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Date: Tue, 14 Sep 2004 19:00:51 +0200
From: [unknown]
To: PML <phylocode@ouvaxa.cats.ohiou.edu>
Subject: Re: Phylogenetic Notation
----- Original Message ----- =46rom: "T. Michael Keesey" <mightyodinn@yahoo.com> Sent: Tuesday, September 14, 2004 12:53 AM > > At this point in history, I don't think it's a noticeable exagger= ation to > > claim that every scientist speaks English. > > Yes, but what about Latin? This seems to be a compromise to the botanists, who are still obliged= to write short diagnoses of newly described taxa in Latin... except if t= hose taxa are fossil, AFAIK. > And will definitions written in either of these always be unambiguo= us? If the registration database administrator is vigilant enough, probab= ly they will... :-} > > I'll try to retrieve the system I proposed a month or so ago (it'= s simpler, > > uses non-ASCII characters but only such that occur in iso-8859-1 "Western > > European", and is not capable of expressing the more complex of y= our > > examples), to see if I could find something about your system to = quibble > > about... :-) > > I'd be very interested to see that. Perhaps it can be instructive i= n making the > system more accessible. Here is it, updated from my post from June 15th (and another from the= 18th that seemingly didn't get through). In fact, I think all characters a= re ASCII after all. ------------------------------------------- A through G are taxa, M is an apomorphy. Parentheses indicate optiona= l additions, such as more than two specifiers. Node-based: {A(, B, C...) + D} "{}" used instead of "Clade()" because it's shorter, already = used on a few websites, language-free, and avoids confusion with the method t= o write a tree -- (A + (B + C))). It keeps definition and description apart. = The identity to the brackets used for mathematical sets is a fortunate coincidence. "+" used instead of "and" because it's shorter, in widespread= use (abstract booklet!) and language-free. Stem-based: {A(, B, C...) # D(, E, F...)} "#" used instead of "not" because it's shorter and language-f= ree; instead of ">" or "<--" because the direction of the arrow would conf= use people either way, and because "<--" is painfully ugly, unless replac= ed by a real arrow; instead of "=AC" because this (the mathematical "not" sig= n) is poorly known and poorly available on keyboards. My English teacher us= ed "#" for "opposite", probably because it's similar to the mathematical "un= equal" sign ("=3D" with one instead of two "/" through it). Its use for "num= ber" seems to be restricted to English-speaking countries and is not under= stood elsewhere. Apomorphy-based (should those be allowed): {M @ A (+ B, C...)} "@" is the chemical "in" sign (e. g. http://gaus90.chem.yale.edu/window.html), probably because it looks s= o _en_circled. Should this be deemed too little straightforward, we cou= ld spell "in" out; "in" is Latin, English, German and more, so some internationality would be retained this way. Hey, wait!!! Actually we don't need _any_ mention of "in" her= e. We could just write {M A (+ B, C...)}, couldn't we? :-) (The apomorphy itself would still have to be written in a lan= guage. Theoretically, this could be used as an argument to ban apomorphy-bas= ed definitions -- but if the apomorphy is well enough described and figu= red, _this_ shouldn't produce any problem in the real world.) One kind of qualifying clause: {[...] \ G} "\" is the mathematical "without" sign, and exists on every c= omputer keyboard. Does not work for Art. 11.9 Example 1, but for Example 2: *Lepidosauriformes* =3D {*Lacerta agilis* + *Crocodylus niloticus* \ = *Youngina capensis*}. (Should math be preferred, this could be "{*Lacerta agilis* + *Crocodylus niloticus*} \ {*Youngina capensis*}" instead; however, th= is can make it confusing to tell how many definitions there are or where it = ends.) Another kind of qualifying clause: {[...] | [condition]} "|" is the mathematical sign that is used in a similar way. L= et's see... it works for Art. 11.9 Example 1: *Pinnipedia* =3D {*Otaria by= ronia*, *Odobenus rosmarus* + *Phoca vitulina* | flippers @ *Otaria byronia*, *Odobenus rosmarus*, *Phoca vitulina*}. More examples will need to be= tested to see if this notation can become confusing. (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 wou= ld be _the very same clade_ if it were defined {*Otaria*, *Odobenus* + *Pho= ca* [your favorite terrestrial Carnivora]}.) Several conditions could be separated with ";", for example. Stem-modified crown definition (Note 9.4.1): {=A5 A # B} =A5 is the symbol for "crown-group". Totally straightforward.= It depicts a cladogram with a node that is marked by double underlining.= =3D8-) =3D8-) =3D8-) Disadvantage: Not available on German keyboards, at lea= st. Advantage: Seems to be ASCII. Perhaps this could be shortened to {A =A5 B} -- if this is no= t 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 tha= t there is nothing alive that's closer to A than to B.) Apomorphy-modified crown definition: {=A5 M @ A} Ancestor-based definition (like "*Homo sapiens* and all its descendan= ts"): {A} A is the ancestor. The format is straightforward because a sp= ecies or specimen cannot by itself constitute a clade if it has any descend= ants. Not applicable for Panbiota/Nominata/Nominanda*; its definiti= on would have to be interpreted as apomorphy-based, {life @ *Homo sapien= s*} respectively {life *Homo sapiens*}. * Jon's abstract said *Panbiota*. His talk said *Nominata*, the "name= d ones". I wonder if he meant "those that are to be named/those we will= name", which would be "nominanda". Never used so far, but node-modified crown definitions are imaginable= : {=A5 A + B} Would mean "the crown group of the clade (A + B)", implying that A is= extant and B fossil. But this type of definition would probably be indistinguishable from a stem-modified one with the same specifiers (= A internal, B external). Hmmm... it would be _exactly_ identical. Right= ? And now the big test: Can I manage to express the definition of *Ichthyornis*? {*Ichthyornis dispar* # *Struthio camelus*, *Tinamus major*, *Vultur gryphus* | amphicoelous cervical vertebrae, [rest of the list] @ *Ichthyornis dispar*} I think this works. Does it?