Final answer:
The most likely reason for two genes on the same chromosome assorting independently during lod-score analysis is that they are far apart on chromosome 12, allowing for frequent recombinations and independent assortment.
Step-by-step explanation:
When two genes have both been mapped to the same chromosome but appear to be assorting independently during lod-score analysis, the most likely explanation is that the two genes are far apart on chromosome 12. The fact that they are on the same chromosome was initially established by somatic-cell hybridization analysis. However, if during lod-score analysis the genes seem to be inherited independently, it implies there is enough distance between them that recombinant gametes are frequently produced as a result of crossing-over during meiosis.
This is consistent with the principles of genetic linkage and recombination which state that, while linked genes are typically inherited together, those that are far apart on the same chromosome may not always be transmitted as a pair due to the likelihood of recombination occurring between them. Therefore, they can exhibit Mendelian independent assortment despite being located on the same chromosome. This concept helps geneticists in constructing linkage maps and understanding the inherited traits.