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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).