" This is why the term inbreeding depression exists and is a real phenomenon."

There is no question that inbreeding can lead to loss of vigor, even to the point where reproduction fails entirely or disease issues become unmanageable.  Someday we may get smart enough to understand why this happens.  In the meantime it is 100% clear it is not due to loss of allelic diversity.  Consider the evidence from guppies or mice as just two examples.  You start a breeding program with related individuals.  You mate brother to sister every generation.  Each generation you make some selection.  Generally the first thing you select for is vigor.  Some lines get so weak they fail to reproduce and are lost.  Other lines continue to get weaker until roughly the eight generation.  They then level out in vigor and start to improve.  By the time you have done 20 consecutive generations of brother to sister matings you can be back to the vigor you had at the start of the program and it will continue to improve after that.  This continued improvement drives Toxicologist nuts because they can not repeat a study done 25 years ago with the same inbred strain of mice because the new ones are more vigorous than the old ones.  This is particularly true in reproduction studies.  By that point you have long since eliminated genetic diversity, even in the immune system.  Obviously, loss of genetic diversity is not the cause of inbreeding suppression.  The general public thinks both inbreeding suppression and hybrid vigor are easy to understand.  Professional geneticists are happy to tell you they do not understand why either exists.

Another aspect is how many generations back is inbreeding important?  In my last post I mentioned Wright's inbreeding coefficients.  Well, a big problem with that calculation is how many generations back do you go?  Five?  Ten?  Fifty?  Take humans as an example.  If you go back for 3000 or 4000 generations we as a species are horribly inbred according to that kind of calculation.  Likely much closer than 1st cousins.  Push it back a few million years and the calculation would say we are 100% inbred.  Obviously after some number of generations such calculations are meaningless.  It probably is not many generations either.  Some number like ten is probably as far back as meaningful.  So, it makes no real difference if our bees were genetically bottle necked 50 years ago.  All that really matters is what happened in the last ten.  I see no evidence that any bottle necking has happened recently in commercial honey bees.  We have exactly one single gene where honey bees require  diversity.  That is at the sex determination locus.  In the US there is no evidence we have lost enough allelic diversity at this locus to cause any problems and that locus would be expected to be the first to show evidence of too much inbreeding.

Dick

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