Note: this is the first instalment in my series “Common Misconceptions in Genomics“.
One of the most misunderstood relationships in genetics, and the whole biology? The confusing relation between homology and similarity.
“The proteins show a low degree of homology”; “the genes are highly homologous”. These are two examples of how NOT to talk of homology.
Homology is a binary concept, not a gradient. The question that homology answers is “do the elements share a common ancestor?”. Yes, they are related, and therefore homologs, or no, they are not. There’s no in between answer, there is no partial homology.
In the instances above, homology is confused with similarity. Similarity is indeed expressed as a gradient. It tells us how much genes or proteins resemble each other. How are they similar? Usually, in two ways: thanks to identical stretches of nucleotides/residues, or because their sequences, albeit different, maintain similar chemical properties (like presence of charged or hydrophobic residues), and, as a result similar 3D structures.
This confusion in terminology derives from how we infer homology, that is by asking how similar two genes or proteins are. The assumption is that genes and proteins descending from the same ancestors will be more similar than those who don’t share a common evolutionary history.
But beware! High similarity is imperfect evidence of homology.
Why imperfect? For two reasons:
- Similarity doesn’t always imply homology: genes or proteins can exhibit a high degree of similarity without sharing a common ancestor. This is not a case of homology but of analogy. Analogs are genes or proteins that have similar sequence because they serve a similar function: they evolved, independently, multiple times, to solve the same problem, in a similar a fashion, in multiple unrelated species. This mechanism—evolution driving different species towards the same solution—is called “convergent evolution“.
- Homology doesn’t always imply similarity: genes or proteins can exhibit a low degree of similarity while still being homologous. Homology does not require similarity. Elements descended from a common ancestor can accumulate, over time, enough mutations to obscure their similarity and common origin. A main mechanism driving this phenomenon is the relaxation of evolutionary constraints when an element’s function becomes non-essential in one or both species. With reduced selective pressure, mutations that might otherwise compromise function are no longer eliminated and accumulate over time. This is an example of divergent evolution.
Obviously, these few words can barely scratch the surface of the intricacies of evolutionary relationships. But I hope I have helped you clarify its most glaring, and common, misconception!
WritinGenomics 
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