For example, imagine this Feynman diagram:
This is analogous to mutational homoplasy.
When comparing haplotypes, there are many possible tree topologies. Under maximum parsimony, we ignore suboptimal tree paths which certainly occur sometimes in reality. For example, imagine the following two haplotypes:
1: C A T T G
2: C A T A A
There are two mutations that make these different.
Maximum parsimony may infer this intermediate, not directly observed haplotype:
C A T A G
If we move from 1 to 2, the tree looks like:
C A T T G --> C A T A G --> C A T A A
However, the following is also possible:
C A T T G --> C A T A G --> C A T T G --> C A T A G
C A T T G --> C A T T C --> C A T A C --> C T T A C --> C A T A C --> C A T A C --> C A T A G
The not-directly-observed haplotype is analogous to the virtual particle. The directly observed haplotypes are the non-virtual particles. One could construct Feynman diagrams that look similar except have haplotypes instead of particles.
It is possible to imagine that some less-likely haplotypes actually are more harmonious with the observations. It seems that perturbation theory may help.
I don't have completely formalized thoughts on this. I am wondering if this has actually been used before to make a mutation process framework (e.g., an improvement to the infinite alleles model).