[continued from previous message]   
      
   > I do think that evolutionary models need to deal with the genetic load   
   > and inbreeding.  I believe that the deleterious genetic load in the   
   > population is very important in maintaining genetic variation and   
   > selection progress in a population.  It may be a major factor in why   
   > populations fail, and why others take over.  Why is the spotted owl   
   > currently being out competed by the midwestern subspecies when they   
   > normally come into contact each warm interglacial period when Canada   
   > becomes forested instead of being covered with ice.   
   >   
   > The Wrangel Island mammoth went extinct due to inbreeding depression. We   
   > can get ancient DNA samples and the ice age megafauna of past ice ages   
   > were less inbred and more genetically diverse than the last couple of   
   > ice ages.  My guess is that the longer cold periods of the last half   
   > million years has allowed over selection for cold adaptation, and the   
   > variation that was needed to adapt to the warmer interglacial periods   
   > was mostly lost.  A couple papers have noted that more ancient   
   > populations had more warm adapted variants segregating than the most   
   > recent ice age populations.  They had adapted to cooling conditions for   
   > a couple million years, but had maintained the genetic variants needed   
   > to deal with the warmer interglacial periods until this last cold   
   > period.  Even though the populations reexpanded during this last glacial   
   > period and their populations recovered to what they had been during   
   > other glacial periods their genetics remained inbred.  It seems that   
   > fewer isolated populations survived to remix after their territories   
   > reexpanded to allow the previously isolated populations to come together   
   > and restore genetic diversity to the species.  My guess is that   
   > inbreeding depression was a major cause of the extinctions of the mega   
   > fauna when they were again isolated to small populations during the   
   > current interglacial.   
   >   
   > I was involved in the first genome variation analysis of the domestic   
   > chicken population.  The paper was published in PNAS.  With genetic   
   > markers spread across the genome we could estimate inbreeding levels for   
   > each population that we had included in the study.  We could also   
   > conclude that the commercial lines only had a minor fraction of the   
   > genetic diversity found among the populations that we had tested.  Some   
   > of the commercial population were highly inbred (Fst over 0.8). Multiple   
   > breeder companies were involved in the study, but several of them   
   > objected to the findings.  We had an internal peer review that was more   
   > rigorous than any that I had previously been associated with. Everything   
   > was cross checked and assumptions verified and or noted.  In the end the   
   > results were just what they were, and several companies removed   
   > themselves as authors on the paper.  What we did not put in the paper   
   > (because the breeder companies did not provide the pedigree information)   
   > was that the inbreeding levels were much lower than we expected them to   
   > be.  It is well known that commercial breeders try to limit inbreeding   
   > to less than 1% per generation in order to maintain genetic progress due   
   > to selection, but some of the lines had been closed lines for over 50   
   > generations, and we started with birds inbred due to being bred to a   
   > standard.  Before the modern commercial breeding industry started in the   
   > 1950's nearly all breeders sold chickens bred to a physical standard   
   > (the American Standard of perfection).  The commercial industry started   
   > with birds like White Plymouth Rocks that had been bred to the standard   
   > since the 19th century.   
   >   
   > Somehow commercial breeders had selected for heterozygousity within   
   > closed lines under intense selection.  Our birds were less inbred than   
   > we expected them to be.  My take is that we were able to detect   
   > inbreeding depression (dominance and gene interactions) and were able to   
   > identify the least inbred (alleles identical by descent) sibs by   
   > phenotype.  This means that nature can do the same thing.  So   
   > deleterious loci would be important in the selection and success of a   
   > population, and we do not have the tools to detect and quantify the   
   > dominance and gene interaction effects that are significant even though   
   > when we look with our current models and analytical techniques we   
   > usually do not find these factors to be significant.   
      
   If you try to model genetic load and inbreeding depression in   
   populations.  What the above results indicate is that as long as the   
   selection intensity remains high you can select against inbreeding   
   depression and maintain genetic diversity when inbreeding is an issue.   
   This is likely due to the homozygotes being differentiated from the   
   heterozygotes by phenotype.  I can't divulge my companies selection   
   intensity numbers, but it is high because of the number of progeny that   
   individuals can be responsible for, but we always generate the same   
   Pedigree breeder population size.  For dairy you have to consider that   
   there are millions of Holstein dairy cattle, but the effective   
   population size is estimated to only be around 50 due to selection in   
   the elite herd that produces the dairy bulls.  To counter inbreeding   
   depression you need a large number of progeny produced and high   
   selection intensity.   
      
   The population bottleneck that humans went through to leave us with   
   about 1/5 the genetic diversity found in most species (even as decimated   
   and chimps are they still have 3 times the genetic diversity as humans)   
   the effective population size went down to around 1,000.  This has been   
   considered to be a near extinction event, but it may have been a   
   speciation event.  The population became more inbred and lost genetic   
   diversity, but we must have also lost a lot of the genetic load.  It may   
   have been chance due to founder effects, but we think that humans have   
   such a low genetic load (Japanese quail have a genetic load estimate of   
   8.0) because hominids reproduced in small family groups where there was   
   often close inbreeding (Neanderthal and Denisovan DNA indicate   
   inbreeding in their family units).  So family groups would either purge   
   genetic deleterious loci or they would fail to reproduce.  So for humans   
   it was likely the number of family groups that determined whether or not   
   our species survived.  Genetically healthy family groups would multiply   
   and split and where there was inbreeding depression those families would   
   be lost.  Somewhere along the line our ancestors figured out that   
   inbreeding wasn't such a good idea, and enacted cultural genetic sharing   
   between family groups, and created taboos against breeding within a family.   
      
   Like the quail example high genetic loads can be maintained in a healthy   
   population.  There are species like the Wood Rat, that are obligate   
   outcrossers, and do not mate with relatives, that have a genetic load of   
   15.  The quail are derived from the Asian migratory quail that have a   
   high reproductive rate.  They can actually breed during their migration   
   like Monarch butterflies.  The quail sexually mature in six weeks and   
   breed again, during their migration from Asia to Africa.  If these   
   species suffer a population bottle neck they would go extinct.   
   Researchers have been unable to create a highly inbred line of Japanese   
   quail.  Some have gotten to 0.5 inbreeding, but the actual inbreeding   
      
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