rooting distance based tree

joe at removethispart.gs.washington.edu joe at removethispart.gs.washington.edu
Sun Jun 15 00:15:21 EST 2003


In article <bcaes6$4tc$1 at mercury.hgmp.mrc.ac.uk>,
Peter A. Cejchan  <cej at gli.cas.cz> wrote:
>suppose we have a distance based phylogenetic tree, plus a
>hypothetical ancestor (derived independently). sequences are believed
>to diverge *before* the ingroup did.
>I believe one *cannot* simply root the tree between the two ingroup
>members who are closest to the hypothetical common ancestor. Please,
>correct me if Im wrong!!!

You are correct that that is not where you root the tree.  You root it
on the line that connects the outgroup to the rest of the tree (on the
branch leading to the outgroup).   Thus if we have the great apes plus a
macacque as outgroup, and the macacque connects to the apes via a node
that connects to the macacque, to the gibbon lineage, and to the rest
of the great apes, the root is on the line between the macacque and
that node.

-- 
Joe Felsenstein         joe at removethispart.gs.washington.edu
 Department of Genome Sciences, University of Washington,
 Box 357730, Seattle, WA 98195-7730 USA
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