would that fit on a cladogram? Why would one even try to fit a known hybrid on a cladogram?





"By 1751 Linnaeus considered most species to be of hybrid origin (Olby  1985)"

This is from Loren H. Rieseberge's and Mark E. Welch's Gene Transfer Through introgressive Hybridization: History, Evolutionary significance, and Phylogenetic Consequences.

Chapter 18 in Syvanen's and Kado's anthology Horizontal Gene Transfer

The same article notes the often cited statistic that 80% of all plant species arose through hybridization. Cladistic analysis cannot account for hybrids due to restraints of the model, and, if a model of evolution cannot account for 80 percent of the organisms in a major phylum, then it is not a very useful model.

If you find this kind of stuff interesting (Like I do :smile:) then you might want to check out that anthology. I'm sure it is available in you university library.


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OfflineNWDude
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Re: Taxonomical Significance of Microscopic Characters. [Re: ToxicMan]
    #7954222 - 01/30/08 01:06 AM (16 years, 2 days ago)

Hey, guys I dont know any thing about this stuf but is it posible for basidia and cystidia to form on a spore?


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OfflineStrophariaceae
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Re: Taxonomical Significance of Microscopic Characters. [Re: NWDude]
    #7954234 - 01/30/08 01:10 AM (16 years, 2 days ago)

Quote:

NWDude said:
Hey, guys I dont know any thing about this stuf but is it posible for basidia and cystidia to form on a spore?




No.


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OfflineAlan RockefellerM
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Re: Taxonomical Significance of Microscopic Characters. [Re: NWDude]
    #7955132 - 01/30/08 11:15 AM (16 years, 2 days ago)

> Hey, guys I dont know any thing about this stuf but is it posible for basidia and cystidia to form on a spore?

Excellent question, I have often wondered that myself.

The answer is that it is not possible.

It is possible for basidia to form a spore, and it can do that while it is next to a cystidia. I hope that is close enough for you.


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InvisibleAnastomosisJihad
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Registered: 01/01/08
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Re: Taxonomical Significance of Microscopic Characters. [Re: Alan Rockefeller]
    #7955240 - 01/30/08 11:54 AM (16 years, 2 days ago)

A spore starts as a bulge in a special gill cell called a basidium. Usually two or four bulges will begin simultaneously, giving a crown or fingered look to the basidium.



Wikipedia basidium



As the bulges form, a vacuole begins expanding at the other end of the basidium. As it expands the vacuole pushes all the guts of the basidium into the forming spores. Once the spores are full, the cell walls close and the spores launch themselves off the gill edge in a process that Strophariaceae describes here.


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