Looking over that figure one more time, it does not look like the branch lengths are drawn to scale. That means we do not exactly expect this tree. Nonetheless, this question still stands:
We would want to see the actual tree, with branches drawn to scale, to make a better assessment.
A Scaled Graph
This scaled tree from the same paper is more helpful, even though it does not have vertebrates. Focus on Chordata (dark blue):
The branch length or divergence width of chordata does not seem particularly notable compared to other groups. The branch length and spread for vertebrates will be smaller that that of chordata, because vertebrates are fully contained within chordata. So the vertebrates would be less remarkable than chordata.
As negative controls, look at Arthopods (bottom), Nematodes (pink), Ascoela (red), and Platyhelminthes (light green). There seems to be far more information gain and/or spread in these taxa.
Consider the Myzostomida
The long thin (red) clade Myzostomida deserves some attention. This are a diverse bunch of worms that are very phenotypically diverse, very different from other clades, and very genetically similar to one another.
To reiterate:
- Very genetically different from other clades.
- Very genetically similar to one another.
- Very phenotypically different from one another.
How do we reconcile the divergence between genetics and phenotype (2 vs. 3)? If we understand its difference from other clades as a measure of FI, then we should not expect to see much phenotypic diversity in the clade, but we do. Likewise, if phenotypic diversity much to do with FI (measured this way), we expect there to be a high spread in genetic diversity for a phenotypically diverse group such as this. We really need to reconcile this divergence between genetics and phenotype, as it demonstrates that this approach to measuring FI lacks validity.
A key finding from the neutral theory is that, on bulk, genetic changes are more a marker of history than functional changes. That means we do not expect there to be a strong link between FI and genetic divergence. That solves the riddle, but in a way that undermines this analysis as a measure of FI.
How would @Gpuccio solve this riddle?