More on the 'cladistics' of sequences

[HJJACOBSON at AOL.COM]

In a message dated 6/6/2004 3:01:15 PM Pacific Standard Time,
rjensen at saintmarys.edu writes:

> Here is an unrooted tree:      A      C
>                          \____/
>                          /     \
>                         B      D
>
> There are five internodes and rooting at each one produces a different tree,
> hence, a different set of hypotheses about character evolution (i.e.,
> homologies and homoplasies)
>

To all those who disagree with my question let me say that I don't disagree
that different root points will suggest different character evolution. However,
in theory, there is only one root point. In practice, of course, we don't
know what it is. Therefore if changing outgroups changes the character
hypotheses, we need an objective way of selecting the outgroup. I think this is what
John is trying to say: What are your objective criteria for selecting outgroups?

I don't think that:

 "I find it much easier to include a suite of outgroup taxa
that have differing degrees of closeness to the ingroup. It can make it
easier to feel confident about the attachment of the branch leading to
the outgroup taxa, even if some of the more distantly related outgroup
taxa are hard to align with the ingroup."

I don't see "easier" as objective and I don't see how "degress of closeness"
is objective, let alone "feel confident."

"This sometimes works, sometimes doesn't - depends on what outgroup sequences
you have at your disposal."

 "Sometimes it works" come on, what is is your objective criteria?

"This idea that one would try to work out in advance of the analysis
which characters are derived by outgroup comparison seems too biased to
me."

I agree! I don't agree with John at all on this, as he will be the first to
tell you.

Herb