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The outgroup problem

harley at uctvax.uct.ac.za harley at uctvax.uct.ac.za
Fri Jun 4 04:03:36 EST 1993

I have a topic which might engender some constructive debate, and can be put as
the proposal *the outgroup is not appropriate as a way of rooting molecular
phylogenies*. This is, of course, a bit extreme, but I am coming to the
conclusion from looking at a number of sequence data sets that one is caught
between the devil and the deep blue sea: if the outgroup is too close it may
not really be a valid outgroup, if too far then the number of sites genuinly
identifying the plesiomorphic state may be too few, and mixed with so many
homoplasies (back & parallel mutations, esp if there is a high transition bias)
as to be worse than useless.
Put another way, is there a statistical method which will define a window  ( of
distance ? of shared sites ?) within which a particular taxon can be used as a
valid outgroup. What is good for morphologists may not be so good for gene

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