Consider a hypothetical population of 1000 organisms.
(a) 300 of these 1000 have a T to G substitution at a specific position 1.
(b) 200 of these 1000 have an A to T substitution at a second position 2.
(c) All of the 200 with the substitution at position 2 (b) also have the substitution at position 1 (a).
As a non-geneticist, I would call the second mutation a refinement of the first mutation. Would that seem reasonable, or is there a specific technical term for this phenomenon?
The description of the second mutation depends on the nature of its relationship to the first mutation.
If the first mutation reduces fitness of the organism, and the second mutation tempers the fitness reduction, then the second mutation would be compensatory.
Compensatory mutations are common in bacteria that acquire antibiotic resistance. Consider a strain of E. coli that acquires resistance to streptomycin by mutating the rpsL gene, which encodes a 30S ribosomal protein targeted by streptomycin. In the presence of streptomycin, the rpsL mutant is obviously more fit than wild type E. coli. In the absence of streptomycin, however, ribosomal mutations lead to inefficient translation. Compensatory mutations may then arise elsewhere in rpsL or within another gene involved in the ribosomal complex, partially alleviating the fitness defect caused by the initial mutation to rpsL.
If, instead, the mutations are synonymous and otherwise unrelated in their functional potential, I would simply call those mutations coincident in the genome, though this isn't really a "technical" term. If you wish to describe the relevance of these synonymous mutations in context of the three distinct genotypes given in the question, you could say that the first T to G transversion differentiates strain X from ancestral Wild Type, and the second A to T transversion differentiates strain Y from ancestral strain X. This assumes that both of these mutations occurred once in the genetic history of this population.
