"Crested Gecko, Foundation Genetics"... a living entity, in pursuit of knowledge - Part 2, Traits, Interactions and Morphs!
Updated: 10/05/22, v1.1
Welcome to Part 2 , Traits, Interactions and Morphs!
Part 1, of the Foundation Genetics Guide, was specifically designed to prepare you for the explanations in Part 2. A solid understanding of the genetics guide is necessary to properly identify traits in combo morphs and to understand how those traits interact with one another. A lack of understanding of expanded genetics will result in misidentification of interactions and mislabeling of genetic traits. Part 1 was intended to ease the reader into the world of more complex genetic interactions like polymorphism, epistasis, and epigenetic interactions to identify how they take place in crested geckos and other species. Genetics in reptiles is more complex than the pea plant genetic interactions that were covered in Mendelian genetics and more complicated than what you can learn from the discussion found on social media sites. Another point that needs to be addressed is that the reptile community has oversimplified genetics for many decades and we incorrectly use most of the genetics terminology. This was another main focus in Part 1, to help correct and stop using words improperly such as; Het, Visual, non-visual, and codom, and to relearn genetics so we can have a solid understanding of how this all works. Part 2 outlines traits that we have identified to behave like single locus genes that contribute to the overall phenotype or “paint job” of the animal. We will follow up Part 2, with Part 3, to help with the standardization of crested gecko morphology within the community.
Crested gecko morphology within the community.
We want to take a moment to thank the members of the community that have reached out to us to contribute. We also want to give special thanks to all of the breeders who have shared their information and feedback to help corroborate our findings. It seems many of you have noticed the same trend while breeding that we have and are excited to see new information about gene interactions with this species. We have incorporated several ideas and descriptions from the community into the guides and will continue to make amendments as information and explanations improve. We have also appended all TOC items to be clickable links to let you fast-travel to any section of the document and to aid in directing others to specific sections of the document.
If you managed to finish reading, and understood, Part 1 you may still be wondering how everything works. In Part 2 we outline individual traits, assign letters to them for genotyping, recording results, and use in Punnett table calculations. We will also be explaining how these traits interact with others to create different phenotypes. Remember we will always be dealing with more than one gene that makes up a phenotype, so keep that in mind. In Part 3, The Interactive Morph Guide we will feature depictions of each trait, isolated on the animal, on a stylized image. All colors are sampled from real-life animals and averaged to give an accurate depiction of the best-looking specimens that trait may produce.
With a new system being presented it is easy to attack the authors with the burden of proof. With decades of experience from each contributor combining collected data, we are summarizing the findings in this document. Presenting the herpetological community with a 1000+ page book of results doesn’t serve the community well. Rather we want to present a working system of summarized results, which took decades of work, years to collaborate on the data produced by each contributor, and more than 5 years to write. This is a living document, which means we will periodically be updating the document as new information reveals itself. As we learn more by combining the efforts of the community and taking those results into account, we will paint a clearer picture of how everything behaves. This will significantly improve how we identify new genes that have yet to be described and mapped. This is an evolving endeavor and will continue to grow as we learn together.
The goal here is to provide information for you to take away, incorporate the ideas and breeding practices into your own collection and label your breeders with the traits each one has once you’ve identified and successfully proved them through breeding results. With that information, you can begin to accurately map your current breeders and design future pairings to attain your goals. Mapping what your breeders are, genetically, allows you to identify traits in the offspring sooner and understand what they will develop into. Finally, we want to help standardize naming conventions and how morphs are defined in the community by providing guidelines that let you know how to identify traits. This can be achieved by using inheritance to define morphs instead of characteristics that are open to broad interpretation. We feel this is an important point, as it will be paramount to outline and identify future phenotypes more accurately and identify the difference between traits, morphs, and interactions between traits versus characteristics.
Table of Contents (click to travel to each section)
- Contributors
- Background on our authors
- History 1998-2001 - Where we came from
- How we derived the morphs
- Correlation vs Causation
- Common Misconceptions
- Current Breeding Practices
- Genetic Lineage
- Stacking
- Advanced Patterns and Morphs
- How we're listing the morphs
- Variants
- How to develop your own line
- Inbreeding/Intercrossing/Line Breeding/Outcrossing practices
- The Morphs
- Base Color Morphs
- Pattern and Color Morphs
- Phenotype Base Color Variances
- Combo Morphs
- Characteristics
- Structural Characteristics
- Polydactyls
- Old Age
- Thank you!
- Comments
Guide Contributors
- Anthony Vasquez & Jessica Vasquez – Lil Monsters Reptiles
- Tom Favazza - Geckological
- Phillippe de Vosjoli
- Allen Repashy
- Matt Parks – Pangea Reptile
- Donald Hendrickson – Reptile City Korea
- Mark Orfus – Northern Gecko
- Hannah Quellhorst – Greeks Gecko
- Amanda Gavel – Wicked Arboreals
- Cindy McDannell – Gecko Haven
Anthony Vasquez
I started in the hobby with leopard geckos and ball pythons, around 1998, where genetics played a big role in the market when breeding and selecting animals. When I started with crested geckos in 2001-2002 the explanation was that their genetics were polymorphic and unpredictable, and this was repeated for the next 20+ years. I hatched my first crested gecko in 2003 and bred different species over the years. However, I noticed patterns in crested breedings only after a couple of seasons. This left me suspicious about Polymorphism, and so began my research. While studying genetics in my spare time I learned that we had not been describing and had been using several terms incorrectly. Many of these terms and descriptions are embedded in phrases that get repeated without any fact-checking. Realizing the community was based heavily on perception rather than strict breeding practices and record keeping I took most information online as opinion rather than fact. In reading The Rhacodactylus book there was a paragraph in the morph section that struck a chord with me and sparked my project. “Further research will be required to determine the genetic relationship of the different morphs. A possible hypothesis for the polychromatism in this species is that the number of traits related to color and pattern are determined by co-dominant alleles.” Even the original founders and authors of the book could recognize what was happening and left it to the community to work out. This is where I wanted to focus my breeding efforts from 2005 onward. I then did a deep dive into genetics, studying, purchasing books, making friends with geneticists, and educating myself by cross-referencing all my information. I teamed up with Jessica in 2007 and we continued to map how each trait appeared to behave in crested geckos. Many post-it notes were used over the years. Jessica’s crucial contributions to peer reviewing everything and resources from her university were also extremely useful in making the information within the guides comprehensive.
Anthony & Jessica Vasquez
We began our experiments by trying to distill traits back to their base form and then redevelop them back up using animals that would inherit or have lost certain characteristics. This wasn’t too difficult as we started breeding in 2003 and had some early stock through Repashy and Phillippe. They helped us with information to know what to do and how to test for traits and inheritance. On average a pair will produce between 2-6 different phenotypes. We began testing how the same sire reacted with different females and was able to add, remove, or reduce the effect of certain traits, depending on what that female added or lacked. Using baselines like this we started understanding how phenotypes were comprised of multiple traits. In testing we needed a control, so we used a few phenotypes for this. One was a base flame morph, and the other was a phantom. A strong trait and one that seemed to behave recessively. With this framework, we could swap base colors on a single phenotype, add or remove pinstripe, change pattern and color, and could produce the majority of all phenotypes in varying degrees of refinement. This behavior resembled how combo morphs interact when multiple alleles contribute to the phenotype and more complex forms like incomplete dominance affect the look and produce a variety of phenotypes. Crested gecko phenotypes fall outside of simple Mendelian genetics, just like many other species in the hobby. After several years of successful breeding results, we began to reach out to breeders with our data, Phillippe, Allen, and Anthony were the first breeders we discussed this information with. We exchanged information and we took those notes to further develop more and more trait interactions and refine our ideas. AC and I worked closely and focused on phantoms, tangerines, and citrus animals. Noticing the correlation of tangerine with each phenotype, we began to find several more interactions that also pointed to epigenetics being at play and epistatic gene interactions began to reveal their play in several phenotypes. Simply put, epigenetics is when one gene shows a stronger expression or a weaker expression through environmental factors, with selective breeding being the environmental factor. While epistasis is better described as, if trait A or B are present then display C, if absent then do not display C. Not all alleles are equal though, as line breeding practices have modified how similar traits behave, so we can have a dominant mutation begin to seem as though it is incomplete dominant due to breeding for multiple genes that contribute to the expression of a particular gene. We took this data and began to write a description of the morphs, initially, this work was called the Crested Codex. Which changed when we began to collaborate with more breeders.
Tom Favazza
In 2005, Tom began keeping, breeding, and observing crested geckos. He became involved with many reptile forums and has a very good grasp on the history of our hobby and how our breeding practices have affected the hobby today. Having years of experience, beginning with the same noob experiences we all go through, he has gained a perspective that helps with the initial assessment and development of our theories. Tom is adamant about keeping things simple, referring first to the known wild-type traits, and factoring in historical breeding practices. By making friends and connections in the hobby, as well as in the science community, he has been mentored in the genetic aspect of our hobby. His contributions, to the studies of leachianus parthenogenesis, have aided in this endeavor. As Tom’s knowledge base grew, many of his theories and tests began aligning with the science. The phenotype spreads and interactions formed logical patterns and an overall understanding began to form. Tom’s breeding practices have included breeding to isolate specific traits. This resulted in base animals that have been used to help identify traits in the animals that were bred to them. Once specific traits are known, they are combined with the intent, to design animals with specific phenotypes in mind. The first animals used in this manner were hypo red phantoms… before we understood what phantoms really were.
Tom has had an understanding of hypomelanism, in our hobby, for over a decade. The hobby is still struggling to understand or believe this today and was not accepting of this idea in the past. Very few people noticed this trait and they could not speak about it without being chastised. An article was written, by Tom, about five years ago, to hint at this idea and to see how it was viewed by our community. There was little response back then… a hint that things were changing. After the discovery of a new hypo trait, Tom openly displayed and discussed these animals, as well as the hypo red based animals he discovered early on. Today there is an outpouring of inquiries along with the critics. It is a much better community response than we have seen in the past.
Collaboration
Tom, from Geckological and I began talking, over a dispute about the verbiage used on a post made by Lil Monsters. We found that many of our ideas aligned while discussing how genes in the species work and behave. We shared several theories and realized that we had been independently doing much of the same work. We also noted that our collections came from vastly different places, were several generations separated from each other, and yet had been getting identical results. This separation was crucial in eliminating line breeding as a factor for similar results. We decided to combine our theories to form a unified work that yielded 75% to over 90% accurate results in predicting phenotype ratios. Over the next year, we spoke daily to iron out any inconsistencies in our models. Tom’s theories with tigering, and how it worked, also pointed to a fixed dominant trait in the species, that I noted was nearly identical in behavior to the gargoyle “BR morph”. The BR morph was also a combined effort by Phillippe, Allen, and Frank who combined research with other breeders to redefine the Banded and Reticulated morphs under a single morph. This was nearly identical to the effect of tiger or tigering in crested geckos and accounts for all areas of pattern separation. Tiger is responsible for pattern breaks, freckling, flames, pattern crossing the dorsal or being restricted and causing what was called reverse pinstripe. Once we had a working model, we compared hundreds of results and discussed our analysis. We also created a method to check one another. If a theory was presented by one of us, the other would play devil’s advocate to debunk the theory and test if it held water by presenting counterarguments and phenotypes that challenged the theory. If you haven’t noticed yet, Tom and I breed in completely different methods, which meant we could challenge theories by approaching them from different directions. This is where we began to see results above 85% accuracy, in phenotype predictions, as our base theory evolved. Using a decade of breeding results from each collection our inheritance was checked, in every trait listed below, for Het and Hzg examples. Keeping Caponetto in the loop with how all of our work was beginning to take form in a document, we continued to gather more breeders to contribute additional data that we felt would contribute significant results to our research, and so decades of work from different breeders was combined to form a framework we could share with the community.
If there is any one important thing Tom and I can impart to the community, it is with the methodology and success of this collaboration. Despite our differences in opinion, we were able to respectfully disagree with one another and use data and logic to better prove our results. Our opinions were respected and challenged when working to find evidence. With so much in-fighting, mocking, ridicule, and cancel culture or defamation on social media, we hope to inspire respectful discussion and collaboration. If you see this poor behavior, don't participate. We want this collaboration, having so many involved, to help lead us in the right direction with one another. Differences in personal opinion, husbandry, and virtually every aspect of the hobby can reach a middle ground. There needs to be a willingness to discuss topics and a responsibility to others to use your platform in order to promote good collaboration.
One important note about our collaboration in this document is how much Tom and I were able to disagree with each other respectfully when we had a difference of opinion. It was never taken as personal attacks, but rather as brainstorming sessions with the pursuit of a common goal. We scientifically looked at a multitude of results, analyzed offspring, observed multiple combo interactions, and resolved the data into the most precise description of how certain traits behave and the best way to describe them. We both have strong personalities so we sometimes spent weeks to months on a single trait analysis. In some cases Tom was right, in some I was, and in others, we were both wrong and we had to follow the data and what it told us. There are differences of opinions, amongst hobbyists, but hearing out the logic and respecting others' perspectives, will lead us to an overall better understanding.
Where We Came From 1995-2006
Allen Repashy, Philippe De Vosjoli, Frank Fast and Anthony Caponetto have supplied some excellent historical data for us. Here you can find some of the information from the 2006 Symposium where Allen and Phillippe first documented and shared their selective breeding results over 6 years. At the time the Morphs include patternless, bi-color, Tiger, Dalmatian, white-fringed, chevron-back, fire or flame, and pinstripe. Included with these were structural morphs normal head size, crowned heads, and reverted crested geckos, with a narrow head. The progress made on the animals below is from wild-caught to F1-F7 stock. We also have slides provided by Philippe that we made digital copies of that were taken during the first trips to New Caledonia when the original stock was collected on the Isle of Pines. Contrary to popular belief that the original stock was around 200-400, the actual number was around 100 animals between 95'-98'. (Source: Allen Repashy).
If you want to really dive into the history of the species and learn about the early captivity of the species and the breeders and scientisc behind this part of the herpetoculture hobby I urge you to find and copy of "Rhacodactylus: The Complete Guide to their Selection and Care." This book covers the two islands where the species has been found, it's history before rediscovery, the expedition when they were first collected, features in the wild, morph descriptions, Breeding, sexing, and care. Information that is difficult to find online, and in details that are not often covered in social media platforms.
2006 Symposium
Here are the original pictures that appeared in the famous blue crested gecko Reptiles magazine article that was showing early success breeding this species in captivity.
Here you can see some of the early flame patterns.
Here you can see F1-F8 phantoms, reds, dalmatians, tigers, and brindles.
Here you can see the early beginnings of pinstripe in an F4, and a full pinstripe in an F7.
1998 - 2001 Original Import Animals and Island Photos
PDV Pine Island Photos
This is Pine Island, where the cresteds were originally collected from. Here are some examlpes of what the fauna was like on the island. Click Here to see the island on Google Earth.
How We Derived the Morphs
Breeders who have been breeding for several years have developed the skills to make educated guesses on what a pair will produce. After hundreds of breedings, patterns begin to emerge, and we develop an intuition based on our previous breeding results. The results produced from breeding a pair is called the phenotypic ratio. In simple terms, this is the different phenotypes produced by a pair. If we don’t know the formula being used, we can use the answers to derive it, it’s like reverse engineering what is in the parents. All offspring should reveal what the parents have as each inherited 50% of their DNA. We do this by observing results and filling in a Punnett table with traits that pass on. We then take the hypothesis and test it with the offspring produced over multiple generations. Using this workflow we were able to confirm inheritance for individual traits. As well as discover which are not traits but rather interactions of multiple traits which we describe as characteristics. We then took that data and labeled parents for further testing and future pairings. This is the point when we began to see predictions increasing over 50% of the time. As we found more and more trait interactions we refined the system and our predictions increased. Fast forward 15 years and we are in 2020. This is when we met Tom who was also working on a system. Together we set out to describe variables for dominance fighting between traits. These variables are the ratios between pattern, tiger, and pinstripe which helps us to predict the interactions we’ve created due to selective breeding development over the past 20+ years.
Just like any species, traits can overlap with how they affect the chromatophore. There are hundreds of different interactions that can occur with a genetic variant and if you look at the rest of the hobby you can find plenty of examples where phenotypes overlap and make similar-looking animals using different genes. When it comes to this species though, we have multiple traits contributing to the appearance of the animal, so the chance of overlap gets even wider. This is why it has been so hard to nail down what's happening. We have seen we can use phantom to make animals that look similar to some capps, and other combos. We can even use phantom to make axanthic-looking animals. There is however a technical explanation for what makes an axanthic. If we look across multiple species, lines can get a bit blurry when compared to one another. So as technical as we can get with the definition, we need to be a little loose with the definition and not get too hung up on how perfectly the animal meets the criteria of a singular definition. As long as it satisfies genetic inheritance, shows predictability, and we do due diligence to try and add weight to our words when we describe these things, then I think we’ll get it sorted in the long run and start agreeing with each other more.
I (Anthony) get asked a lot by other breeders, "did you prove this information out?" We can't just speculate on this information, it must be proven! Another thing I get told is that none of this can be proven until you map the genome in a lab. Please see my response in the Misconceptions section for that. I agree mapping in a lab is helpful but not the only way and it is only partially correct, and YES I did work to prove nearly every trait in this document, and so have several of the contributors in this document. For those I was unsure of, I reached out to the breeders that did have the numbers to share their data to collaborate on mapping the trait and finding any allelic traits we could. The guide also includes the 10% of phenotypes that are produced that break the results in the Punnett table below. This is because we don't yet know everything, but starting from the framework in this document and promoting better record-keeping practices we can begin to uncover why those phenotypes are produced. This is something that will be impossible to do only using the lineage system commonly in use now. Below is an example of some of the methods used to map how genes behave. Working backward we can use the phenotype ratio to work out the genes. Breeding these animals to get to the LCD or fixed traits and then building them back up to the combos is what we've done since 2005, when I began to notice the patterns for what we were hatching. Once we plugged the numbers into a chart we could see how it could take several seasons before seeing the same phenotype hatch out again.
Example of a simple pairing producing a large number of results and various phenotypes.
Correlation vs. Causation
We are all breeders that will receive a unique set of results that account for our collection’s diversity and our own personal taste in breeding what we like. We may find that when we repeat a breeding in our collection, we get a result that seems conclusive and develop a hypothesis without thinking to test the theory at a deeper level. We have had many conversations discussing correlated breeding results before finding the cause. For example, in one person’s collection they may have many Het phantom yellows, something that could be caused by several yellows coming from a single parent or source that was phantom, which produces all Hets. Leading them to conclude that maybe Het is carried with yellow or all yellows are Het phantom. Another example could be someone using yellow animals to create lavenders and therefore concluding that yellow is the single major factor needed for lavenders. When the cause may be the yellows that originated those animals were all hypo. Therefore, yellow in these examples is correlated to the results but yellow is not the cause of the phenotype that is being produced. We have seen many examples of this over the last several years and breeding every possible combination would take decades to develop conclusive results for an individual breeder, trust us we know how exhausting it can be =).
As a note, while reading, if you find you have unique results, look at different morphs and trait descriptions below, to see if there are other avenues for arriving at the same phenotype. We will do our best to try and cover this, but a full understanding of part 1 and 2 and several years of breeding will be required to have a full grasp of every concept presented here.
Another correlation issue we have seen is attributing a gene to an effect of multiple traits. The brindle name is often referred to as being a gene when in reality it is the ratio of tiger to pin and pattern that causes the characteristic brindle morph to appear. This is why it seems unpredictable when trying to reproduce it. A good off-topic comparison is pancakes, you need the correct ratio of ingredients to make them, too much of any one thing and you get watery batter or something else that’s not a pancake. For genetics, this can be Het for one trait, Hzg for another, which causes a unique phenotype, the phenotype itself is not the trait but a combination of two or more. The other cause of a characteristic has been found to be the right amount of dominance fighting between two traits causing the pattern to form in a particular way. A phantom lilly for example having a faded pattern in a completely different way than another phantom lilly showing more or less white. The traits are correlated but dominance fighting is the cause due to how the pattern forms, not any one particular trait.
Common Misconceptions
- The only true Mendelian traits in crested geckos are Lilly White and Axanthic, the rest are polymorphic traits.
FALSE. Mendelian genetics describes recessive and dominant morphs that occupy the same locus. The incomplete dominant, codominant, multiple non-allelic or epistatic phenotypes, that make up the polymorphs, are part of non-Mendelian genetics, and fall under expanded genetics. In fact, the majority of reptile genetics falls outside of Mendelian genetics. They require a more complex system to determine inheritance and properly describe it. Lilly is incomplete dominant and falls under expanded genetics. None of these were explained in Mendel’s experiments. Karl Correns described these terms. The different variations in lilly white animals only confirm the inheritance of the other traits discussed below and how they behave. The phrase "The only true Mendelian traits in crested geckos are..." is often overused, always makes me think of a quote from Neil deGrasse Tyson "One of the great challenges in life is knowing enough about a subject to think you're right, but not enough about the subject to know you're wrong." Part 1 of Foundation Genetics focuses on these exceptions to Mendelian genetics to help fast-track hobbyists into the world of more complicated genetics and was written to help combat arguments like this. Remember… We’re all still learning and must keep an open mind in order to discover anything new.
- All the other traits are line-bred traits and not true traits.
FALSE. This argument is just poor circular logic stacked with not understanding genetics. It’s like saying “Math doesn’t exist, I have calculated it.” The premise of this argument requires just as much proof as the conclusion. Breeders who use this argument but then sell animals with labels of “strong genetics,” seem to be contradicting themselves. So, is it genetic or not? If it is genetic then there must be traits associated with the phenotype that produced the animal and therefore there must be inheritance. What then is the point of using lineage trees if there is no genetic inheritance and if everything is random? Aside from how often this phrase is repeated and the amount of contradiction it produces, line breeding and why it works so well is due to traits and how they are expressed, which is…you guessed it…genetic.
- Traits can only be confirmed by sequencing the genome.
FALSE. We often see this phrase repeated to invalidate breeding results and breeding data, which is silly because the same people that use this argument use the same argument that only lilly and axanthic are "true morphs". Which have also not been sequenced, so they are arguing against themselves. This argument is usually just another ploy to bring discussions to a halt rather than trying to figure things out as a community.
A good point used to counter this argument is when Mendel made the 3 laws of Mendelian genetics there was no method to sequence the genome of the pea plants he used during his experiments. It wasn’t until the 1940s and 1950s that McClintock discovered transposition and used it to demonstrate that genes are responsible for turning physical characteristics on and off. This was almost 100 years after Mendel. The majority of ball python morphs and other specie’s traits have been determined without genomic sequencing. Lastly, even with genomic sequencing we still need to make phenotypic observations based on real-world breeding results in order to relate the phenotype to the sequenced data, in short, both are necessary for genomic sequencing to tell us anything. Knowing the letter sequence that lies on a locus doesn’t tell us anything until we make observations through breeding results.
- Lineage and the term “proven”.
Lineage has become an all-consuming requirement for many breeders. Since the traits were not properly defined, it is based on the overall look, color, and/or “morph” perception. What is even worse is when lineage is used with the term “proven”, without knowing what the actual traits are, or if they have ever been proven through breeding trials or genetic analysis. Many hobbyists see similar phenotypes being produced and call them proven. Something else that is very common is the buying and trading of animals from other hobbyists and breeders. Until those animals are bred out, over multiple generations, to trait documented animals… you don’t really know what you have and how those traits interact with known traits. Some of the base traits/appearances give a partial idea, but the whole picture is still blurry. When you see breeders showing their breeder lineups, and most have other breeder’s names as “produced by”, how much control over outcomes do you think they have? Giving greater value to an animal, that states “proven” is very subject to inaccuracies… at least in today’s hobby climate. If you believe in the old hobby definition of polymorphic and/or think that only Mendelian genetics can be at play, then using these terms is contradictory to yourself.
- What is a Het or a visual vs nonvisual? Is it codom?
Het is one of the most misunderstood terms in the hobby. Along with codom, visual, and non-visual language to try and make more technical terms such as recessive and dominant easier to understand. However, it has only created a flurry of misunderstood terms and confusion in the hobby. If we instead use the correct terminology, you will find that once you know a trait's inheritance you will have most of the information needed regarding how to breed that morph and what you may expect from the offspring being produced. Adding additional gene data to that and you can improve predictions dramatically.
Het in the hobby means the animal has one copy of the gene, most people use it to describe recessive traits. This means the animal doesn't show an outward appearance of the trait, so it is often accompanied by the phrase "non-visual".
- "Visual" in the hobby is usually used to describe an animal that displays the trait on its body, and often times used to describe recessive traits. Therefore the animal is a Hzg recessive.
- "...carrying a Het". You can literally Google the word Heterozygous to learn that it has no mention of recessive. Yet everyone uses it in place of recessive
. I have no idea how the Het thing has made it so far into the herp hobby that no one has tried to correct this misunderstanding. Anyway, they are trying to say that Het is used to describe recessive mutations that do not show a visual representation of the gene on the animals' skin. If you understand recessive and Het independently then you'll hav e a much happier time discussing genetics. - Codom..., so far no codom genes have been found, everyone really means incomplete dominant.
- How are new morphs just now popping up? Are they recessive or hidden traits in the parents?
This is an excellent question. The traits that seemingly appear out of nowhere can be caused by many factors, googling this information you will find a ton of human factors, but for the ones we’re discussing here, they usually occur in the egg during fertilization. These genes that mutate are best described as variants. New variants can occur at the same locus and when that happens a complex for the variant can form, leading to multiple allelic traits that are usually different in the phenotypes they produce. It is often impossible to tell exactly when a new variant happened. If the initial phenotype was “oddball” marked like they usually are in the community, then it can be released into the population, bred and other offspring carrying the gene can go off to reproduce until someone recognizes it as a gene or stumbles on the Hzg complete or “Super” form of the trait.
- Big breeders have "Closed Collections." Therefore, you shouldn't buy from big breeders because you can't track the lineage.Â
FALSE. Many big breeders have excellent collections. One of the most powerful tools at their disposal is the size of their collections. It allows them to have much deeper diversity pools to choose from when outcrossing lines. Outcrossing keeps heterozygosity high, which is the key to reducing the chances of inbreeding depression. Big breeders didn't become big by inbreeding their collections and selling genetically weak animals. Big breeders share experiences with each other as they refine their groups and are ultimately responsible for building the foundation that most of us stem our collections. Many known large-scale breeders like Repashy, Pangea, ACR, and Northern Gecko are very responsible breeders. They track groups, outcross, and ensure good genetic diversification when breeding their lines, otherwise, they would have crashed decades ago. Instead, we see them coming out with new traits, new phenotypes, excellent structured animals, and they have good fertility rates. That is simply crucial to be effective as a business. This is afforded to them due to the sheer size of their collections and being able to choose from a large pool of animals to continue to maintain that diversity. These pools of animals can be anywhere between 400-7000 in some cases. Different projects represent new genetic diversity potential when outcrossing to unrelated animals, which creates more genetic diversity and higher heterozygosity. If not for this long line of good breeding practices we would have crashed the gene pool by now.
In contrast to small breeders with long lines of lineage, large collections are necessary, small collections make up only a small percentage of the overall genetic diversity amongst the species in captivity. This is why it is important to keep lineage to help avoid sharing related animals and genetically crashing niche pools of the market that circulate within small populations. Something we have seen in the past with reds where the phenotype produced undesirable structural traits. Small breeders overall have less genetic diversity within their collection. In some cases, several can trace lineage back to the same source of pins, yellows, or high patterned animals. Mathematically speaking, if you were to add up the number of pools of genetic diversity within captivity, big breeders have on hand the greatest pool of genetic diversity. This makes the odds of purchasing something too closely related much lower. Another advantage they have is that they have worked with each other to diversify their collections. Trading many animals that represent new bloodlines being outcrossed into their groups regularly. Weak genetic diversity can be spotted as small head structure, underbites, low fertility, and other strange physical characteristics. Something we do not see happening in "closed collections", rather being traced back in shared lineage, and associated with smaller corners of the market.
This discussed misconception is part of a bad cycle of information being passed on by people who are trying to do better but don't understand the genetic key, which is maintaining and rebuilding heterozygosity within your groups. The reliability of breeding records, that have been passed on, has proven to be unreliable. Many breeders have seen an uptake of misrepresented lineage by customers who have lost or incorrectly recall lineage records. Ego, greed, and laziness lend themselves to lies, guesses, mislabeling eggs, and overvaluing animals. Human nature has no place in genetic calculation.
- Phantom is linked to Pinstripe...
This is genetically misrepresented, along with other descriptions found only in the reptile community, and the verbiage is confusing. Traits can be linked but they do not carry each other along for the ride. Linked traits are linked because they are on the same gene or located on a particular chromosome, like sex-linked traits that only females or only males have. The phantom trait is located on its own locus and a pinstripe trait on its own locus. There is no “link” associated between the two and if there were located on the same chromosome this is where genome sequencing would be required or extensive phantom breeding to prove it along with acknowledgment that phantom is a trait and not a "fluke". Another type of link or association we can test for is epistasis this would make a better argument for linking. This means that a gene’s effect is only visible when another trait is present. So far breeding tests only reveal that there are a lot more phantoms mixed with pinstripe but the two do not interact in any way other than contributing to the animal's phenotype.
Here are the first signs and results of pinstripe documented in the hobby by Repashy.
- C2 is a gene that stands for Citrus.
WRONG - If we are going to use names like this in the community we MUST know where they came from so we don’t accidentally confuse ourselves more. Here is an excerpt from the original C2 in 2006 and a 2002 article from Allen Repashy discussing the possibility of a unicolored cream animal. This is history at its best and if you want the condensed version, here it is:
"C2 comes from the cream on cream, Anthony Caponetto coined it C2... think cream squared. These animals exhibited the hypo trait stacked from 2002-2006. Breeding this into the citrus line of yellow tiger animals he produced a new line which he coined C2 Citrus Glow. The naturally hypo citrus morph combined with hypo to produce glowing orange yellow and cream animals. New breeders now thought C2 meant citrus. The original C2 project was not worked on as much. C2 is not a gene but a combo and the gene responsible for their coloration is hypo!"
Allen Repashy Article - Rhacodactylus ciliatus The Perfect Pet Gecko
Current Breeding Practices
Although many of our current breeding practices will remain the same, we expect that trait identification and labeling of animals will improve significantly. We also hope to see trait inheritance making more sense to breeders and find fewer “oddball” description animals pop up. This should get better as people begin to label animals as Het for recessive mutations and understand how heterozygosity works in dominant traits. The oddballs will now have an explanation because of tracked genetic lineage. Improvement in these areas of the hobby will help advance our understanding of morphs. Finally, we have found that "tiger" is a unifying term that explains a significant contribution to phenotypic differences within related siblings. Genetic Lineage is the new system we propose being used. It helps to identify what traits have been passed on to which offspring. This system should give a better prediction of what genes are being inherited and which are not.
Either way, those who do not agree with our findings should not be scrutinized in any negative way. We really do not want breeders to feel pressured to conform or change their practices. The only thing we want to encourage is learning, and a more open-minded community, and hope this information helps to develop lines further. Just have fun!
Genetic Lineage
As mentioned previously, lineage has become an all-consuming requirement for many breeders. Since the traits were not properly defined, it is based on an overall look, color, and/or "morph" perception. What is even worse is when lineage is used with the term "proven" without knowing what the actual genetic traits are or if they have ever been proven through breeding trials or genetic analysis. Many hobbyists see similar phenotypes being produced and call them proven. The herp hobby has already created so much confusing terminology and crested gecko breeders are continuing to add confusion by adding verbiage to their animals without any analysis.
In this document, we propose a new system, for understanding the lineage within your animals and providing more accurate descriptions of offspring. Breeders, who track long lines of genetic lineage, will have some base to see what traits are in the animals they are currently breeding and what has or has not potentially been inherited. Lineage is important, but adding the information of the genetics, within the animal, gives significantly more knowledge as to what the animal can be used for. It only takes one animal to add a dalmatian or phantom to a project. Making sure that information is present is important, as phantom behaves recessively and can be difficult to identify in the animal. The absence of dalmatian spot lineage means nothing to keep it out of a line if a newly paired animal has dalmatian spots. Dalmatian behaves like a dominant trait and can be added in a single generation. We have seen a single spot occasionally pop up and those animals never produce dalmatians. This may be more similar to a freckle. We have also found that some paradoxing is more like birthmarks where there is a chance of it passing on but is a genetically more complex mechanism.
To summarize, genetics that has been passed on visually, and those that are being passed on recessively, should be labeled as Het with lineage of the parents. This helps to reveal the phenotype that is present in the offspring. Something to remember with inc-dom traits… depending on stacking and expression levels, each individual trait can blend and become more or less dominant over other traits. This and the effect of tiger is what accounts for the range of expression within the phenotypes. The same phenotype, displaying the same traits, can have many visual variances. This is one reason why it has been so difficult to define the traits. With a greater understanding of base traits and their interactions, there is greater hope that hobbyists will be able to use the terms "lineage" and "proven" in a genetic sense. This will pave the way for a logical approach to real value and breeding practices. It will bring greater visual impact at a faster rate than we have ever seen in our hobby. Wouldn't it be nice to know what traits you need in order to produce your goal animal? How about being able to purchase or produce what you need, because of known trait lineage? Do not be bound to the old, incorrectly repeated, information. A solid genetic foundation is the way.
Stacking
Stacking is a term that we use to make dominance, through breeding practices and is simple to understand. It also works very well with what is happening from a genetics standpoint. By breeding animals back to other animals, that carry the same trait, we are "stacking", or increasing the dominance of that trait. If we take a trait and stack it up for multiple generations, we see an increase in the level of dominance and expression, of the trait, and the animal passes it on to its offspring. Using a ratio, or levels of stacking, of pin to tiger, tiger to pattern, or all three, pin to tiger to pattern, is useful to describe how orange pattern, white pattern, and tiger develop and affect one another. This helps to describe the animal’s appearance and account for the variation in phenotype development.
Advanced Patterns and color layers
Anthony comes from the entertainment industry where shows are programmed by manipulating video or image layers to create compositions and visual art. Some traits’ influence on color and pattern may, at times, be so strong that they mask each other. Even though the animal still, genetically, has the gene, it is no longer displaying it visually. This is due to another trait suppressing the expression of that trait or overtaking it with a strong coloration. A good example here is melanistic and leucistic traits. These traits are so extreme that you need to breed the animal out to find out what other traits are there. An analogy I use for this is with regards to color, if you reach a maximum white, adding any color to it still yields pure white as all the colors RGB are at their max already. On the other side, melanistic traits add so much black melanin that it is difficult to see if any other trait is there. To describe this effect we use the word “mask.” One common example is the phantom trait, which can mask patterns, creating a patternless-looking animal. This analogy works well to describe how the axanthic, cappuccino, lilly white, and phantom traits work to mask other traits that the animal may genetically have. Additionally, we use “suppress” to describe how the same traits can suppress coloration, but still show signs of the effect of the trait on the animal. A few examples would be how lilly masks dalmatian and sometimes suppresses it. When phantom is involved dalmatian can express again. Phantom suppresses white coloration down a lilly’s dorsal and lateral. The super cappuccino Masks most traits with how significantly it affects the chromatophore by effectively turning off the pipe of yellow and red coloration and directly inhibiting color produced by xanthaphores.
Although this is new verbiage being used that is not common in the community, it does however better align with how things are defined genetically and the well-thought-out concepts in genetics and expanded genetics. This verbiage holds more weight than the marketing terms invented by the hobby that has, so far, led to confusion. Most of this verbiage can be picked up in Part 1 which we will be amending soon.
One last concept here, with reference to layers, is specifically related to the chromatophore. Colors are formed within a 3-layer structure that produces 6 distinct colors and all of the hues in-between. I will occasionally refer to some patterns causing an interference pattern to form. This happens when 2 layers of color are interacting, to create a unique appearance, that is a result of several factors affecting a single part of the animal. An example of this is phantom and cream animals. Say we breed two red base, WP, harleys and they are Het phantom. They will on average produce 25% bicolor red base phantoms. The bi-color dorsal is the cream coloration of the harley phenotype being suppressed by the phantom gene. If it were an orange patterned harley, the animal is more likely be patternless. The darker coloration is not a new gene separate from harley and phantom, but the reaction of both coming together. The concept works well to explain how two distinct things can come together, to create something that is new and unique, and sometimes makes it difficult to see the cause.
How We’re Listing the Morphs
The morphs are going to be divided into Morph Categories to better outline how each interacts with one another. Understanding the data in part one means the morphs here will let you understand the genotype and phenotype differences, giving you the power to use Punnett tables to better predict results and better understand how rare or difficult some phenotypes are to reproduce. Information is outlined under trait details and will list if there are any known or suspected allelic traits. The details will be followed by a brief description, photos, and animal depictions. Under the “with-” section we will describe how other genes affect the phenotype or gene. There are many details and traits that still need work, research, and data. Although we have many morphs and interactions outlined anything that still requires data will be labeled as WIP until we have better descriptions and data on how they work.
EXAMPLE:
Trait or Characteristic name
Description and History of the trait and how it presents in the hobby in its purest form.
Trait details:
CATEGORY: Base, Color, Pattern, Characteristic
GENOTYPE: The letter here can be used for Genotyping in Punnet Squares
PHENOTYPE: Recessive, Dominant, Incomplete or Dominant
ALLELIC WITH: This describes if any known traits occupy the same loci
with-TRAITS
Here we will describe How the individual trait interacts with other traits, and what characteristics we've noticed when both are present.
Variants
Many of the traits we’ll be discussing may have variants, these are unique gene mutations that occupy the same allele. We suspect there to be several we are unaware of in the community and will list that information where appropriate. Some variants are still a WIP as we do not know of every single one out there but using the framework here will help to develop good breeding practices to test the theory if any are found.
It is often impossible to tell exactly when a variant happened, especially if it is recessive. The practice of how we breed most animals and just how widespread they are only make it that much more difficult to know how or when a variant occurred and who was the source. Like we stated in Part 1 the person who identifies and describes the trait is usually the one credited for naming the trait or morph. Even if you have the same gene in your collection and that gene works to produce the same Hzg form then it should still be called by the primary name. Often times the argument of not being able to trace lineage is used to try and stake a unique claim to a name, but in general, a new name is not accepted by the community as it just further adds confusion. Usually the first name proposed is what is used. The reason for this is not just to alleviate confusion but also statistical. The odds of the same trait mutating are low but the odds of the same gene mutating and creating the same exact mutation are so low we have yet to find an exact occurrence of this happening that can be documented in a controlled isolated environment. Therefore it is usually best to just use the primary name followed by your line name to delineate that it is a group that has less lineage tracing to the person that originally described it. A good example of this is axanthics where we have AE Line, MSL Line, and Obscural line. So far the lines seem to all work with each other and likely have the same origin point regardless of how obscure the connection may be.
How do you know if you have a variant?
The best way is to document the phenotype ratio. Calculate the ratio and breed it with the popular form to see if it produces a unique form. Let the math speak for you and hold your animals back to see how they develop to define the new variant properly. You must note Het and Hzg differences if any and define the heritability as dominant, recessive, incomplete, or codominant. Finally, breed it to various other combos to see if you in fact are producing a unique variant as it should be able to be bred to other combos.
Morph SHOCK Warning!!!
Several of the following descriptions for morphs and traits are being modified to accurately depict trait inheritance, morph interactions, and combo morphs. We are keeping almost all the old names but modifying the definitions to describe its behavior as a trait, not a characteristic. Now we can refer to a characteristic, like reverse pin, as being caused by a gene combination, rather than a gene that doesn’t exist. It is the result of pinstripe and tiger interacting with each other. Characteristics are open to broad interpretation by individuals. It is one of the biggest issues with misidentification and breeders making newcomers feel isolated. Having a better understating of an animal's worth, or genetic value will bring a better understanding across the experience levels in the hobby. It will help cull deceitful marketing practices and make for a better community.
In this document, we cover the confirmed traits and popular combo morphs. Additionally, we cover popular combos to denote all the variations that can be produced. Animals we use to depict the traits will be used from the collection of the contributors and are some of the best representations of the trait being described.
How to Develop Your Own Line
This is a basic workflow for starting a line of animals and maintaining heterozygosity for undesirable traits, such as underbites, small crest structure, and other abnormalities that can occur by not outcrossing. Outcrossing animals gives you a large pool of offspring to use to develop a line and add other traits to it down the line. Outcrossing allows for better genetic diversity in the founding groups and throughout the hobby for animals that are sold. This is an important practice to stick to as too many breeders are rushing to produce their own new line. If that line or trait they want to work with is recessive then that means for any recessive mutation to display, relatives with the trait MUST produce a visual trait offspring. Outcrossing these animals gives us the heterozygosity needed to make sure we are not breeding for expressed deformities, which are usually recessive. This chart shows intercrossing done responsibly. Revealing this information and how to do it responsibly is more beneficial than not discussing it. We want to avoid practices such as breeders pairing siblings for several generations in a row. Breeding siblings for several generations in a row limit genetic diversity which, and as seen in other species, could result in shorter lifespans and poor fecundity and genetically weakened animals. This could be simply overcome through regular outbreeding practices and selecting only the most vigorous offspring in each generation. Note that intercrossing is something that focuses on a line to develop a trait, while regular outcrossing and using new animals with a similar appearance is more akin to a project. Until something is established or can be reproduced you do not have a line, you have a project.
In simple terms a line starts with a point that is dragged out to form the line. This means there's a source, and that the line can be traced back to an origin point. Using the word “Line” indicates you have put in due diligence to breed and prove out something. However, too many new breeders just buy new geckos and start a “Line” without knowing what that can produce or prove out any heritability. Lines in general produce something unique and distinct to add to the genetic pool. This isn’t to say a line of harley isn’t viable, as you may take it in a direction that produces a unique and consistent combination of characteristics. Therefore you may produce a type of harley that passes on a desirable flame pattern or freckling and that is the characteristic your line is based on. Whatever “IT” is you must put in the work to solidify the characteristics of that line and be familiar with the phenotype variability it can produce. As AC says when choosing animals to start your line or project.
"Dalmatian is a dominant trait you can easily breed out. Unless your project is at the pinnacle and cannot be improved upon, sometimes it's worth buying an animal with spots even if you don't want them.
In the ball python world, pastel is like that. We are very smart about what we buy with Pastel in it. Sometimes it can't be helped, but if it can, we avoid it. What we don't do, is pass on a snake that will do big things for us because there's an annoying gene present."
NOTE: Direct siblings should be outcrossed for one more season before the first intercross, not depicted below to save on horizontal space.
Inbreeding, Line Breeding, Intercrossing, Outcrossing, and Selective Breeding
Inbreeding is the practice of breeding directly related animals together, especially over many generations. This practice is frowned upon as it can cause issues within a species. Line breeding is selective breeding to closely related lines, in an effort to enhance traits. This practice is more acceptable because it utilizes at least partially outcrossed animals. This method brings in a greater percentage of genetic variance than inbreeding. The important factor is continuing to bring a greater level of genetic diversity into your breeding groups. This level of genetic diversity is called heterozygosity.
Inbreeding and linebreeding reduce heterozygosity to different degrees in their progeny. The loss of genetic material comes along with the gain of stacking some of the same genes that do get inherited from the related animals. These types of breedings are done with many species and are used to enhance or improve specific traits. It helps target single traits, rather than possibly mixing up similar-looking traits from unrelated animals. It creates better odds and shortens development timelines. The loss of some heterozygosity can be easily restored through outcrossing. As long as you outcross to unrelated or less related animals there is no credible threat of inbreeding depression. The stigma of having a limited gene pool, from a small number of originating animals, has not caused the captive population to crash. With every new generation, there are new genetic variances and due to our selective breeding practices we push these variances further. In other words, it means that we have different variances or forms of the same gene. Aside from single genes, each animal has an equal contribution of genes from each parent. The moment you outcross an animal the progeny inherit half of the genetic material from each parent. This shows that one outcrossing can significantly increase heterozygosity.
When hobbyists make you think that we are heading towards a crash, if you don't track family tree type lineage, know that they don't have a clear understanding of heterozygosity and population dynamics. For prolonged development of any trait, with a single point of origin, it is important to outcross in multiple directions. This means that you breed your single or founding animal/s to multiple unrelated animals or groups. Those animals produced from each group will have a different genetic profile, while some will have the desired trait. Those with the desired trait are chosen for continuing the development process. These less related animals can be further outcrossed, bred across the less related groups or bred back to the originating animal. This process creates a stacking of the desired trait. Repeating this process for each set of outcrosses can grow your groups exponentially and lead to having many animals in your project. This is the best method to maintain healthy heterozygosity and expedite development.
Selective breeding is simply selecting for desirable traits and continuing to refine those traits while avoiding inbreeding practices. This causes stacking of the traits we are selecting for when choosing animals. We can also stack multiple traits in multiple directions producing complex advanced phenotypes with several traits contributing to the phenotype. Continuing this trend inevitably creates Hzg forms of the selected traits and produces consistent offspring with less divergence from the parents. Using multiple lines in the same direction is recommended in order to cross those lines together further down the line, these animals do not have to be related.