Mini-thought experiment about the nested hierarchy

[evograd (Blogging Graduate Student)]

Only using “phylogenetically informative” sequences in phylogenetic analyses is not the same as sorting data in such a way to bias the results towards resulting in a consistent nested hierarchy.

Phylogenetic “informativeness” is measured based on internal consistency, not consistency with other phylogenetic analyses. Nothing about choosing sequences that provide a statistically significant “signal” inherently guarantees or even biases that the trees implied by those signals should be consistent between studies covering overlapping parts of the tree of life.

We’ve discussed this a bit before, if you recall. In comments #14-25 in this thread:

Beyond Reasonable Doubt? A Test for Common Ancestry

Hi all, this is first time starting a thread on this site, so I decided to go with something simple and uncontroversial, so we can all get along in unanimous agreement. Universal common ancestry. I’ve been browsing a few different threads here recently and one topic that I’ve noticed pop up repeatedly is formal tests of universal common ancestry - whether they have been performed, or are even possible. One paper that is often brought up (and not surprisingly so given its title), is Douglas Theobald’s 2010 paper A formal test of the theory of universal common ancestry. It’s worth a read if you haven’t already, but without getting into the details, I think it’s generally acknowledged at this point that Theobald’s statistical methods were flawed, so let’s put his paper to one side for a moment. What other research exists to fill this void? Well, as it happens I wrote a blog post a while back outlining one such piece of research. I’ll let you read the blog post and/or paper to get the …