The few babies that are moving out of Dad's cave all look normal colored & short finned.
Can anyone explain the genetic variation for me ?
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Genetically speaking, that would imply that in long finned Ancistrus, the control mechanism does not work. Adding a mechanism that does work, will result in a working system, and thus short finned Ancistrus. Which are carrier for long finnedness, and breeding the ofspring will bring back some long finned Ancistrus.
Assuming finlength is on one gene, I would expect 1/4th being long finned
For the color green a similar approach will help. Apparently, greenness is the result not of green genes, but of the disfunction of genes for other colors but green.
Now, in order to make pigment, one needs a series of enzymes, all doing a small part. And all of them can be incorrect, resulting in lack of that color.
Apparently, the male had his errors on another set of enzymes than the female, and the result is a funtioning set in the offspring. But, they do carry genes incapable of making colors.
Now the problem is, a normal colored Ancistrus has brown, yellow and, apparently, green or blue, resulting in yellow and blue = green. Lack of yellow might result in a seemingly normal Ancistrus - I could not tell.
Therefore, your normal looking offspring might still be lacking yellow.
Breeding the offspring will result in animals lacking brown, and perhaps these will be green again. Others will still be normal, and this will be the majority. Depending on the complexity of normal color and green color, the result will be differend.