Conflicting molecular tree topologies? - examples?

[Kent E. Holsinger]

Volker Knoop <volker.knoop at biologie.uni-ulm.de> writes:

> 
> Hi, out there.
> Anybody having good examples for conflicting tree topologies obtained
> with two different molecular data sets for a similar set of taxa?
> We are in the situation that we obtain different trees with 18S rRNA and
> a mitochondrial protein encoding gene (with and without ists intron) at
> a special grouping position for a set of land plants.
> Any pointers to references reporting similar things or useful comments
> appreciated
> 

(Shameless plug follows.)

You might want to check the following paper.

Sullivan, J., K. E. Holsinger, and C. Simon.  1995. Among-site rate
   variation and phylogenetic analysis of 12S rRNA genes in sigmodontine
   rodents.  Mol. Biol. Evol. 12:988--1001.

In it we describe a similar situation in the genus
Peromyscus. Sequence data from cytB is concordant with a well-accepted
phylogeny for the group. Similar data from 12S rRNA is not. This
result was particularly striking to me for two reasons:

1) Both topologies score well on all measures of internal consistency
   we examined for their respective data sets.
2) cytB and 12S rRNA are both mitochondrially encoded, so the
   differing topologies cannot represent different gene trees.

-- Kent