Gpuccio: Functional Information Methodology

[swamidass (S. Joshua Swamidass)]

@glipsnort

When using conservation it’s possible, even likely, to underestimate the total FI present while overestimating the change in FI.

@glipsnort

Some functional sequence is likely to have changed on the branches between rodents and primates without losing function, while other functional sequence has been lost and gained in each branch.

Which is, once again, why it is important to do this analysis with a phylogeny. As @John_Harshman, an expert in this area, comments:

@John_Harshman

I would like to know why gpuccio is using the crude measure of pairwise BLAST scores rather than actual reconstruction of sequences on a phylogenetic tree.

Like this: Lee et al. 2013. Rates of Phenotypic and Genomic Evolution during the Cambrian Explosion. Current Biology 23:1889-1895.

Note that the paper he links too does a great job at the analysis you are attempting to do. It would be valuable to look it over to determine where you disagree, agree, or could learn from it @gpuccio.

Furthermore, I reiterate my question from early on:

@swamidass

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.

And:

@swamidass

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.