Convergence in molecular evolution
In bats, there appears to be a case where similarity of genes is due not to homology, but to convergence:
Prestin codes for a protein of the outer hair cells – the tiny structures in the inner ear that help to give mammals their sensitive hearing. Important mutations occurred during the emergence of mammals that led to the evolution of Prestin from similar proteins. Since mammals evolved, it has been argued that the Prestin gene has changed little.
The researchers studied the Prestin DNA sequence in a range of echolocating bats and fruit bats, which do not echolocate. They found that parts of the gene appear to have evolved to be similar in the distantly related echolocating species. Source
This might seem like typical case of evolution happening, then conservation of crucial adaptations. The reason this is not believed to be the case is that some echolocators apparently are more closely related to fruit bats, and fruit bat DNA indicates that they likely have never echolocated:
Furthermore, they could not find any evidence of genetic changes in the Prestin of fruit bats that might be expected from a loss of high frequency hearing.
“In recent years, scientists have discovered the curious fact that echolocating bats do not all group together in the evolutionary tree of life, but instead, some are more related to their non-echolocating cousins, the fruit bats. This has raised the question of whether echolocation in bats has evolved more than once, or whether the fruit bats lost their ability to echolocate. Ibid.
It would seem that evolution can sometimes happen relatively deterministically. Presumably, Prestin would have changed in the separate lines under heavy selective pressures, so that much the same changes occurred.
Anyway, I thought it was an interesting evolution story, especially since similar biomolecules are typically believed to be due to common origin and conservation. In this case, the similarity does indeed seem to be due in part to common origin, but then to similar adaptive evolution.