Understanding Indigo Genetics

When the Eastern Indigo Snake was federally listed in 1978, it effectively froze the available gene pool at a time when the species was at a low population. The result is that today every wild Eastern Indigo is assuredly related, at least to some degree, to every other wild Eastern Indigo.

And of course the impact on the captive bred gene pool was the same, if not more significant, because it was and is an even smaller population. There is no doubt that, particularly in the early years of protection, there was significant poaching, and wild specimens were contributing some genetic variation to the captive pool. But while speculation remains as to the extent of wild poaching today, it is certainly far less common and likely no longer a significant factor in varying the captive gene pool, as the occasional introduction of a few wild individuals would not impact the captive population as a whole. As with the wild population, every captive bred Eastern Indigo is related, to at least some degree, to every other captive bred Eastern Indigo.

Certainly the various agencies and organizations currently involved in captive breeding and reintroducing the Eastern Indigo to portions of its former range are keeping extremely careful track of the genetic diversity of their breed-and-release animals, albeit unfortunately they are not publishing those details. We must assume that these various entities (including: US Fish and Wildlife Service [USFWS], Alabama Department of Conservation and Natural Resources [ALDCNR], Florida Fish and Wildlife Conservation Commission [FWC], Central Florida Zoo & Botanical Gardens, Orianne Center for Indigo Conservation, Orianne Society, Auburn University, The Nature Conservancy, US Forest Service, Zoo Atlanta, Welaka National Fish Hatchery, Zoo Tampa, Joseph W. Jones Ecological Research Center, Georgia Sea Turtle Center, Alabama Natural Heritage Museum, and others [Ref: Central Florida Zoo: About the Zoo]) are doing their utmost to maintain genetic diversity and avoid extreme inbreeding. Unfortunately to date neither these organizations nor federal or state Fish & Wildlife agencies have shown the slightest interest in engaging with the captive breeding community. Both communities — and more importantly, the species itself — could mutually benefit from cooperation, but unfortunately we are at present left to merely imagine such future interactions. Imagine, for example, if sperm samples from wild populations could be used to artificially inseminate captive populations, to freshen and vary the captive gene pool? No doubt a handful of breeders would pay significant fees, that those in charge of managing the species in the wild could doubtless put to good use. The mind boggles.

Meanwhile we can only speculate as to the degree of inbreeding within the captive bred population. At first these issues were not at the forefront of awareness among the tiny community of captive breeders. I certainly wasn’t thinking about it when I first bred my wild-caught specimens in the early 1970s. It seems likely that captive breeders, selecting at face value for traits like size and color, were at least for a time engaging in some degree of indiscriminate inbreeding and “line breeding,” that is, deliberately breeding offspring back to the previous generation in an effort to produce animals with desirable traits.

In more recent years, however, concerns and awareness have grown, and respected breeders have clearly made an effort to consider relatedness when choosing pairings. Much speculation and mythology is repeated in online groups about faulty traits such as spinal kinks, split ventral scales, and dwarfism, yet the science is lacking as to which if any of these traits are actually due to inbreeding versus incubation issues, an entirely different matter. Wild charges are sometimes circulated against this breeder or that, often depending as much or more on grudges and other personal antipathies rather than falsifiable evidence, and yet in some extreme corners such innuendoes are taken as fact rather than myth, and science rather than mere gossip.

Most responsible veteran breeders are open with their customers, sharing some degree of information about their collections and histories. When a breeder claims to be maintaining diverse genetic lines, the customer relies on reputation and relationship when making a judgment call, while some at greater distance are eager to offer critiques and complaints.

One change that has had an impact is the existence of a genetic testing program developed by Therion International LLC who, according to their website, “is the recognized leader in providing reliable and accurate DNA-based testing services for addressing questions concerning the genetic identity of animals.” The Therion genetic testing for Drymarchon species was developed in an exclusive business relationship with Mr. Alan Brutosky, who charges a fee and serves as intermediary between his customers seeking testing and Therion who actually performs the tests. Presumably, several hundred specimens have been tested since the program began. As of mid-2023, however, reports indicate that the owners of Therion are retiring and closing the lab. Time will tell if another lab picks up where Therion leaves off, but we can safely assume such efforts are underway.

In brief, the Therion testing looks at 10 pairs (originally it was 11) of alleles, or pairs of genes, characteristic of Drymarchon DNA. This test represents a small fraction of the genome of this genus and species, which have yet to be completely mapped, but so far this is a better-than-nothing approach that provides information about relatedness between individual specimens. This is independent of identifying actual genetic traits, and selecting for healthy traits versus unhealthy traits is actually of greater concern in the eyes of many experts, because we know that pairings with high relatedness can produce perfect offsprings, while pairings with low relatedness can produce flawed offspring. While some would insist that the 10 allele pairs currently being tested by Therion are the end all and be all of genetic issues in breeding Eastern Indigos, the truth is otherwise and far more complex. As the saying goes: Every problem has a simple solution, and it’s usually wrong. It is not my intention to elucidate all of these issues here, but merely try to identify them in simplified form.

The game changer in this regard will be DNA testing by Rare Genetics, Inc., the company founded by genetics tech entrepreneur Benson H. Morrill, PhD. Rare Genetics currently provides low-cost DNA testing to identify sex in a wide range of snake species. But they are actively engaged in dramatically expanding their range of abilities, and are now identifying morph DNA in Ball Pythons. This development will undoubtedly serve to dramatically transform the captive breeding industry in the next few years, because buyers will no longer have to take a vendor’s word for what the snake they are buying at an expo is “het” for or not when it comes to non-expressed traits. Times change.

Further, Rare Genetics is hard at work on mapping complete genomes for multiple species — including Drymarchon couperi and other Drymarchon species! — so as to be able to determine relatedness, and create large databases similar to what firms like 23andMe now offer in tracking human DNA and family trees. It’s only a matter of time before Rare Genetics will be able to test Drymarchon for far more than a mere 10 pairs of alleles.

This material is intended as a brief summary introduction to what is a complex and sometimes controversial subject. As I discuss in Chapter 4 on the Husbandry page, buyers need to do their due diligence, develop relationships with responsible breeders, and use their best judgment when choosing a source. Reputation, longevity, experience, expertise, and of course the actual quality of animals, all must play a factor in making these decisions. And see the Resources page for a number of informative articles about snake genetics.