A website dedicated to explaining and exploring the harlequin appaloosa gene in alpacas is one of my many back-burner projects, so for now, let's go through a review of what it means to be a harlequin alpaca.
First, the pictures of Caine. This is the first picture that I posted, and people were skeptical, understandably. He is not spotted, not even on his face.
The logical next question, which I have not yet been asked, is: "What makes you so sure?"
... In some cases, I'm not. If I'm not, I don't call it a harlequin. In the case of the fawn "possible harlequin" crias we had born this year, neither of them have yet changed color or developed spots, so I have to assume that they are, genetically, just regular old fawns.
In a case line Caine's, I'm pretty danged sure. He started life looking like this (photo by Spring Grove Alpaca Ranch):
That sort of dramatic color change is so indicative of the harlequin gene that, even if he didn't have a harlequin sire, I would have to believe that one of his parents was a carrier of that gene somehow. Many alpacas change color after their cria shearing, but a dramatic change from fawn to dark grey pretty much tells you this is a harlequin.
As to why he doesn't have those tell-tale spots like his brother does, that I am less certain. One possibility is that Caine is a harlequin appaloosa without the appaloosa. We know that there are harlequin appaloosas without the harlequin -- appaloosa alpacas from known harlequin-producing lines, who are clearly expressing the "harlequin-associated" appaloosa gene, who never change color and become grey. Our boy Kubota is an example of one. His mother is a classic grey harlequin (and grey fleece champion at one of the Southwest USA's largest shows, by the by). Kubota is clearly an appaloosa, but he shows no indication of darkening to grey. Here he is at age two:
Another option is that Caine is an example of variable expressivity. Most alpaca breeders know about the "white spot" gene, which can result in pinto coloring and which causes the blue-eyed white phenotype when bred with tuxedo grey. Most breeders also know that the white spotting gene can range anywhere from a classic pinto -- cow-spots and all -- all the way to one single tiny spot that is smaller than a dime. This is an example of variable expressivity. The loud pinto and the tiny white spot on a black alpaca both derive from the same gene; it's just that they are expressed differently in different animals. It's possible that Caine represents the harlequin appaloosa equivalent of a "white spot" alpaca with only a teeny, tiny spot. (He does, in fact, have a very small spot on his groin which is actually visible in the shorn photo.)
It is clear that the harlequin appaloosa gene can manifest in an extreme variety of ways. We have solid silver harlequins, classic harlequins, classic appaloosas, extreme (leopard) appaloosas, and all sorts in between. In all likelihood, some of these are distinct variants of the gene's expression that are caused by the effects of other color genes. Some are likely due to variable expressivity.
So, that is why I am confident that Caine is a harlequin. He also has an absolutely bitchin' fleece, and that is really what the gene is all about.