Re: human population bottleneck

On 12/25/2024 4:40 PM, erik simpson wrote:

https://www.science.org/doi/10.1126/science.abq7487
 Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition
 Abstract
Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.
 We had a narrow escape from extinction.  When I read the news, sometimes I think it's too bad we made it.
 

The estimate for when this bottleneck occurred has been going back further in time for decades.  The initial estimates at the turn of the century that I recall were less than 100,000 years ago, but those estimates were biased by the fact that nearly all DNA sequence came from individuals of non African ancestry, so they were getting an estimate of the subpopulation that made it out of Africa.
The estimate of around 1,000 individuals has been around for a long time, but it sounds like the loss of ancestors occurred over a fairly long time period due to reduced population size and likely truncation of existing families.  There were more than 1,000 individuals breeding during the low population levels, but a lot of lineages went extinct during that 117,000 year period.  It could even be a speciation event where a subpopulation took over.  The chromosome fusion creating human chromosome 2 has been estimated to have occurred 900,000 years ago. Such fusions (if they are associated with reduction in viable gametes) can be fixed in a small population.  As this small population expanded in size it could interbreed with individuals that did not have the fusion, but gene flow would be reduced (hybrids would produce fewer viable gametes).  So even as the fusion containing population expanded, they would displace more than integrate other populations.  The take over may have taken a hundred thousand years.  The initial population may have been a lot smaller than 1,000 individuals with the fusion, but they would have picked up genetic variation from surrounding populations, but the gene flow would be restricted.
Ron Okimoto