Phantom is widely accepted as a recessive mutation that suppresses coverage pattern (Harlequin), but all evidence actually points to Harlequin being the gene that adds coverage pattern to Phantom. Because of the typical inheritance ratios we find between Phantoms and Non-Phantoms, these traits cannot inherit independently from one another.
The only possible inheritance scenarios are:
1.) When Harlequin is absent, what remains is Phantom. Geckos with only one copy of Harlequin will be able to produce Phantoms directly, while those with two copies (higher expression/extreme Harlequins) will not. Inheritance in this scenario behaves exactly as if Phantom were an independent recessive mutation.
2.) Phantom is a recessive mutation that suppresses Harlequin...however for this to be true and follow observed offspring ratios, Harlequin would need to be the "Wild Type" (innate pattern).
Below are some important points to consider:
Historical Context: Wild populations and early hobbyist collections were predominantly "Patternless" (Phantom). The emergence and subsequent selection for the visually striking Harlequin pattern dramatically shifted the phenotypic landscape. The term “Phantom” only entered the hobby ~2007, (thirteen years after its inception) when “Patternless” geckos were produced from “Patterned/Harlequin” individuals. This occurrence should be considered in the two inheritance scenarios mentioned above…
Harlequin is Dominant to Phantom
Phantom suppresses Harlequin
Harlequin Evolution: The significant changes in Harlequin expression observed within the hobby over time demonstrate the selection for a gene's expression.
Het Impact: The presence of Harlequin in heterozygous form correlates with specific base color combinations that predict the potential to produce Phantom offspring (ie. Yellow non-Phantoms, Red Harlequin). This phenomenon is not characteristic of a recessive mutation. There is currently no explanation as to how this correlation falls in line with the recessive "suppression" definition.
Finding - Harlequin has a mechanism that can be tracked. Harlequin impacts Yellow base color to create Orange and White Pattern. This can be tracked by observing Base Color inheritance between Phantom and Non-Phantom phenotypes.
A tremendous amount of flexibility surrounds the current “definitions” of Phantom; however there is actually no evidence to support Phantom’s recessive “suppressor” definition that cannot be more intuitively explained by the lack of Harlequin’s impact! Adopting the new viewpoint below will enable us to correctly track and attribute other genetic variables and Base Color inheritance.
Phantom likely represents the ancestral, "default" state.
Harlequin is the gene that introduces pattern and modifies base color.
The apparent "recessive" nature of Phantom stems from the absence of Harlequin's influence.
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