I've studied at uni, I have a major in genetics, I've been breeding reptiles over well over 10 years, I've visited some of the biggest and best snake breeding facilities in the world. I don't believe inbreeding in snakes is a big concern in terms of their health while in captivity. There are countless cases of snakes being inbred for many generations producing no observable problems.
There are some cases of inbreeding causing problems; blindness in the geckoes mentioned, Jaguar Carpets carry a lethal recessive allele (quite likely the one which causes the jaguar trait), and a few others. In those cases, the situation is very simple and avoiding it is not a problem.
There are very few documented cases of inbreeding depression in wild reptiles, but it is known in Cunningham's Skinks - a species highly unusual in its breeding, in that they will sometimes actually prefer not to reproduce rather than reproduce with a close relative. The fact that they have such incredibly unusual behaviour among reptiles and are one of the few species with inbreeding problems speaks volumes; it is strong evidence that it isn't much of an issue for other species.
Inbreeding depression was observed in the Vipers as mentioned. This is a classic study of inbreeding depression, and a very interesting one. My studies in genetics (including having this viper example being used in courses I've taken, and one I've been examined on multiple times), and my background in herpetoculture lead me to be almost certain that if those wild vipers had been brought into captivity they would have been perfectly healthy and bred without any troubles at all. In the benign conditions of captivity, inbreeding depression is often not observable or important....
As we know, rats and mice (mammals by the way) have been inbred for countless generations and are perfectly happy and healthy in captivity, but release them into the wild and unless they're lucky enough to find a nice place to live near human dwellings, they will drop dead quickly. They have retained everything required to thrive in captivity, but have lost abilities essential in the wild.
To give hypothetical examples, let's say that most of a population had the ability to resist a type of tick often occuring in the wild. We established a population in captivity and by chance one of the founding animals was heterozygous for a fault which made them highly vulnerable to the tick, and by chance the whole captive population ended up losing the resistance. We'd never know, we'd never care, but release those snakes and bang, they're all going to die. This same principle applies to countless traits (cold resistance, toxin resistance, ability to digest certain animals, ability to recognise certain prey, ability to avoid predators, I could list thousands), and when you remove the selective pressures of the wild, some of these will be lost (they'll actually be lost whether or not you inbreed, but they'll be lost more quickly if you do). To our snakes in captivity it just doesn't matter. Yes, it does mean that multigeneration captive snakes will often be very poorly suited to release, which is actually probably a very good thing since they are almost certainly not going to be needed for release and many will accidentally escape. What I've described here are Mendelian traits. Similar situations exist with multigenic and complex traits, but describing them would take far longer than a page or so, and it wouldn't be understandable by most reptile forum users (and if anyone could understand it they'd already have studied complex genetics anyway!).
Kathryn: it's cute that you're studying genetics and want to teach us all about what you've learned, but what they teach you in first and second year university genetics are generalised principles which mainly apply to mammals (and sometimes they'll cover plants too). As you'll learn if you continue studying genetics, things are extrememly complicated in the world of genetics. There is an exception to every rule and there are cases where just about everything imaginable happens. For reasons geneticists don't yet understand, reptiles are genetically far more robust than mammals and birds. The types of hybrids possible with reptiles (Woma x Ball for example) would be genetically unthinkable in a mammal context. We have parthenogenetic reptiles, but mammals are genetically incapable of such a thing. Mammals have things like genetic imprinting to deal with, which reptiles do not. Some of the principles you're learning apply very well to reptiles, but some do not. As you learn more you'll start to learn how to tell the difference, but keep in mind that even the best geneticists get completely thrown by reptiles if they're unfamiliar with them. Theory is great to use as a guide, but never let vague theory get in the way of a mountain of demonstrable evidence.
Good luck with your studies though! It's great to see you applying what you've learned, and in time I hope you'll become one of the precious few learned geneticists in our ranks. If you'd ever like to talk genetics, get in touch
