More on the 'cladistics' of sequences

[John Grehan]

At 08:35 PM 6/8/04 +0200, pierre deleporte wrote:

>I think that using several outgroups at the same time is a partial answer.
>Different outgroup species will have different character states for the
>same character. Hence you can't always decide for sure which is the
>correct plesiomorphioc state (unlike what is suggested by John Grehan's
>method as far as I understand it), you can have one, or SEVERAL putative
>symplesiomorphic states for some characters. Anyway if all your outgroups
>root in the same place, the congruence criterion optimizing the topology
>and rooting for all characters will have done the trick.

I am not sure about the need for several outgroups if one chooses a
sufficiently broad single outgroup. Thus for the orangutan-human
synapomorphies the context I am looking at is ALL other primate species
collectively and that is quite a lot of species. Most of the characters
stand up pretty well in that regard, and even those of lesser distribution
may be supportable (e.g. lack of ischial callosities which is unique to
orangutans and humans among Old World monkeys and the apes could be
reasonably treated as an apomorphy rather than as a plesiomorphy inherited
all the way from the split with New World monkeys which lack the
callosities). This is just an observation, to necessarily a criticism of
using several outgroups. Similarly, in examining the phylogenetic
relationships of a single genus of ghost moths comprising about 12 species
I am using the entire family as the outgroup. The family comprises 500
species and while I have not looked at every one I have at least endeavored
to look at most, and eventually all, genera.

One thing I have noticed said about morphological synapomorphies is that
they are either difficult to determine and/or that there is a lot of
parallelism. I wonder whether the former is a product of degree of
familiarity and/or the ability to generalize a structure (something that I
have found can be a real challenge to understanding or recognizing
comparability), and the latter to the use of too many marginal characters
(in the quest for large numbers the inclusion of features that might be
assumed to be comparable rather than demonstrated). Again these are just
observations from a personal point of view and I am entirely open to
thinking about these matters quite differently from people who have
undoubtedly many more years of detailed experience than I.

John Grehan