[continued from previous message]   
      
   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.   
      
   PNAS paper, this became my 4th most cited publication, and was my second   
   publication accepted as submitted without revision, probably, because we   
   had revised it and checked it out multiple times before submission:   
   https://pubmed.ncbi.nlm.nih.gov/18981413/   
      
   Ron Okimoto   
      
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