"With 10% being ligustica, and 90% being
carnica, what 10% was ligustica?"

Drawing a global conclusion based on haplotype is meaningless.  Haplotype is simply some short conserved hunk of DNA..  In bees it has to be pretty short due to the super high cross over rate.  Then you also must remember we do not even know the DNA sequence of the honey bee very well at all.  For perspective on how well we know total sequences consider the situation in humans.  Clinton had a big press conference and announced we knew the total human genome in 1998 or 99.  Within weeks the scientists involved realized the data was garbage and no one has looked at that data since as it was replaced by "better" data produced by Craig Venter within a month after the press conference.  Since then periodically another announcement has been forthcoming saying we actually know the human genome this time and have corrected the errors in the prior versions.  Maybe in another 25 years we will get it right for humans.  Now, another perspective.  Humans are easy compared to the honey bee from what I have read.

So, what you have is a mess in terms of detailed knowledge of the total DNA sequence, an animal known to experience a very high cross over rate during sex cell production and a short hunk of DNA that is well known and called a haplotype.  What conclusion should you draw from such data?  Probably the best conclusion is none at all.  That haplotype likely tells you nothing at all about how the colony behaves and for sure nothing at all about the 99+% of the genome outside the haplotype section.

By the way, just to make things even more complex it is well known that cross over rates are under genetic control and thus can vary wildly from one individual of a given species to another individual of that same species.  Thus to say that the cross over rate between two loci is say 25% can be true if the rate has been measured in a few hundred unrelated individuals but is a meaningless statement for a population if measured on only a small number of  individuals, particularly if they happen to be related.

Color you can see with your eye is also meaningless.  Color, like the quoted haplotype simply tells you something about a very tiny hunk of the total DNA and nothing at all about the vast bulk of DNA.  It would be perfectly reasonable for an It colored queen to head a colony that had classic Carny behavior or to have a black as your hat queen that headed a colony that had classic It behavior.

Forget genetics for a moment.  Rather, consider money.  Say that I tell you that six different people each have a penny as part of their bank savings account.  Now, one of those people might have $1 million in the bank and another might have $35 total in the bank.  Knowing each has a penny tells you zero about anyone's total balance.  Just like knowing a tiny hunk of DNA in the queen tells you zero about the total behavior of some colony of bees.

Dick

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