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Offlinefalcon
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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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OfflineStrophariaceae
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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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Offlinexmush
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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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OfflineStrophariaceae
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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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InvisibleAnastomosisJihad
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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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Edited by AnastomosisJihad (01/23/08 07:35 PM)


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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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InvisibleAnastomosisJihad
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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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OfflineStrophariaceae
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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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OfflineToxicManM
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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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OfflineAlan RockefellerM
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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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OfflineStrophariaceae
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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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