Message 2004-10-0100: Re: Phylogenetic Notation

Wed, 15 Sep 2004 09:54:06 -0700 (PDT)

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Date: Wed, 15 Sep 2004 09:54:06 -0700 (PDT)
From: [unknown]
To: Mailing List - PhyloCode <>
Cc: David Marjanovic <>
Subject: Re: Phylogenetic Notation

--- David Marjanovic <> wrote:

> From: "T. Michael Keesey" <>
> > These (and node-based clades) are already provided with shorthand
> > notations (which are also ASCII-friendly) in the current draft of
> Yes... I just like mine better. :o)

I dunno, usage of "#" for "not" is pretty nonstandard.
> > Didn't know about that usage of the "backslash".
> It's amazing how different school mathematics seems to be in differ=
> countries. I've been taught to use it in expressions like "the irra=
> numbers are the real numbers without the rational numbers", I =3D R=
 \ Q
> (written with those broadened letters).

A contraction for I =3D {x /member of/ R | x /not member of/ Q}?

While I'm at it, backslashes aren't necessarily the best method for w=
riting the
non-ASCII symbols. It occurred to me that angle brackets or quotes mi=
ght be
more legible:
I =3D {x <member of> R | x <not member of> Q}
I =3D {x =ABmember of=BB R | x =ABnot member of=BB Q}

One problem with the first style is that angle brackets are used in c=
(for original authorship of a supplanted homonym).

I'd like to emphasize that this ASCII-friendly version would only be =
for casual Internet discussion, *not* the actual definitions or in pa=

> > I don't think that's a problem, since there is clearly an operato=
> > bridging the two expressions.
> ||*Lacerta agilis* + *Youngina capensis* \ *Crocodylus niloticus*||
> ||{*Lacerta agilis* + *Youngina capensis*} \ {*Crocodylus niloticus=

"||" means "or" in C-based computer code. I see this symbol as redund=
ant and
potentially confusing, since there's no distinction between the begin=
version and the ending version.

> 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 cro=

Better, yes.

> > > Ancestor-based definition (like "*Homo sapiens* and all its
> > > descendants"):
> > > {A}
> > >         A is the ancestor. The format is straightforward becaus=
e a
> > > species or specimen cannot by itself constitute a clade if it h=
as any
> > > descendants.
> >
> > Here's where I really dislike this notation, because it looks lik=
> > "the set of A".
> OK... ||A||.

And then what do we use for species definitions? For lineages? For ot=
her types
of taxa covered in future editions of the Code?
> > [snipped]
> > > And now the big test: Can I manage to express the definition of
> > > *Ichthyornis*?
> > > {*Ichthyornis dispar* # *Struthio camelus*, *Tinamus major*, *V=
> > > 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 ques=
tion is
> > hwo far back they go. The actual prose definition is worded not s=
o much as
> > definition with a qualifying clause, but as an intersection of tw=
o clades.
> > Rendering this is not really possible in your notation or the sho=
> > proposed in PhyloCode.
> If my attempt is read as "those members of [the stem-based clade] f=
or which
> it is true that they have [all the apomorphies] homologous to those=
 in *I.
> dispar*", "for which it is true that" symbolized by "|", then it wo=

The problem here is that, in your system, "M @ A" means "the apomorph=
clade stemming from the first ancestor of A to possess character M ho=
with that in A". I would read your expression as "the clade stemming =
=66rom the
first ancestor of _I. dispar_ which is not also ancestral to _Struthi=
camelus_, _Tinamus major_, and _Vultur gryphus_ such that the clade s=
=66rom the first ancestor of _I. dispar_ to possess amphicoelous cerv=
vertebrae, etc. homologous with those characters in _I. dispar_", whi=
ch is a
bit nonsensical. "Such that the clade stemming from ... homologous wi=
th those
characters in _I. dispar_" what? Such that it exists? Of course it do=
es. But
you haven't related it in any meaningful way to the first half of the

> The
> question is now how to make the notation so unambiguous that people=
> read it the way it's supposed to be read. The "subset" symbol would=
 come in
> handy here:
> *Ichthyornis* =3D || [subset] {*I. dispar* # *S. camelus*, *T. majo=
r*, *V.
> gryphus*} | [apomorphies] @ *I. dispar*||
> Is this better?

No, because the second half is still not related to the first, and th=
e original
definition is ambiguous as to which clade is more inclusive. It's not=
question of subsets, it's a question of set intersection.
> > Illegible?
> Lengthy.


> > More legible than the mathematic symbols? Equally difficult?
> I think it's similar. It requires one to think around three more co=
> than is probably necessary.

This is why the shorthand definitions are incorporated. If all you wa=
nt to do
is discuss those types of definitions which have shorthand notations
(ancestor-based, node-based, stem-based, apomorphy-based, modified cr=
clades), you don't need to use all the set and Boolean notations. But=
 if you
want to go beyond that, there's a rigorous and powerful notation styl=
e which
the shorthand is defined by.

> Besides, if it looks too mathematical, it
> might drive some people away who might think we were all pattern cl=
adists or
> pheneticists (especially if they are already prejudiced and next to
> uninformed).

Yeah, using math in science? That's absurd!

=3D=3D=3D=3D=3D> T. Michael Keesey <>
=3D=3D=3D=3D=3D> The Dinosauricon <>
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