"My question, is the loss of allele diversity and a genetic bottleneck the same thing?"

The only practical way to cause a genetic bottleneck is by purposely inbreeding for some generations.  In nature this can happen if a species is nearly wiped out resulting in all survivors being closely related.  So inbreeding will cause a loss of allelic diversity.  An exception might be something like the sex chromosomes in bees where there is very strong selection pressure to maintain diversity.  But, you can lose diversity in a large population also simply due to statistics.  Say you had some allele that existed in some population at a rate of .001%.  All it takes to lose that allele is one generation where it does not get passed on unless the population is so huge it becomes statistically improbable that it would fail to get passed on.  Pretty minor selection pressure can change allele frequencies in a population, either resulting in elimination or in it becoming much more common.  The blue eye mutation in humans happened only once about 8000 years ago.  Look at all the people today with blue eyes after only about 400 generations.  There must be some selection pressure to have caused the frequency of that mutant to grow to today's state.

In animals where both sexes are diploid you find lots of hidden recessives that are not favorable at all when homozygous.  Some are lethals when homozygous like the CF mutant I carry.  Many are sub lethals.  In honey bees such mutants get eliminated very fast as drones are haploid and die when they get such a mutant.  Likely a lot of the genetic diversity in honey bees is either simply noise that does nothing or mutants in the gene control regions where changes are better tolerated.  Noise can be lots of things.  A big one, in terms of how often it is seen, is base substitutions in the protein coding region that do not change the amino acid coded.  About 1/3 of all single base substitutions fall in this class.  As there is no change in the protein such mutants seldom have any impact on survival of the critter.  It is not at all uncommon to sequence one modest sized gene in 25 random  individuals and see ten or more such silent mutations.  Inbreeding would reduce the frequency of such mutants in the population but have no impact on survival.

I feel this is not a very satisfactory answer, but do not know how to do better.

Dick

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