You’re confused. The question is not whether some of the differences between similar genes found in different species have particular physiological effects that affect their function, and therefore affect how they interact with other genes in the species. Some of those differences are there because they do have a functional consequence of some sort, this is not in dispute.
The question we are considering is whether the types of mutations in similar genes shared between different species, that have functional consequences, should be expected to constrain independently inferred phylogenetic trees to converge on a similar topology.
Before we proceed on this question, do you understand this distinction?
not according to this article:
Phylogeny: Rewriting evolution | Natureyou can see that these are completely different trees and no similar at all.
That’s actually not correct. In both trees, cow and dog are more closely related to each other than to everything else. In both trees, both rat and mouse are more closely related to each other than to everything else. The main differences seem to be which clades nest into which. Little to nothing can be concluded on the basis of what appears to me just a drawing made for emphasis.
Second, even supposing those two are real phylogenetic trees inferred from data, the significance of the incongruence has not been worked out anywhere that I can see, and the question is how that would change with a larger taxon sample or more loci included in both data sets. It also isn’t clear what methodology, or data sources, were even used to infer those trees.
I looked up Kevin Peterson’s google scholar page, and since that pop-sci article has been written, Kevin Peterson and colleagues have proceeded to publish an actual mammalian tree based on a superalignment of 16,050 pre-miRNA genes, and compared it to a tree inferred from protein coding genes. This is their result:
These trees look almost completely congruent to me. As far as I can see there are only three mismatching branches, and that’s because some branch from each tree is missing which is present in the other.