So, what's the specifics behind bee mutation?

[Awoigre]

We've been getting into a bee world lately and with all the breeding I've been wondering what exactly goes on behind the scenes with bees, specifically regarding species mutation and hybrids. Getting a new species is easy enough to understand; for example, Noble Princess + Majestic Drone has an 8% chance of making an Imperial Queen... fine, no problems. However, what if I don't get a mutation, but instead get a bunch of hybrids?

I assume (I think I read this somewhere) that the bee traits (of which species is one) are based on Mendelian mechanics, i.e. Punnett squares. So, purebreds have both their dominant and recessive (defined ingame as active and inactive) traits as their species, which we can represent as Mm (Majestic's active and inactive majestic genes) and Nn (same for Noble). Therefore the combinations are MN, Mn, Nm and mn. In the case of Nm and Mn the active gene wins out. However, what happens with the other two cases, where MN and mn come into play? There seems to be no way to get a purebred out of putting two pures of different species into one hive.

Of course, that's just two pures. What if we have a hybrid princess and drone, with Nm and Mn? We end up with NM, Nn, Mm and nm. Seems like combining two hybrids of the same species has a 50% chance of producing a pure of either species, but what happens in the NM or nm case?

On top of that, what about mutation chance? I'm pretty sure I've had drones with one gene as a new species (in this case, Imperial) and the other gene as either of the source species. How does this work? With two purebreds it tells us the chance is 8% of an Imperial queen (according to NEI). Does this work on a genetic level i.e. each time a Noble or Majestic gene gets selected (regardless of dominance) does it have an 8% chance of turning into an Imperial gene if the accompanying gene is Majestic or Noble? If this is the case, then no wonder pures work better; all 4 of their Punnett square results have N and M combinations, whereas only 2 of the hybrid ones do, so with hybrids you'd have half the chance of getting an Imperial gene mutated in... I think?

I think this post is long enough for now (I haven't even touched on pure + hybrid combination, or three-species combinations...). I should point out that I'm not a biologist by any means, and this is just my speculation on the mod's workings; for all I know it could be written entirely differently. If anyone has a better understanding of the mod or the genetics here, feel free to correct me

 

[MilConDoin]

confusion about mutation and inheritance mechanics

Forestry has four aspects which you need to look at:
1) Primary/Secondary genome: Each bee has two genomes, containing all the chromosomes a bee has.
2) Chromosome: Commonly referred to as a trait (e.g. species, effect). Contains two alleles, one primary and one secondary.
3) Active/Inactive: If you view a bee in the Beealyzer, it has two columns (+ the names of the chromosomes). The left one is the active one, the right the inactive one. How a bee behaves is only controlled by its active column. Normally the active column contains the primary alleles for each chromosome, but dominance can change this.
4) Dominant/Recessive: Displayed as red colored allele (dominant) and blue colored allele (recessive). Normally the active allele per chromosome is the one from the primary genome. Exception to this is, when the primary allele is recessive and the secondary allele is dominant. Dominance is fixed by flavor of the allele (e.g. fertility 1 and 2 will always be dominant and fertility 3 and 4 will always be recessive).

A queen knows the primary and secondary genomes from both parents.
Now when a queen dies the following happens for each descendant (1 princess and 1-4 drones):
1) Check (50/50 chance if 1a or 1b is checked) if
1a) Princess.species.PrimaryAllele mutates with Drone.species.SecondaryAllele.
1b) Princess.species.SecondaryAllele mutates with Drone.species.PrimaryAllele.
2) If yes, set the primary and secondary genomes from the parent princess to the mutations base genome.
3) Check (50/50 chance if 3a or 3b is checked) if
3a) Princess.species.PrimaryAllele mutates with Drone.species.SecondaryAllele.
3b) Princess.species.SecondaryAllele mutates with Drone.species.PrimaryAllele.
4) If yes, set the primary and secondary genomes from the parent drone to the mutations base genome.
5) For each chromosome (species, effect, ...) individually choose randomly the primary or secondary allele from the parent princess and the primary or secondary allele from the parent drone. With a 50/50 chance set either the chosen allele from the princess or the chosen allele from the drone as the new primary allele of that chromosome for the descendant. The other one will be the new secondary allele.

If two drones won't stack, despite looking the same in the beealyzer, most of the times it is because you have at least one chromosome where one allele is dominant and the other recessive. This chromosome then has for one drone the primary allele as the dominant one and for the other drone the secondary allele as the dominant one.

 

[MilConDoin]

Here is a complex example, focused mainly on the species and thus the mutation mechanics.
Let's say you have a princess with Noble/Cultivated and a drone with Common/Majestic. The Noble/Cultivated bee will be displayed in the Beealyzer and the tooltip as Cultivated/Noble, since Noble is a recessive (blue) trait and Cultivated a dominant (red) one.
Now let's use the algorithm mentioned above for the descendant princess:
1) Roll a 2 sided die, result: 1a)
1a) Will Noble mutate with Majestic? Capability yes, random roll (8% chance) says the mutation happens.
2) Result for 5) is treated as if the parent princess was a purebred Imperial with 100% default traits.
3) Roll a 2 sided die, result 3b)
3b) Will Cultivated mutate with Common? Capability yes, random roll (10% chance for Noble) says no. Random roll (10% chance for Diligent) says no.
4) nothing happens.
5) Chromosome species: Roll a 2 sided die three times. First result: princess.primary; second result: drone.secondary; third result: princess/drone. So the new princess has Imperial/Majestic as the primary/secondary species. Since Majestic is dominant and Imperial is recessive, the new princess will have Majestic/Imperial as active/inactive, so it will behave like a Majestic bee (no Royal Jelly for you). Just remember, that later mutations will have Imperial as the princesses primary allele.
{Now do step 5 for all the other chromosomes for effect, speed, ...}
After this do the same routine for all the produced drones which can result in different results, e.g. a Diligent/Imperial drone.