Oragnutan relationships

pierre deleporte pierre.deleporte at UNIV-RENNES1.FR
Tue Apr 9 15:00:23 CDT 2002

Strange enough... molecular analysis using parsimony doesn't require the
definition of an ancestral sequence, outgroup rooting is sufficient exactly
like for morphological data. The same way, morphological data do not
require a priori statements of polarity. Outgroup rooting has largely
lowered the requirement for primary homology assumptions whatever the data
sets you use. I think that molecularists are generally less interested in
homology (not only primary assumptions of putative synapomorphy)
particularly at the level of sites in sequences, because they generally
have no evolutionary hypothesis for the presence of a given base rather
than another one at a given position in a sequence... but the method is the
same for molecular and morphological data in basic parsimony analysis.
Approaches involving more elaborated models of character evolution differ
(e.g. molecular clocks have hardly an equivalent in "morphological
clocks"...). This question of underlying models is important and may be
different for molecular and morphological traits, but the question of a
priori / a posteriori synapomorphy statements seems largeley irrelevant to
me in this comparison. As stated by Richard Jensen, assessing synapomorphy
is always a posteriori, with reference to an accepted phylogeny ("secondary
homology" sensu de Pinna). If primary homology statements were to be
preferred, why perform phylogeny inference at all ? Another question is the
possible differentiel weighting of characters, but this leads us back to
the question of assumed models of character evolution...


A 08:29 09/04/2002 -0400, John Grehan wrote :
>>Aren't all synapomorphies "identified a posteriori?"  I don't see how you
>>can id
>>a character as a synapomorphy unless you already have the phylogeny worked
>>Richard J. Jensen
>I was using Schwartz's terminology and I appear to have created confusion
>by not providing the complete context of his statements which are as follows:
>As such, molecular synapomorphy is identified a posteriori, after the
>phylogeny is generated, rather than as a result of broad outgroup
>comparisons that yield hypotheses of character polarity, some of which may
>be in conflict. Molecular synapomorphies,however, can take the form of
>either entire sequences of specific sites in sequences that are identified
>only as a consequence of the clustering analysis used. Thus, there never is
>any character conflict within a particular molecular study, only trees of
>differing lengths. Whereas hypotheses of morphological synapomorphy can be
>used in attempts to falsify other hypotheses of synapomorphy, no such
>methodological procedure can be applied to phylogenies generated from
>molecular data because the guiding principle in the latter endeavor is one
>of "minimum number of steps" needed to achieve the most parsimonious theory
>of relatedness.
>In a morphological cladistic analysis, the issues of determining character
>polarity are dealt with first and then competing theories of relationship
>are generated from the alternative combinations of character states.
>Basically, features are investigated prior to the phylogenetic assessment
>of taxa. In molecular analysis, polarity is determined by specifying a
>particular taxon (and thus its molecular attributes) as primitive relative
>to the taxa of interest and then generating a tree based on nested sets of
>increasing overall similarity among the non-rooted taxa. Molecular
>synapomorphy is subsequently defined in the context of the
>already-determined branching sequence.
>John Grehan

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