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Discussion in 'Codex taxinomiae plantarum (CTP)' started by Braem, Nov 19, 2006.

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  1. Nov 26, 2006 #41

    Heather

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    No kidding...I spend all my time reading and moderating this forum. ;)

    If I were to read the books, I'm afraid I'd fall asleep. :poke:
     
  2. Nov 26, 2006 #42

    Braem

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    Now that is fine. I can live with people not reading the taxonomy books. But in that case, they should not complain about taxonomy.
    And generally speaking (and this is based on many years of experience): I know lots of people that spend LOTS of money for orchids (of which a fair percentage is sent to orchid heaven within a fairly short time) but who will not send 50 US on a book about those orchids.

    I wish all of you would be honest and tell me how much money they spend for orchids over the last five years and how much for orchid books over that same period of time.

    And when I read a book on maths, I fall asleep too. But I don't complain about maths.

    Guido
     
  3. Nov 28, 2006 #43

    kentuckiense

    kentuckiense

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    Since I started growing about 6 months ago:

    Books: $420
    Orchids: $305

    However, about half of my plants were gifts, so that skews that figure a bit.

    Yikes. I've spent way too much. No orchids this winter!
     
  4. Nov 28, 2006 #44

    VAAlbert

    VAAlbert

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    I would never call my my work to have been molecular taxonomy, but rather molecular phylogenetics. True enough, a taxonomy - mine - resulted from a molecular (+ morphological) phylogenetic reconstruction, but this taxonomy was non-objective concerning taxic circumscriptions and use of hierarchies vis-a-vis nomenclature. Not only that, I produced 2 taxonomies based on the same results. Nothing was verified at any stage, and certainly nothing was completed. Alpha taxonomy supplies the phylogenetic investigator with names that can be used to circumscribe individuals used in phylogenetic analysis. Plant individuals are what are extracted for DNA. The more the better. Not only that, more individuals and more DNA sequence is better still. Even better will be coding microsatellite data that can be transferred well among all (e.g.) Paph species.

    Concerning development of morphological characters for phylogenetics, one must make leaps of faith in deciding what features are homologous vs. not, and how to encode the variation seen. I have certainly made such leaps. But I have in no way verified anything, nor would I ever think that to be possible. We can only corroborate, and the greater the corroboration, the more robust the working conclusion.

    Finally, let us not take alpha taxonomy nor molecular phylogenetics too seriously re: defining what species really are. There is a body of debate out there on what a species is or isn't (biologically and philosophically), and the situation in plants is especially difficult given frequent propensity for interbreeding in nature. Species, as we use them for slippers, are merely constructs of convenience; no investigator sees or analyzes the full range of variation in nature, so there is no use for even the 'best' taxonomist or phylogeneticist to pretend otherwise.

    Taxonomy does not necessarily equal biology, and many useful taxonomies have been not been very biological. If we could marry evolutionary history with slipper species concepts - and do so robustly (i.e., with strong corroboration) - a slipper taxonomy should become stable.

    Best wishes,

    Vic
     
  5. Nov 28, 2006 #45

    Braem

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    Victor,

    you very much have a point. What your branch is, is the DNA Analysis. After that, it is statistics. But still, it has its purpose (although you know well that I have always been critical). The problem is that the "general public" out there has been led to believe over a series of years that so called "molecular taxonomy" is the best thing that happened since Eve gave Adam the apple [of course not saying that it wasn't an apple either], that one can solve all problems with the new method, and that alphataxonomy should be forgotten. That, of course is nonsense.

    Now, to those people thinking of the definition of a species: First of all a species must be a workable unit (a real population) within a workable system. Philosophical thoughts on that do not fit in biology (of course, I use "philosophy" here in the modern sense and not in the sence of the "natural philosophy" of pre-darwinian-times.)

    I am sure (and I have pointed at that in earlier posts) that the molecular work is evolving and will give some new insights. It will, however always have to stay "one tool among many tools". If taxonomy can only be done in the lab, we have lost the idea of "useful classification".

    As far as taking taxonomy (whatever it comprises) serious, I differ with you. If we don't take classification (and naming) serious, we are letting the system slip into chaos. And I have pointed out that some parts of the system already are nothing but chaos.

    As long as there is "democracy" on this planet, there never will be general consent on what a "plant species" is. Therefore, we should not have illusions about finding the ultimate taxonomy within any given group, including the slippers.

    You have used Mexipedium as an example in other posts. Now, no-one would like to deny that it is a slipper orchid. And no-one can deny that the differences (in respect to the plants as well as in respect to its flowers) between Mexipedium and all other slippers is readily visible with the naked eye, and can be described in simple terms. Therefore, I would be very interested in hearing your opinion on the alternative to considering Mexipedium a separate (autonomous) genus.

    regards
    Guido


     
  6. Nov 28, 2006 #46

    VAAlbert

    VAAlbert

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    Dear Guido,

    Well that isn't quite true. I wear several hats. I have in fact described about a dozen new species (in Gentianaceae), and a new genus (also Gentianaceae). I've even worked with Gentianaceae floristics! And phylogenetics isn't just statistics! See my edited book, e.g.,

    Albert, V. A., ed. (2006) Parsimony, Phylogeny, and Genomics. Oxford Univ. Press. 229 + pages. Paperback edition, revised.

    The first chapt. is available at http://folk.uio.no/victoraa/index_files/slide0002.htm


    Well, as I said, there's a lot of debate out there, and your opinion is yours! What, e.g., is a real population? That's a good one. I'm working these days on a metapopulation in the Lamiaceae.

    Well, we must be serious, but what I said and meant is that we shouldn't take ourselves too seriously. Nomenclature is serious, to be sure, since we need valid names. But classifications, species circumscriptions, and the nature of species are less to get jumpy about because they are malleable to mere opinion.

    Well, it's a very easy matter to say that the conduplicate-leaved slippers have far more in common with themselves as a group than any of the three genera (Mex included) do by themselves. I also presented the alternative: establishing Mex cleared the way for readily used key characters to distinguish sp. xerophyticum, Paph, and Phrag. Otherwise, I argued that sp. xerophyticum blurred the Paph/Phrag boundary, at least for visible, non-gestalt traits. The DNA data supports either argument. You choose -- key chars. that unite conduplicate slippers, or key chars. that dsicriminate 3 condup-leaved genera. Or choose an alternative that I think is less useful, like sp. xerophyticum in Phrag, where it would disrupt key chars. for paph and Phrag. The bulk of the community seems to have chosen Mexipedium, so I am fine with that.

    Yes, taxonomy should be useful, and there are often multiple alternative taxonomies that can be equally useful depending on where you cut the line between characters that can be described discretely vs. those available only as gestalts. And of course what is discrete vs. gestalt is subject to opinion!

    DNA sequences and other DNA markers are in fact objective, which I like -- but that doesn't mean I believe that DNA is 'the answer' to slipper taxonomy -- it can't be, because it can only reveal relationships, not taxonomist's opinions!

    Best again,

    Vic
     
  7. Nov 28, 2006 #47

    Braem

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    Dear Victor,

    Yes, Taxonomy is a serious business, but taxonomists should not take themselves too serious. That is very, very true.

    I will have to get your book.

    I am afraid I can't quite follow you on Mexipedium. I understand that Mexipedium is different from Paphiopedilum, Phragmipedium and Cypripedium. That is why it was established as Mexipedium. I don't see it is blurring any boundary by any visible traits. Look at the flower, look at the leaves. Furthermore it does not interbreed with any phrag. There is no need for DNA result here, but if you want to use them: they support an autonomous genus. Even if and when you argue that the DNA result may possibly also support an other interpretation, the alphataxonomic evaluation is clear. Thus Mexipedium is a good autonomous genus, well-defined and well-separated from all other slippers.

    The only alternative I see is to put _all_ slipper orchids together again in Cypripedium. But a) there is no point in doing that, and b) it would hardly be accepted by "the general public."

    And yes, your DNA "markers" are objective [assuming the procedures were carried out properly], but their choice is subjective, and the interpretation of the cladistics made on the basis of them is very subjective indeed.

    best regards
    Guido



     
  8. Nov 28, 2006 #48

    kentuckiense

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    Dr. Braem-

    Correct me if I am wrong, but I believe that M. xerophyticum does blur the boundary between Phragmipedium and Paphiopedilum if the unilocular ovary in M. xerophyticum is homologous with that of Paphiopedilum. Is it possible(or has it already been done?) to determine if the unilocular ovary of M. xerophyticum is an ancestral trait or if it is simply an adaptation due to decreased size and drier habitat?
     
  9. Nov 29, 2006 #49

    VAAlbert

    VAAlbert

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    Yes, Kentuckiense,

    The locularity of the ovary is at issue. Paph is unilocular; Phrag trilocular; Mex unilocular. Whether or not the unilocular Mex condition is a parallelism as regards Paphiopedilum, its presence at ovary midsection destroys locularity as a key character for identification purposes. Of course, the possibility of parallelism is interesting from the evolutionary perspective.

    As I wrote in my original description, Mexipedium can still be diagnosed readily from Paph based on another character. Mex has branched inflorescences like some Phrags, but unlike Paphs.

    The phylogeny supports Mex as as independent, but again, the data are ambiguous as to whether it is sister to Phrag (as published) or to Paph, or to both. Any of these ways you still run into the taxonomic key-character issue of the unilocular ovaries.

    Guido, I don't agree with your comments on Mex, Paph, Phrag & Cyp. If one ignores the locularity feature altogether (remembering that this would also implicate Cypripedium, which is unilocular, whereas Selen is tri), there is a suite of characters that support the conduplicate leaved taxa -- to the exclusion of particular generic-level boundaries. These features are described in my two Lindleyana papers:

    Lindleyana 9(2): 115-134, 1994
    Lindleyana 9(2): 133-139, 1994

    And many of these previously by Rosso:

    Journal of the Linnaean Society of Botany 59: 309-341, 1966

    And Atwood:

    Selbyana 7: 129-247, 1984

    Cypripedium has a rather different vegetative anatomy, for example, shared to considerable extent with Selenipedium.

    No, the conduplicates are easy to separate from the plicate-leaved slippers, but the conduplicate genera are much more narrowly defined unless one looks into the microscope for chromosomes (Phrag and Mex are much smaller than Paph; Phrag has a different base chrom. number; that of Mex is not yet certain, but is fascinatingly 2n=26 like basal Paphs), considers geography and interbreeding more important than morphology (only the former can be a direct field observation!).

    To dissect the interbreeding issue, we know that no combination of Mex, Phrag, or Paph can interbreed. But as I have argued elsewhere, interbreeding should not be used as a generic-level character among orchids, or we would run into big problems given that many recognized genera *can* in fact interbreed, whereas others can't.

    And although we slipper freaks can easily wade our way between the Paph, Phrag, and Mex gestalts just by looking at a flower (or even a plant), we can't expect non-specialist botanists to automatically perceive these overall differences.

    As regards molecular markers, when we pick a certain gene, that is subjective indeed. However, now that we have genomic-scale technology, we pick up genes at random -- thousands of them, which can then be 'mined' for markers based on criteria such as presence of potential nucleotide repeat elements that might be variable among individuals.

    As regards the interpretation of phylogenetic results and its subjectivity, I have already addressed the point that one phylogeny (e.g., the one I performed to erect Mexipedium) could support several different taxonomies -- you choose where the hieracrchic boundaries for names lie.

    Finally, again, the bulk of the community likes Mex, so do you, and I'm also perfectly OK with this alternative!

    Best wishes,

    Vic
     
  10. Nov 29, 2006 #50

    Braem

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    Kentuckiense & Victor,

    OK - Granted. But in that case, the marker "number of locules" in the ovary is no longer good to distinguish between paphs and phrags. Fair enough. But that is just one single characteristic. The boundaries between paphs and phrags remain clear enough without that marker. There are many more. Thus, all you can say is that the discovery of Mexipedium xerophyticum has shown that the marker "number of locules in the ovary" is no longer full proof for this group of plants.

    Now, if anyone is uncapable of differentiating Mexipedium from the other slippers by eye-sight, he/she needs either glasses or is ....
    Thus, you rule out Mexipedium and if you want, you can use the "locule-trick" again.

    Anything else in this respect is of purely academic importance and hardly of any practical use.

    To the question whether the number of locules in the ovary is adaptive or not, I cannot say very much. We would have to see whether something similar occurs in other plants that grow in similar conditions, and even so, that would be some indication, but no proof.

    Guido




     
  11. Nov 29, 2006 #51

    VAAlbert

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    Guido:

    Please elaborate that list! And please try to make those differences discrete enough to be used in keys.

    You and me, but what about a novice, or a specialist in Gentianaceae who needs a workable key to do the job?

    This is your opinion on what is practical! And, what is academic, I think. 'All conduplicates = one genus' could be considered practical by others. There are no overlapping species epithets, to my memory, so no new ones would need be erected as replacements. Your claim throughout these pages has been that taxonomy is an academic discipline, so I take this to mean that you'd agree with the view that practicality in taxonomy should also have an academic basis? No tongue-twister intended.

    Best again,

    Vic
     
  12. Nov 29, 2006 #52

    VAAlbert

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    Oh,

    Forgot to mention that the branched inflorescence character in Phrag is not uniform in Phrag, so it is not a perfectly clear identifier. Maybe then 'all condups = one genus' is better supported...

    Many other morphological traits will fall into this category, for example, outwardly folded labella (only some Paphs), infolded labella (Mex, Phrag, only some Paphs), infolded and apically fused labella (only some Phrags), etc.

    Maybe you like staminodes better? Leaf texture? Give us the list!

    BW,

    V
     
  13. Nov 29, 2006 #53

    Braem

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    Dear Victor,

    OK let me do this one first:

    You are quite correct that the branched inflorescence character in Phrag is not uniform. But that is in Phrag. Thus the character is not fool proof within the given genus. It is however useable to differentiate between the genera of the slippers (and that is what we are talking about, the differentiation between Mexipedium and the othere genera of the slippers and not the differentiation between the various species of phragmipediums.)

    Staminodes is a similar problem. You know that staminodes are variable within a number of species (for example very much so in the brachypetalums). But there is no staminode in Phragmipedium that can be confused with the staminode of a Paphiopedilum.

    While I am at it: plant size
    Yes, that is no good within any given species and no good in many other cases. But within the slippers, it is an excellent criterion to differentate between Mexipedium and anything else.

    The same applies for leaf texture. The same for flower size, the same for overall flower morphology, the same for flower colour. I must have slept deeply if I have missed the description of _anything_ that looks in anyway similar to Mexipedium. And again, we are discussing slippers here. Nothing else.

    As a trained taxonomist, I know very well that all this _may_ possibly not apply to the Gentianaceae, Scrophulariaceae, or whatever. And I too wear several hats having worked on the sixteen families of plants in which there is "carnivory" and having worked on Tulipa (Liliaceae). But that is not the subject of our discussion.

    regards
    Guido



     
  14. Nov 29, 2006 #54

    Braem

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    Victor,

    I have dealt with your first two points in my other reply. Again, we are discussing the problems in the taxonomy of the slippers. Not the Gentianaceae, although that are very interesting plants indeed.

    As far as expressing my own opinions. Of course they are my own opinions. It would be bad if I were to express nothing but the opinions of others. But you will have to grant me that founding a taxonomy on DNA studies is not exactly practical (besides the fact that it does not work). Or maybe you can ask how many people of the somewhat 35000 members of the Orchid Societies world wide (admittedly a rough estimate) have access to a lab in which they can do molecular biology.

    And I maintain, that if we can differentiate between certain plants and plant groups by looking at them with the naked eye, it is very unpractical to blur the issue by anything else. I have shown on other occasions that the molecular studies in Paphiopedilum and in Phragmipedium on the species level or below species level are non-stable thus impractical if not simply non-applicable. Above that level, to differentiate sections, subgenera, and genera, they confirm (or if you wish to use another phrasing: they do not contradict) alphataxonomic procedures. I know of no instance within the study of slipper orchids that molecular studies have revealed anything that was not recognizable with alphataxonomic means.

    Sincere regards
    Guido







     
  15. Nov 30, 2006 #55

    VAAlbert

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    Hello again, Guido:

    Just some counterpoints; having some fun!

    Best wishes,

    Vic

    Well, if inflorescence branching isn't constant within Phrag, then it doesn't discriminate Mex and Phrag perfectly -- if a novice compared Phrag caudatum with Paph and Mex based on this character, he might group Mex with Paph. Throw in a branched-inflor. Phrag, and the situation becomes more complicated.

    Again, it is true that staminodia of Paphs and Phrags are dissimilar at the gestalt level, but those of Mex and Phrag are not particularly! Again, overlapping suites of characters can make identification -- using keys -- difficult for non-specialists.

    Come on now! What about Paph barbigerum or helenae? To be picky, we could even throw in some of the tiny Cyps. True enough, the leaves of Mex show xeromorphic adaptations, as do those of Paph druryi. So, again, we need to say 'very thick-leaved plants that are very small, X cm by X cm'.

    These features are mostly in the realm of gestalt! For the first, compare Paph druryi with Mex, for the second, compare Paph hangianum with Phrag kovachii, for the third and fourth, maybe get confused between Paph delenatii and Phrag schlimii. You and I can tell the difference, but a practical system is one that suits multiple users of different backgrounds. *Not that I'm saying we shouldn't have a system with separate Paph, Phrag and Mex* -- only, as the Devil's Advocate, that one genus is an alternative, based on the bulk of the character data that supports a conduplicate-leaved lineage more than it does the specific 3 genera.

    I won't grant you the first one in its entirety, Guido. Nobody doing molecular phylogenetics works with entirely unknown groups of plants; i.e., virtually all plants studied have already passed through the alpha phase and (hopefully) have valid names and fall into somebody's classification. Molecular data, as applied to such plant groups, can be very useful in determining whether supposed plant taxa have a single evolutionary origin, or several. The latter was found to be the case with Flacourtiaceae some years back, and after morphological/anatomical investigators took a second look, they found decent characters that support the separate origins. So in this case, molecular phylogenetics helped to redefine a plant family, since the 'true' Flacourtiaceae group could only include those plants related to the type species. Now, the taxonomy of former Flacourtiaceae groups has been changed, and accepted by most taxonomists. For *many* similar examples, please flip through Peter Steven's Angiosperm Phylogeny Website -- http://www.mobot.org/MOBOT/Research/APweb/welcome.html . Of course, similar stories exist within the generic level.

    So far as practicality goes, the members of orchid societies don't need to do this work! Results are easily disseminated, and when taxonomy might change as a result, implications for morphological diagnoses can be well elucidated. Who would suggest using direct molecular research to identify that non-blooming Paph plant on your windowsill, just collected (illegally, maybe) in Borneo? Let it bloom first! Then, if it doesn't match other species' descriptions or photos, bring it to the attention of a specialist or two. Then, maybe it'll get described and put into a taxonomic system. Then somebody might want to do molecular work to see what species it might be related to (genetically). Just an example.

    OK again, but let's talk about forming a classification that has a key. That's the issue so far as I'm concerned. And remember, I don't object to Mex, Paph, & Phrag -- since they can be keyed out, AND they form separate evolutionary groups! (so long as you are willing to consider a monotypic genus a group)

    Come on now! Molecular phylogenetic research has, e.g., cleared up the issue of whether the Paph delenatii group (Parvisepalum, at whatever hierarchical level) is distinct from the Paph concolor group (Brachypetalum/Concoloria). Different taxonomies exist, but this research has shown that the 'parvisepalums' and 'brachys' branch off sequentially from the base of Paph, such that one subgenus or section for both would not constitute a natural group.

    And if one gets picky with your usage of the word 'study', molecular research has certainly helped us to understand floral evolution among the slippers. Given that Paphs and Phrags at the base of their respective sub-trees have infolded (and usually inflated) labella, that Mex also does, and that Cyp (for the most part) and Selen also do, one can readily infer that such floral morphologies are 'primitive' within Cypripedioideae. This has consequences when one tries to interpret the gestalt floral similarity between, say, Paph delenatii and Phrag schlimii. Cribb hypothesized parallel evolution based on pollinator similarity, but molecular phylogenetic studies suggest this (basic) similarity to have been derived from shared, primitive characteristics. The Lorifolia Phrags and the vast majority of Paphs are more evolutionarily 'advanced'. Interestingly, the phylogenetic tree strongly suggests that the evolution of fly pollination has occurred several times in parallel among the slipper orchids, from basically bee-pollinated flowers.
     
  16. Nov 30, 2006 #56

    Braem

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    Dear Victor,

    indeed, this is fun. Will reply in detail later. My internet is "kaputt" and I have to use a friend's system. So please, bear with me for a few days.

    Guido
     
  17. Nov 30, 2006 #57

    NYEric

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    Wow! Am I the only one whose head is spinning from all the big words?:crazy:
     
  18. Nov 30, 2006 #58

    Braem

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    Eric, if there are any words we use that may be confusing, please let us know. I will be glad to explain and remove blurs (in as far as I can), and I am sure that Victor will be willing to do the same.

    regards
    Guido

     
  19. Nov 30, 2006 #59

    Kyle

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    Hi Guido,

    Gestalt - I have never heard that word. Please let me know what it refers to.

    I really enjoy this thread,
    Thanks,
     
  20. Nov 30, 2006 #60

    VAAlbert

    VAAlbert

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    Agreed! Very happy to describe terms.

    From Webster's Third New International Dictionary, a gestalt is a "configuration of physical, biological, or psychological phenomena so integrated as to constitute a functional unit with properties not derivable from its parts in summation."

    In other words, a general, overall perception that can defy description by a series of explicit attributes. So, with a Phrag, maybe you can tell it is a Phrag by just looking at it, but you can't really say why.

    V.

    Best,

    Vic.
     

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