I have no idea how the leopard got its spots, but scientists have figured out how horses got their leopard spots!
Scientists have known for a few years that it is mutations within 'transient receptor potential cation channel subfamily M member 1' (TRPM1), that cause leopard spots and sometimes night blindness in horses. It turns out the bugger causing both of these phenotypes is a retrovirus that decided to plop into TRPM1.
The retrovirus did this in an egg or sperm, so it became an endogenous retrovirus. At some point, the two LTRs overlapped and cut out the 'virus' part of the ERV, so there is only a single LTR left. This happens the majority of the time with ERVs, but these solo LTRs are still disruptive.
In this case, the presence of the LTR results in a partially dominant fur/vision phenotype.
ERV-/ERV- horses dont have white patches on their horse butts, and have no vision issues.
ERV+/ERV- horses are white/have white patches on their butts WITH leopard spots, and have no vision issues.
ERV+/ERV+ horses are white/have white patches on their butts with NO leopard spots, and DO have vision issues.
Random mutations leading to phenotypic diversity!
Though the insertion does cause, what we would call a 'negative' phenotype (reduced night vision), the insertion has been maintained in the horse population for about 17,000 years.
THAT is how the Appaloosa got its spots (and some other breeds) :-D
Huh. It'd be interesting to find out how many different species have similar variations. I just recently found out I have something called "multiple lentigines syndrome" -- basically, I'm spotty everywhere, which I knew -- apparently the syndrome can also include eye and heart issues. My eyes are ok (for my age), but turns out I also have an inverted T-wave. Nothing serious though.
Here's the dl on the genetic variation in humans: http://ghr.nlm.nih.gov/condition/multiple-lentigines-syndrome