There is more than one comparison of tRNA's, and there are molecules other than tRNA's that are being compared. The correct usage is the plural form.
Genome Res. Mar 2007; 17(3): 293298.
mtDNA phylogeny and evolution of laboratory mouse strains
Ana Goios,1,2,6 Luísa Pereira,1,3 Molly Bogue,4 Vincent Macaulay,5 and António Amorim1,2
Inbred mouse strains have been maintained for more than 100 years, and they are thought to be a mixture of four different mouse subspecies. Although genealogies have been established, female inbred mouse phylogenies remain unexplored. By a phylogenetic analysis of newly generated complete mitochondrial DNA sequence data in 16 strains, we show here that all common inbred strains descend from the same Mus musculus domesticus female wild ancestor, and suggest that they present a different mitochondrial evolutionary process than their wild relatives with a faster accumulation of replacement substitutions. Our data complement forthcoming results on resequencing of a group of priority strains, and they follow recent efforts of the Mouse Phenome Project to collect and make publicly available information on various strains.
mtDNA phylogeny and evolution of laboratory mouse strains
We have directly observed that evolution produces a nested hierarchy. We know from direct observation that mutations are random and blind with respect to both fitness and species. All known mechanisms of evolution will cause species to diverge through lineage specific mutations. This necessarily will produce a nested hierarchy.
Nowhere in the theory of evolution does it say that it is the only cause. All theories are tentative. All scientific theories use the same inference. If you claim that testing hypotheses through observations is a logical fallacy, as you are doing here, then you are claiming that all of science is a logical fallacy. Good luck with that.
People DO NOT create nested hierarchies, as I have explained over and over and over and over. Human designs do not fall into nested hierarchies. Cars do not fall into nested hierarchies. Computer programs do not fall into matched nested hierarchies. For example, a web browser on an Apple and a PC will look almost identical from outward appearances, yet they differ drastically at the level of machine code. Not so for life. Even more importantly, when humans design organisms (i.e. genetically modified organisms) they regularly violate a nested hierarchy. For example, the Glofish has an exact copy of a jellyfish gene, something that should not be there if that gene evolved in vertebrate fish.
Let's see how that works. Lower levels of the Air Force and Navy use exactly the same planes while other lower levels in each division do not. That is a clear violation of a nested hierarchy. You have divisions of the Air Force and Navy that share a feature while those lower divisions do not share the same features within each branch of service.
Why would an intelligent being go to the extra effort of making life look like it evolved when it is not necessary to do so? Do humans go through the extra effort to make sure that only one lineage of car has an airbag, and then find completely different adaptations for safety in all other lineages of cars? No. Why would humans do that? Humans mix and match features in designs where it makes functional sense, not to make it look like cars evolved from a common ancestor.