Hey out there:

Do any of you want to get going an extended train going on the "taxonomy" of slipper orchids (broadly defined)? Themes could include (1) nomenclature (naming rules), (2) taxonomies (how different scientists group the names or synonymize them), (3) what think about these taxonomies, (4) evolutionary research, and (5) identification technologies (e.g., DNA). My favorite topic among the above is slipper orchid evolution.

I'm also more interested in the evolution aspects and DNA tech info. I would also like to see more info on taxonomy related to habitat preference and pollinator requirements.

[/b]

Hi Rick:

Happy to know there's a kindred spirit out there.

I can provide a pollination story based on the DNA phylogeny of Cox and friends. This is the reference:

Cox, A.V., Pridgeon, A.M., Albert, V.A., & Chase, M.W. (1997) Phylogeny of the slipper orchids (Cypripedioideae: Orchidaceae): nuclear rDNA ITS sequences. - Plant Systematics and Evolution, 208: 197-223.

You can order a PDF copy at:
http://www.springerlink.com/app/home/contribution.asp?wasp=1c9ff39c562f4090a99f6b517468 2388&referrer=parent&backto=searcharticlesresults,1,4;

You can see the phylogenetic hypothesis without the detailed explanation at:
http://www.rbgkew.org.uk/ibis/slipper_taxonomy/slipper.html

If you look at the phylogeneteic tree, you'll see that the "cyp-like" flowers are primitive within the whole slipper orchid group. That goes for Selen, Cyp, and the Parvisepalum Paphs, Mexipedium, and Micropetalum Phrags. Flowers of these plants are, or are strongly thought to be, bee-pollinated. Now when we go up to the "higher" Paphs and Phrags, we see evolutionary change to green-brown colors, warts&spots&stripes, and other evidence for fly pollination. These evolutionary changes from bee to fly clearly happened in parallel in Paph and Phrag. This is very interesting from an evolutionary standpoint, because flowers rarely evolve from intricate pollinator associations with "smart" bugs (like bees) to more general ones with "stipid" bugs (like flies). Recently, a group published a nice paper on Cyp guttatum showing that it has evolved a "Paph-like" pollination strategy -- what they didn't talk about was the family tree of Cyps (from Cox & friends) that clearly shows Cyp guttatum to be evolutionarily derived ("advanced") within its lineage. So, now we have three instances of parallel evolution of "stupid" pollination from within a group of plans that had "smarter" flowers to begin with.

Cribb wrote in The Genus Paphiopedilum (the first one, anyway), that the Cyp-like flower may have evolved in parallel in the Parvis and Micros -- but this seems very much not the case -- instead, these groups show original slipper traits.

With best regards,

Beskriver

Oh, and DNA technology -- what particular aspects do you want to talk about? B.

:? Sorry, the Springer link for the PDF seems to be in error -- if you want the paper, enter the term Cypripedioideae under "search for".

For those not interested in the whole article, here is the abstract:

Phylogenetics of the slipper orchids (Cypripedioideae, Orchidaceae): Nuclear rDNA ITS sequences

Antony V. Cox1 Contact Information, Alec M. Pridgeon1, Victor A. Albert2 Contact Information and Mark W. Chase1
(1) Department of Molecular Systematics, Jodrell Laboratory, Royal Botanic Gardens, TW9 3DS Kew, Richmond, Surrey, United Kingdom
(2) The Lewis B. & Dorothy Cullman Program for Molecular Systematics Studies, The New York Botanical Garden, 10458-5126 Bronx, New York, USA

Received: 18 May 1996 Revised: 5 September 1996 Accepted: 5 September 1996
Abstract Cypripedioideae (Orchidaceae) have been the subject of numerous taxonomic treatments with conflicting interpretations of relationships among the five genera and the 150–170 species. We have produced nuclear ribosomal ITS nucleotide sequences for nearly 100 slipper orchid species and used parsimony analysis to investigate their relationships. Our results demonstrate that each genus, as currently circumscribed, is monophyletic (Mexipedium andSelenipedium being represented by a single taxon). LikerbcL data, ITS sequences placeMexipedium sister toPhragmipedium. Relationships at the sectional level inPaphiopedilum are largely as described byCribb. However, the division ofPaphiopedilum into subgg.Brachypetalum andPaphiopedilum is not supported; subg.Brachypetalum is paraphyletic to subg.Paphiopedilum. Phragmipedium species are divided into the same three major clades as in the taxonomic scheme ofMcCook. The plicate-leaved genera,Cypripedium andSelenipedium, are successive sister groups to the rest of the subfamily, confirming generally held opinions that they display plesiomorphic characters compared to the conduplicate-leaved genera. A survey of karyotypes in the context of the ITS tree reveals a general trend toward increased chromosome number, probably brought about by centric fission. These data also accord with a previously suggested biogeographic hypothesis of a widespread Northern Hemisphere distribution, followed by range fragmentation due to Miocene cooling.

This is all fascinating to me. I was thinking the other day how similar to Cyps. my Mexipedium appears and found myself wondering about geographic distibution and pollinators and such.

Thanks.

Hi Paphgirl -

Yeah, Mexipedium is an interesting case also for geography. The Cox and friends DNA paper puts it as the sister plant to Phrag; Paph is then the sister lineage to these. Since Mex comes from Central(North) America and the majority of Phrags are S. American, the simplest inference is that non-Selen/Cyp slippers were once widespread in what today would be North America and Eurasia -- the majority just dying out when the Earth cooled and dried at least 15 millions years ago. The ranges of "higher" Paphs and Phrags would then have expanded toward the present-day tropics. Whether or not the Paph/Mex/Phrag lineage persisted over the Bering Land Bridge or across the North Atlantic Land Bridge is a matter of timing. The Bering Bridge was broken on and off up until a few million years ago, whereas the North Atlantic Bridge probably closed around 40 million years ago. The Cox & friends paper favors the latter idea. Best from B.

Very cool B.

You jumped way ahead of me with your posts, and I haven't had time to look things up.

Concerning bee-primitive and flie-advanced paradox. I don't know if bees are any smarter than flies, but they are evolutionarily much farther along at obtaining food rewards from plants than flies. Developing a bee fraud orchid may be easier than developing a flie fraud orchid for that reason.

Especially given that some of the flie pollinators are predatory (hover flies with good visual acuity skills) that are looking for aphid targets. How would you progress to that, and from what???

It's a little easier to see the case for stinky Bulbos with your basic carion fly.

This is fun

...puts it as the sister plant to Phrag; Paph is then the sister lineage to these. Since Mex comes from Central(North) America and the majority of Phrags are S. American, the simplest inference is that non-Selen/Cyp slippers were once widespread in what today would be North America and Eurasia.../b]

(I know NOTHING about genetics) but just based on look and growth habit (clumpiness) I would have thought Mexipedium closer to Cypripedium than Phragmipedium. Does geographical location just trump this?

Sorry for such ignorant questions. Hoping to understand taxonomy better. :)

I don't think you can get to excited about growth habit and relationship between Cyps and Phrags. Clumping vs rhizome spreading is probably more of a function of habitat adaptation.

Actually a big split in growth habit between phrags/paphs/mexis and Cyps is that as far as I know all cyps are deciduous, and leaf structure is considerably different (usually plicate and hairy). So from a plant habit basis mexis are not that much more cyp like than kovachii, or schlimii.

I think there is some species of cyp in southern China and northern Mexico that have overlapping ranges with paph/phrag/mexi???

Can anyone verifie that?

RickL, I heard Cribb speak at this year's Paph forum and I remember him saying that there was overlap in China between a cyp species and a paph, although I can't remember either specific species...

As for taxonomy in general, I am in search of a definitive monograph of Paphiopedilum. There are too many conflicts at the moment for my tastes and I am busy amassing reference material in the hopes that I can clarify some of the confusion.

--Stephen

Hi all -

First pollination: bee-flowered plants (except those buzz-pollinated) are usually "high fidelity" with respect to their pollinators. The bee-pollinated slippers are probably more so, given size constraints through the lateral labellum exits. Fly pollination in Paph/Phrag is probably much less species or size specific re: pollinators.

As for plant habit, rhizomatous growth as in Mex is also known from the "primitive" Parvis -- would'nt think too much more from there. There are in fact LOTS of vegetative characteristics that link Paph/Phrag/Mex in any case.

Regarding co-occurrence with Cyp species, Cyp irapeanum from Central America overlaps in range with some Phrags (e.g., P. exstaminodium) and Mex. And definitely, some Cyps overlap with Paphs in China. But again, these range co-occurrences have nothing to do with phylogenetic history.

As to definitive slipper taxonomy, that will always be a subjective venture, since one man's species can be another's variety. That is taxonomy; nomenclature is what names have been assigned, by whom, and when. Taxonomies must follow proper nomenclature. And I strongly belive that any taxonomy should also follow phylogeny.

Best from Beskriver.

Ouch to many big words.... Interesting read I must say, however do we trust the taxonomists?

Hi again -

I think "trust" is not really the issue; after all, as I said, one man's species is another's variety. Variation out there in nature should be described, via the rules, but that doesn't mean that everyone has to accept a certain taxonomy. Remember, nomenclature is different from taxonomy. Take this example:

Paph jackii was described by Hua in 1995; Paph hiepii by Averyanov in 1998; Paph malipoense var. hiepii in by Cribb 1998; and Paph jackii var. hiepii by Koopowitz in 2000. ALL OF THESE are validly published according to the rules of nomeclature. THE DIFFERENCE is ONLY in the accepted taxonomy. Averyanov decided Paph hiepii should be a distinct entity when it was discovered, so he gave it species status. In terms of "lumping", Koopowitz took middle ground while Cribb went for the big bang and sunk both hiepii and jackii into malipoense.

One issue at hand is what a species of Paph really is. There is an ENTIRE LITERATURE out there in the evolutionary and taxonomic community arguing over definitions. My own preference is to recognize diversity in nature with species names. I don't think that most species authors have done great disservice in this area, however, all such authors should (in the best of worlds) be familiar with the full range of variation within the genus and have access to herbarium specimens when necessary to avoid double-naming. Still, not all taxonomists have such access, and hence in works such as Slipper Orchids of Vietnam, we see a number of synonymizations of names. But I for one would like to see JPGs (at least!) of the herbarium specimens -- not just drawings and descriptions -- before I would make synonymies. And it won't help only to look at living material -- too much has already been described dating back over 100 years, so dead specimens simply have to be looked at to see whether a new ID could apply.

Not to mention that taxonomists must show that names they use have been validly described -- for example, I don't see that "Paph crossii" is based on a proper type specimen, so it should clearly be "nomen nudum" (= naked name) just as Cribb has specified.

IN SUM, trust an evolutionary tree more than anything else; names are there to help us describe diversity, although nature has left us Paph diversity that is not always easy to place in packages. Placing given individual plants on a phylogenetic tree -- as could be possible using new DNA sequences along with those available on the public database GenBank -- should provide a means for collectors to "diagnose" what they have according to what other plants an individual is related to. Of course, sequencing all individuals is not very practical, so maybe just seeking a sample of the broadest possible diversity could help out a lot.

Having a fun chat, B.

That was excellent !!!

I enjoyed reading it very much - Can we do it again? :clap:

Thanks heaps for the mono

Cheers
Stephan

OK! Are you ready for some more chat? Next topics are on the table...

Best wishes, B.

I'd like to work on the pollinator issue some more. Right now we are splitting between bees and flies, but I know with flies there has been specific mention of at least 2 (possibly three) distinct groups of flies, and these are predatory rather than carion eaters.

I don't know if the "sweat flies" mentioned as the pollinator for sanderianum falls into the category of the serpheid (spelling???) flies listed as the primary pollinator for Roth type flowers. I also have not seen any documentation at all on phrag pollinators.

I agree with the fidelity issue with the bees, which is why I think that those relationships are "older" (not to imply primitive or simple) than the fly pollination strategy of the slippers. There a lots of be species of bees, with just a variable social, food gathering strategies as the orchids trying to trick them, so any ideas/knowledge on any specific bee/slipper orchid interactions.

Actually after doing a little checking. Syrphid flies are a big group that include the hover flies and sweat flies. In general the adult flies lay their eggs amongst aphids and the larvae eat aphids. The various species as adults eat pollen, nectar, or sweat (and or other bodily secretions).

It also seems that syrphid flies are bee and wasp mimics, which could indicate that they are evolutionarily more recent than bees and wasps.

There seems to be allot of diversity in the group that could be capitalized on by a diverse group of orchids.

True enough re: syrphid flies diversity and mimicking habits. Fly attraction to phylogenetically "advanced" Paphs and Phrags still lower-fidelity than bee-pollination. For "higher" Phrags especially, flower morphology is not diverse enough in my opinion to show much pollinator specificity. Fly-pollinated "higher" Paphs that are sympatric must have pollinator specificity most of the time, but I don't think that many such species are truly sympatric in the first place (REALLY LIVING in the same places, not just overlapping in geographic range). My impression is that such Paph species are mostly allopatric, spatially segregated either by crow-fly distance or altitude. But, then again, I have not done much field work.

The issue with phrags may be even messier with all the adaptations that seem to be occuring for "spontaneous" pollination, and species like exstaminodium.

Maybe the pollination link in phrags is breaking down.

Well, let's face it -- it's still all a matter of taxonomy! How many Phrag species are there? Depends on your point of view.

Maybe we could start discussing taxonomy! Species concepts! Is Paph hiepii a species or a variety? What about Phrag dallesandroi?

Lots to talk about.

And, didn't somebody want to talk about DNA -----------??

Best wishes from Beskriver

[ Is Paph hiepii a species or a variety?

Yes please talk about that. I bought a plant in the spring labled as P hiepii and I would like to know if its a species or a variety of jackii. Mine is far from blooming size. And I don't own malpoinse or jackii to compare the foliage.

Kyle

mannnnnnnnnn you have a hiepii in Canada? Growing orchids in the US sure can be annoying sometimes. Braem and Cribb refer to the plant as P. malipoense var. hiepii. The leaves of var. hiepii are light green as opposed to dark green in var. malipoense. Also, the petals are narrower and hooked at the apex. The distinguishing feature that makes me lean towards calling it a species is the pouch. It is much narrower than var. malipoense and has a distinct hook pointing toward the staminode. It is the only plant within the genus that has such a hook.

As for Phrag dallesandroi, I am inclined to call it a species. The growth habit, drooping petals, and differences in the staminodal shield seem to be more than enough to warrant classification at the species level.

--Stephen

I have my doubts.
The plant was pretty cheap. I think it is probably malpoinsie (sp?). One day I'll buy a mal and compare the leaf color. This ones leaves are pretty light in color....

Here's a pic of my malipoense for comparison (it's in a 9cm pot):

http://i8.photobucket.com/albums/a25/silence882/malipoenseAug05.jpg

If you have or could take a pic of the hiepii, I would love to see it.

--Stephen

I'll take a picture tonight. The plant only came out of flask in june. So it is only growing its first post flask leaf and doesn't have very much mottling yet. I will post a pic regardless.

Kyle

The distinguishing feature that makes me lean towards calling it a species is the pouch. It is much narrower than var. malipoense and has a distinct hook pointing toward the staminode. It is the only plant within the genus that has such a hook.

Take a look at pic of what has been described as Paph globulosum Z. J. Liu & S. C. Chen (2002), scanned from the original description and posted on Tanaka's site. Note also the extremely large staminodium. http://www.orchid.or.jp/orchid/people/tanaka/orchid/org/shinshu/enshinshu33.html

It is of course possible that the lips of globulosum and hiepii are abnormal, but Averyonov probably saw more than one plant in flower at discovery. I should also add that some photos i have seen of "hiepii" fit the characteristics of jackii far better (see Tanaka's site for example! -- http://www.orchid.or.jp/orchid/people/tanaka/orchid/org/newpaph1.html). Note also that leaf undersides of jackii vary from pure green to purple-flushed. Also, jackii does not seem to produce stolons, by which maliopense often spreads with in nature.

In addition, I am surprised to see that "hiepii" is being sold legally in Canada...more likely a malipoense, esp. if dark purple on leaf undersides and bought from a "reputable" dealer...

As for Phrag dallesandroi, I am inclined to call it a species. The growth habit, drooping petals, and differences in the staminodal shield seem to be more than enough to warrant classification at the species level.


What is this? http://www.phragweb.info/phragmipedium/species/photos/display_photo_phrag.asp?photo_id=206&phrag_name=besseae

And this? http://www.phragweb.info/phragmipedium/species/photos/display_photo_phrag.asp?photo_id=205&phrag_name=besseae

The globulosum looks interesting. The staminode is so unique that I would say it would have to be a species, although I would like to see a picture of the flower itself. As for the picture of the var. hiepii, I agree that it looks very much like a var. jackii to me. I would need to see a side view showing the apex of the pouch to make a judgment on the identity. In Braem's 2003 monograph, there is a picture of var. hiepii that clearly shows the laterally compressed lip with the hooked apex.

As for the Phrags, from the staminodal shield morphology, I would say they are both probably besseae. I wouldn't say that for sure though (especially about the second pic) without being able to examine the plants themselves.

--Stephen

OK, time for Devil's Advocate --- :evil:

What makes one stamindode "different" from another? Shape, color, size? Does one in fact throw up one's arms and say "I believe!", when the variation in fact may be nothing more than quantitative?

And lips -- what lip characters warrant calling something a species versus a variety? Shape, color, size? Are these aspects of staminodia and pouches actually functional or just quantitative?

Well, we get down to that old species definition debate, which is a real pain in the butt for all botanists. Plants just don't behave like most animals, which observe the "Biological Species Concept", i.e., non-interbreeding. Get a some "besseae" together with a few "dallesandroi" in nature, have a couple of hummingbirds buzz around and do their thing, and then let's see what we get F1, F2, F3.... :evil:

In addition, I am surprised to see that "hiepii" is being sold legally in Canada...more likely a malipoense, esp. if dark purple on leaf undersides and bought from a "reputable" dealer...

Me to, I'm not very optimistic. I had some money burning a hole in my pocket at the time, so I bought a bunch of flasks from a guy whom I had never bought from. I don't have malipoense or jackii, so at the very least I have one now. The plant was in flask, so I will have to wait a bit for it to get 'adult' leaves. Right now, it doesn't look like much.

Kyle

Hi -

Back on the taxonomy train -- anyone interested in a new subtopic?

Best from Beskriver

One of the things we finally realized in vertebrate DNA work is that when one compares various DNA studies which include multiple genetic region to some of the earlier work based on a limited slice of the genome, some of the trees generated are very different. I see the plant work developing in the same way and it will take some time to have a really good consensus tree for Paphs.
I was interested in the fly vs bee discussion. There are genera of flies (Syrphids sp??) that are specialized bee like flower feeders and I have seen them use orchid flowers. In Alaska I have seen Cyps with many flies around them but no bees. Bees are not as common in the far north as flies. With a circumboreal distribution, Cyps may have come to utilize flies because bees were uncommon.
I welcome Beskrivers suggestion for this type of discussion. Very interesting and nice to have a person available with a good understanding of it. Thanks Besk
Dean

Just wanted to add a quick snippet of info to the earlier discussion of pollinators....

JT Atwood documents the pollination of P. rothschildianum in Borneo by syrphid flies in his article:
Title: Pollination of Paphiopedilum rothschildianum : Brood-site deception.
Source: NATL. GEOGR. RES. Vol. 1, no. 2, pp. 247-254. 1985

--Stephen

I think I saw that reference in Cribbs book on Slippers Orchids of Borneo. Can you get it?

I have a copy that I got from the library a few days ago, actually. If you'd like a PDF of it, just shoot me a PM with your e-mail.

--Stephen

Hi out there --

ANYONE FOR DNA TALK?

Meanwhile some additional references relevant to slipper pollination/reproduction.

Best from Besk

__________________________________

Banziger H, Sun HQ, Luo YB
Pollination of a slippery lady slipper orchid in South-West China: Cypripedium guttatum (Orchidaceae)
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY 148 (3): 251-264 JUL 2005

Schiestl FP
On the success of a swindle: pollination by deception in orchids
NATURWISSENSCHAFTEN 92 (6): 255-264 JUN 2005

Tremblay RL, Ackerman JD, Zimmerman JK, et al.
Variation in sexual reproduction in orchids and its evolutionary consequences: a spasmodic journey to diversification
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 84 (1): 1-54 JAN 2005

Sugiura N, Goubara M, Kitamura K, et al.
Bumblebee pollination of Cypripedium macranthos var. rebunense (Orchidaceae); a possible case of floral mimicry of Pedicularis schistostegia (Orobanchaceae)
PLANT SYSTEMATICS AND EVOLUTION 235 (1-4): 189-195 2002

Lipow SR, Bernhardt P, Vance N
Comparative rates of pollination and fruit set in widely separated populations of a rare orchid (Cypripedium fasciculatum)
INTERNATIONAL JOURNAL OF PLANT SCIENCES 163 (5): 775-782 SEP 2002

Sugiura N, Fujie T, Inoue K, et al.
Flowering phenology, pollination, and fruit set of Cypripedium macranthos var. rebunense, a threatened lady's slipper (Orchidaceae)
JOURNAL OF PLANT RESEARCH 114 (1114): 171-178 JUN 2001

Erneberg M, Holm B
Bee size and pollen transfer in Cypripedium calceolus (Orchidaceae)
NORDIC JOURNAL OF BOTANY 19 (3): 363-367 1999

Primack R, Stacy E
Cost of reproduction in the pink lady's slipper orchid, (Cypripedium acaule, Orchidaceae): An eleven-year experimental study of three populations
AMERICAN JOURNAL OF BOTANY 85 (12): 1672-1679 DEC 1998

O'Connell LM, Johnston MO
Male and female pollination success in a deceptive orchid, a selection study
ECOLOGY 79 (4): 1246-1260 JUN 1998

Banziger H
The mesmerizing wart: The pollination strategy of epiphytic lady slipper orchid Paphiopedilum villosum (Lindl) Stein (Orchidaceae)
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY 121 (1): 59-90 MAY 1996

Is the thread dead??

A couple of dumb qs!
1 - What's divergence?
2 - What's diversification? Are the two related?

Regards Mang

Divergence = amount of change, let's say between 2 species. The term is often applied to the difference in DNA sequence. Chimps and humans, for example are only 1% divergent in their entire genomes, and any random numan is 0.1% divergent from another at the DNA level.

Diversification = the process of diversifying into, say, lots of different morphologies, e.g., by the influence of natural selection. Diversification is the process that underlies biodiversity.

Sorry -- for 'numan', I meant human!

Thanks Besk!

Sorry to pester you again with another dumb q
- if I caught the drift correctly, can I say that in the process of diversifying a species may diverge enough to become a new species?

Regards Mang

Thought I'd alert interested folks to a train on Paph hermannii under Paphiopedilum discussion.......

Besk

What do folks out there think of Paph intaniae? A natural (or intentional) "hybrid"? Or...?

http://www.orchid.or.jp/orchid/people/tanaka/orchid/org/shinshu/newpaph201.html

Best wishes, B

What makes anitum different from adductum?

Check out this new phylogenetic tree based on a new alignment of the DNA sequences used by Cox et al. - note the position of Mexipedium as sister to Paph instead of Phrag!

http://img109.imagevenue.com/img.php?loc=loc38&image=3a0_newtree.jpg

Hmmm, that's interesting. Are they going to add other species as available? Seems like there are a lot of missing species. Then again, I know nothing of the research being done.

Well, there are more plants sequenced for this particular piece of DNA, but the Mex placement is particular to this new alignment of the sequences. This placement can of course change in different alignments. I can't say about relationships among the other species, however, as more species are added and new alignments are tried. What we really need is new DNA data that is variable enough to resolve all of the 'combs' in this tree, not to mention bolster the position of Mex as first cousin to Phrag or Paph. I am personally comfortable with either placement of Mex, or even if Mex were first cousin to Paph+Phrag together! Mex has a very odd combination of traits, which led Albert and Chase to assign the new genus in the first place.

B.

I should have been clearer.
I just wondered where/how the missing species would fit in? For example, besseae and schlimii are linked, but no fishceri, has that just not been sequenced yet? Same for rothschildianum and adductum. What about anitum, I would think it would fit in there also.

Maybe though, I am thinking one thing (family relations) and this (DNA) should be thought of all together differently? Or, is the DNA evidence/grouping grounds for changing taxonomic groupings?

I'm not sure I am phrasing this correctly...sorry!

Think like a family tree!

Yeah, I am, that's what I thought too, but what of the missing species? I guess that's where I'm getting caught up. I'd think that anitum and adductum would be closely linked, but no anitum even listed. :confused:

Someone's gotta sequence an anitum first, then it could be added to the data set.

OKAY!
That's what I was wondering!
Thanks!

Besk, out of curiosity, did you make the graphic? Where did the data matrices come from? If you don't mind the pestering, how would I go about getting the sequences of each species? and then confirming they are from the same location? Cox lists EMBL acc. no., but I have no idea what that means...

--Stephen

Here's the data! Yes, the graphic is mine. Sequences can be downloaded from GenBank, National Center for Biological Information (NCBI) at:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Display&DB=nucleotide

All sequences in EMBL are mirrored at NCBI.

At the field where it says 'Search Nuceotide....for __________' -- input the phrase --> Cyprpedioideae internal

You will then get 183 records spread over 10 pages. The data below does not include all of these sequences. Note also that not all sequences that get input into GenBank are of equal quality, since they can come from different experiments at different times and from different labs.

If you want the sequences, tell it to show 200, display FASTA, send to text. Then copy and paste. You can then enter the pasted text into an alignment program such as Clustal, http://align.genome.jp/ .

After pasting into the box, click DNA instead of protein, and hit execute. This is a crash course, and not a very accurate one. The alignment you get is nowhere near as good as the one below, which required many further adjustments. Make sure you know that the data below is already aligned, and that ???? symbols = missing data or gaps inserted into the sequences as part of the aligning process. The data matrix is set up to be run by the program Nona, http://www.zmuc.dk/public/phylogeny/Nona-PeeWee/. See www.cladistics.com for the shell Winclada, which permits nice graphic visualization and saving possibilities. Last, the matrix below may not be the one that made the consensus tree shown previously since I have several and the alignment is a couple of years old..... Can't give all the details, but you asked, so here it is!

All best!

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

I was close to following the discussion until I got to the last few feet of the last message! There appear to be a few questions raised but that's as far as I could decipher... :D

I expected to see "The owls are watching" embedded in there. 8)

Hey, I see that the giant data set is now deleted for some reason....

Besk, thanks for the help. I got the raw data and will now spend long periods of time when I should be working figuring out how to use all these programs. Do you have any experience with TNT? The website that had the other programs had a readme saying that it was considered to be the best atm (though it's not free like all the others). I am interested to see what trees the programs will come up with. Would excessive computing power help in generating even more accurate trees? I've got a CS grad student friend with potential access to a supercomputing center....

--Stephen

Hi Stephen,

In fact, I used TNT but didn't want to confuse you with a non-freeware application. And no, TNT is so advanced that I was able to solve a 500-sequence, 1428 site data matrix for DEFINITE most parsimonious trees in < 45 seconds on my LAPTOP. I ran the same data on a SPARC back in 1992 for ca. 3 months but got longer trees. Others ran the same data set for over 1 CPU year, and still got longer trees! There is absolutely no substitute for good programming. With the right search strategy, one could use NONA on the 500-seq matrix to get optimal trees in 2-3 weeks, but why bother if you have TNT. Other tree-building methods are also possible, but with prior assumptions about evolutionary processes.

Best from Besk

all the cool stuff.

But one of the problems I keep hitting my head against is the issue of nomenclature including its use for hybrid registration purposes.
So my questions:

Does anyone have access to the International Registrar's "accepted' names for Paphiopedilum species.

Is there an updated comparative list like the one that is placed at the Antec site that includes all the new species vis a vis all the recent taxonomical treatments? If not, shouldnt we build one as a reference tool?

¿Platceme fraters et sorores?

Welcome Jose,
We have a forum member who is working on compiling a lot of this sort of information. I don't know if your request is one he'll include, but he's certainly doing a very comprehensive job so far.

You can see his work here:
http://www.slipperorchids.info/

Wouza!!!! :Party: :Party: :Party:

There is only one thing that I want that seems to be missing ....
And that is the Registrar 's list of 'approved/accepted names....


:Party: :Party: :Party:

Working on it!
I've got a preliminary list compiled, but I have to get in contact with the RHS offices to see about the ambiguous taxa.

I would like to propose that rather than referring to the 'acceptable 'species' from now on, everyone refer to them as 'acceptable taxa.' That way if they allow a variety to be used for registration purposes(e.g., malipoense var. jackii), 'taxa' will still be appropriate (whereas 'species' would not).

Now, to force everyone to speak as I do... Anyone have a mind control gun I could borrow? Anyone? Please? fine then

--Stephen

Sounds right on to me!

(Taxa....taxa....taxa....)

practicing....:)

Taxa and Taxon o man they sound so much like T...A... X :shock: :shock: :shock:

I will try...I will try :roll:

Hello again, I contacted the RHS and they were very helpful in giving me the data for what taxa are acceptable for registration. I am attaching the list here and hope to have a new page up with notes and synonyms shortly. This only takes into account the 'species' at the moment, but I should be able to deal with natural hybrids soon. The only taxon that is still ambiguous is viniferum, which hopefully I can get an answer to soon.

--Stephen

acmodontum
adductum
anitum
appletonianum
argus
armeniacum
barbatum
barbigerum
barbigerum {var} lockianum
bellatulum
bougainvilleanum
boxallii
bullenianum
callosum
cerveranum
charlesworthii
ciliolare
concolor
curtisii
dayanum
delenatii
dianthum
dixlerianum
druryi
emersonii
exul
fairrieanum
fowliei
gigantifolium
glanduliferum
glaucophyllum
godefroyae
gratrixianum
hangianum
haynaldianum
helenae
hennisianum
henryanum
hirsutissimum
hookerae
insigne
jackii
javanicum
kolopakingii
lawrenceanum
liemianum
lowii
lynniae
malipoense
mastersianum
micranthum
moquetteanum
niveum
ooii
papuanum
parishii
philippinense
platyphyllum
primulinum
purpuratum
randsii
richardianum
rothschildianum
sanderianum
sangii
schoseri
species
spicerianum
stonei
sukhakulii
supardii
superbiens
tigrinum
tonsum
tranlienianum
urbanianum
venustum
victoria-mariae
victoria-regina
vietnamense
villosum
violascens
virens
wardii
wenshanense
wentworthianum
wilhelminiae
wolterianum

Thanks a lot for your work. :clap: :clap: :clap:

Finally got the registration page up:

http://www.slipperorchids.info/registration.html

--Stephen

Great information, Stephen. You will have a fantastic site when you are finished.

Thanks ......