Dear Colleagues,
It is probably time for me to make my contribution to the discussion and to
clear up some misunderstandings.
The first point is that I am a specialist of aquatic oligochaetes who, a few
years ago, started a molecular analysis of my group and related taxa.
Accordingly, I do not consider myself as a "molecular-oriented
colleague", as my work on systematics was only based on morphological
data so far. I just tried to use both kind of data, morphology and
molecular, in order to solve clitellate relationships.
The second point is that I have the strong feeling that most of the problem
raised by K. Fitzhugh is due because the problem is considered within
the framework of maximum parsimony (MP) analyses while I only used
the maximum likelihood (ML) method. Briefly, the latter method enables to
obtain the tree which statistically optimizes the probability of observing
the data given a particular evolutive model. The important point here is
that the temporal dimension is included in the model. Hence, rate has
here a meaning since it is considered in a context of time.
>Let's say one has a set of specimens, from which they "observe" that
>position 556 of each specimen has an A. Our perceptions tell us we "see"
>the same nucleotide among these individuals. Most systematists then go so
>far as to say, "this A at position 556 indicates homology."
This is exactly the point. Considered within a "most parsimonious"
framework, this is indeed what most systematists will say. This is also
why the MP method can be misleading when it is applied to molecular
data: the method is unable to detect multiple changes on long branches
(convergent, parallel, or reversed), resulting in the so-called "long branch
attraction" phenomenon. In contrast, it is very likely that the maximum
likelihood of obtaining the observed data, given a particular evolutive
model, requires the following transitions, A-C-T-A, for one specimen,
while for the other one, these successive transitions are not required.
Very roughly, we measured in this study an amount of difference
between the taxa considered (the number of substitutions per site
separating the sequences, according to the evolutive model considered).
We then noticed that some lineages, namely the leeches, leech-like
worms and gutless worms, cluster along long branches in our
phylogenetic inferences, by comparison with other oligochaetes. These
differences in mutation rates were statistically significant, according to
the evolutive model considered in ML analyses. This higher amount of
difference between these groups and other oligochaetes could not be
interpreted as the result of an ancestral condition since both molecular
and morphological data suggest that these groups are located within
oligochaetes. We then concluded that these lineages rapidly evolved.
Hoping that this can be of some help in the discussion...
Patrick MARTIN
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Patrick MARTIN
Institut royal des Sciences naturelles de Belgique
Biologie des Eaux douces
29, rue Vautier
B-1000 Bruxelles
Belgium
Tel : +32/2/627.43.17
Fax : +32/2/627.41.13
Email : martin at kbinirsnb.behttp://www.kbinirsnb.behttp://eea.eionet.eu.int/ec-chm/cbro/country/Belgium.htm#127
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