Agreed linkage disequilibrium (LD) is poorly named. LD is a covariance in the alleles found together at two loci. Negative LD refers to a higher chance of carrying a “bad” allele at 2nd locus if a chromosome carries a “good” allele at the 1st locus.
Recombination shuffles the loci and breaks down LD (much like shuffling cards randomizes them and breaks down associations, such as clubs being near each other in an unshuffled deck). So what builds LD? Many things - which chromosome a mutation lands on, chance genetic drift...
and selection. For example if there’s an extra fitness boost for having two good alleles (positive epistasis), positive LD tends to build, so good-good combos are found more often than expected (as are bad-bad): the loci become positively correlated in which alleles they carry.
Negative epistasis means fitness is lower than expected for chromosomes carrying two good alleles, so those combinations become rarer than expected over time = - LD. (There’s more to share & learn, but that’s a start for Twitter!!)
