Any comments?

Joe Felsenstein joe at evolution.genetics.washington.edu
Sat Nov 4 01:20:26 EST 1995

In article <47dav2$d8s at studium.student.umu.se>,
Ludvig Mortberg <Agneta.Guillemot at historia.umu.se> wrote:
>I claim the following is true:
>When homologous sequences of DNA, aminoacids etc e.g the sequence of
>bases in a gene, are compared between different organisms the
>"phenetic distance" or "unrooted tree" does not always reflect the
>true phylogenie of those organisms.

Of course _no_ method _always_ reflects the true phylogeny.

>     A    B   C
>      \  /   /
>       \/   /
>        \  /
>         \/
>To be short: In a "distance matrix meseurment" (unrooted tree) A and C
>may show up as closer than A and B. 
>I'm not saying this happens every time. I'm just saying it happens
>sometimes. Can everyone agree on this?
>(I believe that the small subunit of rRNA in mammals is "closer" to
>amphibians than to birds.)

Are you inferring rooted or unrooted trees?  From the picture, rooted.
But parsimony, likelihood, and most distance matrix methods (such as
Neighbor-Joining or Fitch-Margoliash) do _not_ estimate rooted trees.
They estimate unrooted trees.  And for three taxa there is only one possible
unrooted tree, so all methods will give the same tree, which is always the
right one, but the whole matter is therefore vacuous.

I can only interpret your posting as based on the total misconception
that distance matrix methods infer rooted trees and do so by clustering
algorithms, which put the closest pair together and then put the root
below that. 

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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