The Palaleoptera Problem

These datasets are from a 2002 paper on the phylogeny of the basal
branches in the phylogeny of winged insects. There are three
monophyletic groups: dragonflies, mayflies and Neoptera, a group
containing all other winged insects.

The genes sequences are rDNA, encoding the ribosomal RNA sequences.
This implies some special characteristics. They are not bound to the
triplet code of protein encoding genes, but still highly conserved as
mutations will disrupt the secondary and tertiary shape of the
ribosomes.

18S and 28S rDNA is commonly used in animal phylogenetics, as these
genes were among the first to be widely sampled and easy to amplify
and sequence with general primers. However, alignment is nearly always
very difficult.

For these datasets, the reconstructed tree is sensitive to the
parameters and method used for alignment. Possible more than the
method used for reconstructing the tree.

You can explore parameters for distance based alignment methods like
Clustal, as weel as optimization alignment with POY and static
alignments build with POY's implied alignment feature. Reconstruct the
tree with parsimony, likelihood and MrBayes.

Rasmus Hovmoller

Department of Statistics and
Mathematical Biosciences Institute
The Ohio State University
Columbus, OH 43210
Phone: +1 614 688-3292