I personally believe that the leopard and pied genes are probably linked. That being said, please forget everything you think about what "linked" means. There is a misconception among ball python hobbyists that linked means these genes must always occur together or are somehow actually two alleles from the same locus, but that is not what the term linked actually implies.
From Wikipedia: "Genetic linkage is the tendency of alleles that are located close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be genetically linked. In other words, the nearer two genes are on a chromosome, the lower is the chance of a swap occurring between them, and the more likely they are to be inherited together."
"Linked" would simply mean that Leopard and Pied are distinct genes located close together. Two mutations are more likely to be inherited together if they were already paired on the same chromosome, and located next to one another. I personally have a leopard het pied which (after multiple pairings to piebalds) appears to have his leopard and pied traits on opposite homologous chromosomes... meaning he is actually less likely to pass them on as a pair... a fact which still supports the "linked" hypothesis (if being on the same chromosome increases likelihood of being inherited together, then being on opposite chromosomes must decrease the likelihood of being paired together). All his offspring have either inherited his pied gene or his leopard gene, never both. Likewise, if many of the earliest animals in this project had their mutations on the same chromosome, it would give the confusing impression that all leopards are het pied, due to the extremely skewed ratios of paired inheritance.
Linkage is determined through statistical analysis of offspring ratios.
If linkage is true, this still allows for the leopard gene and piebald gene to be completely isolated from one another. It allows for the existence of "super leopards." And finally, it explains why so many of the early breeders, and some still to this day, insist that all leopards are pieds.
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