Let's approach this from another direction we can look at nematodes and compare their genome with flies and humans. So researchers compared more than 100 nuclear protein alignments. The original study used the 18S rRNA. In nematodes this has particularly long branches, indicating an increased rate of sequence change. What this means is that, basically, nematodes have an increased rate of nucleotide substitution which creates a longer branch phlogenetically - in essence high rates of sequence change give the appearance of greater age and are pushed further down on the phylogentic tree (called long branch attraction).
Which is where they are placed in the coelomata hypothesis. Supporters of the alternative view argues that this is because of long branch attraction. The writers of the papers linked to above reasoned that if nematodes cluster at the base of the phylogeny because of long branch attraction then the best place to find support for the alternative, Ecdysoza, hypothesis is in slowly evolving proteins. Their results actually supported the Coelomata hypothesis - that is that humans are more closely related to flies than nematodes. They suggest that the linkage of nematodes with flies is an artifact of of analysing only one gene.
But there is another wrinkle, which I will discuss tomorrow.