Wed, 15 Sep 2004 18:21:52 +0200

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Date: **Wed, 15 Sep 2004 18:21:52 +0200**

From: **[unknown]**

To: **PML <phylocode@ouvaxa.cats.ohiou.edu>**

Subject: **Re: Phylogenetic Notation**

----- Original Message ----- =46rom: "T. Michael Keesey" <mightyodinn@yahoo.com> Sent: Wednesday, September 15, 2004 9:31 AM > > Stem-based: > > {A(, B, C...) # D(, E, F...)} > [snipped] > > Apomorphy-based (should those be allowed): > > {M @ A (+ B, C...)} > [snipped] > > These (and node-based clades) are already provided with shorthand notations > (which are also ASCII-friendly) in the current draft of PhyloCode. Yes... I just like mine better. :o) > > One kind of qualifying clause: > > {[...] \ G} > > "\" is the mathematical "without" sign, and exists on eve= ry computer > > keyboard. Does not work for Art. 11.9 Example 1, but for Example = 2: > > *Lepidosauriformes* =3D {*Lacerta agilis* + *Crocodylus niloticus= * *Youngina > > capensis*}. > > _C. niloticus_ and _Y. capensis_ should be switched there, right? <shock> Yes! > Didn't know about that usage of the "backslash". It's amazing how different school mathematics seems to be in differen= t countries. I've been taught to use it in expressions like "the irrati= onal numbers are the real numbers without the rational numbers", I =3D R \= Q (written with those broadened letters). > > (Should math be preferred, this could be "{*Lacerta agili= s* + > > *Crocodylus niloticus*} \ {*Youngina capensis*}" instead; however= , this can > > make it confusing to tell how many definitions there are or where= it ends.) > > I don't think that's a problem, since there is clearly an operator bridging the > two expressions. ||*Lacerta agilis* + *Youngina capensis* \ *Crocodylus niloticus*|| ||{*Lacerta agilis* + *Youngina capensis*} \ {*Crocodylus niloticus*}= || Problem solved, I think. Hmmm... perhaps the best way is: ||{*Lacerta agilis* + *Youngina capensis*} \ *Crocodylus niloticus*|| which avoids the impression of a set with only one element (the croc)= . > > Another kind of qualifying clause: > > {[...] | [condition]} > > "|" is the mathematical sign that is used in a similar wa= y. Let's > > see... it works for Art. 11.9 Example 1: *Pinnipedia* =3D {*Otari= a byronia*, > > *Odobenus rosmarus* + *Phoca vitulina* | flippers @ *Otaria byron= ia*, > > *Odobenus rosmarus*, *Phoca vitulina*}. More examples will need t= o be tested > > to see if this notation can become confusing. > > "|" is usually translated orally to "such that" or "where". But it = seems to me > what you really want here is a conditional, usually written as an a= rrow and > orally translated as "if X, then Y", It's true, I wanted to make an "if" sign of it, which it isn't. > > (Another question is if this is needed at all, even if > > apomorphy-based definitions will be allowed. For example, despite= the > > emphasis on the apomorphy, *Pinnipedia* is a crown-group here; it= would be > > _the very same clade_ if it were defined {*Otaria*, *Odobenus* + = *Phoca* > > [your favorite terrestrial Carnivora]}.) > > No, it could, in theory, still be a crown clade not including any o= ther extant > carnivorans ("fissipeds") AND have an ancestor that did not possess flippers. True. > > Stem-modified crown definition (Note 9.4.1): > > {=A5 A # B} > > =A5 is the symbol for "crown-group". Totally straightforw= ard. It > > depicts a cladogram with a node that is marked by double underlin= ing. > > =3D8-) =3D8-) =3D8-) > > Hehe ... international traders might disagree. Considering how often the dollar sign is used in programming... > > Perhaps this could be shortened to {A =A5 B} -- if this i= s not too > > confusing (A is the internal, B is the external specifier). > > (I have only just noticed that such definitions, too, can > > self-destruct, namely if A is extinct; then there's a possibility= that there > > is nothing alive that's closer to A than to B.) > > Good point, although I don't think there's anything wrong with self-destructing > names. (Nor do you, judging from your abstract.) I just like jumping off the topic. :o) > > Ancestor-based definition (like "*Homo sapiens* and all its descendants"): > > {A} > > A is the ancestor. The format is straightforward because = a species > > or specimen cannot by itself constitute a clade if it has any descendants. > > Here's where I really dislike this notation, because it looks like > "the set of A". OK... ||A||. > [snipped] > > And now the big test: Can I manage to express the definition of > > *Ichthyornis*? > > {*Ichthyornis dispar* # *Struthio camelus*, *Tinamus major*, *Vul= tur > > gryphus* | amphicoelous cervical vertebrae, [rest of the list] @ > > *Ichthyornis dispar*} > > I think this works. Does it? > > Nope. We know that the characters appear in _I. dispar_; the questi= on is hwo > far back they go. The actual prose definition is worded not so much= as a > definition with a qualifying clause, but as an intersection of two = clades. > Rendering this is not really possible in your notation or the short= hand > proposed in PhyloCode. If my attempt is read as "those members of [the stem-based clade] for= which it is true that they have [all the apomorphies] homologous to those i= n *I. dispar*", "for which it is true that" symbolized by "|", then it work= s. The question is now how to make the notation so unambiguous that people w= ould read it the way it's supposed to be read. The "subset" symbol would c= ome in handy here: *Ichthyornis* =3D || [subset] {*I. dispar* # *S. camelus*, *T. major*= , *V. gryphus*} | [apomorphies] @ *I. dispar*|| Is this better? > Illegible? Lengthy. > More legible than the mathematic symbols? Equally difficult? I think it's similar. It requires one to think around three more corn= ers than is probably necessary. -- Besides, if it looks too mathematical,= it might drive some people away who might think we were all pattern clad= ists or pheneticists (especially if they are already prejudiced and next to uninformed).

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