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Re: How truncation works, and how ranks don't work was Re: Sauropodz r kewl



On Thu, Apr 19, 2012 at 7:11 AM, David Marjanovic
<david.marjanovic@gmx.at> wrote:
> Am 18.04.2012 15:53, schrieb Robert Schenck:
>
>>  On Wed, Apr 18, 2012 at 9:33 AM, Anthony Docimo <keenir@hotmail.com>
>>  wrote:
snip
> What I do is press Ctrl+U, which shows the source text of the e-mail in a
> new window.

I'm just going to pretend that you cast some kind of conjuring spell to do this.
(but seriously thanks for the informative explanation).

snip
>
>> > all the extant organisms as closely related to the tuatara as mice
>> > are related to muskrats
>>
>>  In a way we can do that, we can build a phylogenetic tree with
>>  quantified branch lengths, calculate the length from mice to
>>  muskrats, get a number, and then find all taxa at the same difference
>>  from the tuatara. Now, given two researchers, they'll both produce
>>  trees with different branch lengths and thus get different answers.
>>  Hell given two researchers you'll probably get two different tree
>>  topologies too!
>
>
> And what do your branch lengths represent? The number of evolutionary
> changes? That depends (to varying degrees) on the dataset you used even if
> you used the same methods to calculate the tree.

Well, it's kinda a silly exercise to begin with, but it seems
reasonable. At least, insofar as your dataset and tree is valid, the
conclusions would be valid. And it'd be a strange person probably who
was able to examine mice and muskrats at the same level of detail as
lizards and tuataras (in order to produce the dataset in the first
place).

>The age of the branch?
> There we get into all the trouble of divergence-dating methods.

What do you see as the troubles with divergence-dating? (not
pretending it's perfect). Also for the purposes of our imaginary
exercise, I think you'd want character change, not time. Of course
combing the two lets us talk about changes in evolutionary rates, but
that's a different matter.

snip
>
> Not "we have trouble", but "the category of subspecies has been defined in
> several different ways, few of which are ever actually used, and some
> species concepts make subspecies impossible...".
snip

Well, if you want to get all accurate, sure.


>
>
> Yep, that was the idea. It would cause enormous upheaval if implemented, and
> it would almost always assign identical ranks to several nested taxa*
snip
Interesting point, something like a Family Rank, nested within a
Family Rank, something for the philosophers to ponder (a puzzle
wrapped up in an enigma).


-- 
Robert J. Schenck
Kingsborough Community College
Physical Sciences Department
S332 ph# 718-368-5792
Follow Me on Twitter: @Schenck
KCC Class Schedule on Google Calendar: http://tinyurl.com/mqwlcy