Help with genetics about alleles?

So the LD value between these two alleles at this locus is = 1. LD goes from 0 to 1, where 0 = completely independent and 1 = completely dependent. LD is calculated by using information about the frequencies of two alleles at these different loci.

We wouldn't expect them to be physically linked because it tells us they are not on the same chromosome! Since they are two different loci it means that they are on different regions of two different chromosomes. So now we have to use this information to form a hypothesis of why these two alleles (at different loci/genomic locations) occur more frequently together than we would expect by chance?

So now we can use some information from biology and evolution to make a hypothesis of how this could happen. For simplicity we will consider these two loci to produce two different proteins. And each locus/gene can have two different alleles; which means that each locus has two different isoforms of their protein(the alleles AT EACH LOCUS encode proteins which do the same function but just have variation in how well they do it). For example, if our two loci are on chromosome 4 and 8 and named 4a and 8a, respectively. These loci produce two different proteins; 4A and 8B, which do different jobs. Each locus/gene has two different alleles 4a' + 4a'' and 8b' + 8b''. So these two loci produce 4 proteins; 4A' + 4A'' which do the same thing but vary in how well they do it. And 8B' + 8B'' which have a completely different function from the two 4A' and 4A''. But 8B' and 8B'' proteins do the same job and only vary in how well they do it.

Now we can imagine that these two loci produce proteins which have different functions but these different functions are needed for a larger cellular process. For example, if the protein from gene 4a produced a protein who's function was to respond to extracellular signals and then form an association with the protein encoded in gene 8b, maybe this association causes both of them to enter the nucleus and turn on the expression of other genes. This means that these proteins are both needed in order for this communication between the environment (cells nearby, molecules etc) mechanism to work. But if we have different variations of proteins then we can have particular combinations which allow this mechanism to occur faster, say. If an individual has the genotype 4a'/4a' + 8b'/8b' and this allows signalling to occur REALLY efficiently. But the genotype 4a''/4a'' + 8b''/8b'' only allows limited signalling in the cells of individuals which have this genotype. This could be explained by having only protein 4A' working with 8B' means that these proteins work really good together and if you have a different allele and therefore different protein at any of these loci/genes then this process of them working together would occur less efficiently. So we could imagine natural selection to select for this particular combination of alleles to be passed on through each reproductive generation. Even though they are different genes with different proteins on different chromosomes, they are still functioning together. They will evolve dependent on each other; co-evolve.