Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition

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Today, there are more than 8 billion human beings on the planet. We dominate Earth’s landscapes, and our activities are driving large numbers of other species to extinction. Had a researcher looked at the world sometime between 800,000 and 900,000 years ago, however, the picture would have been quite different. Hu et al. used a newly developed coalescent model to predict past human population sizes from more than 3000 present-day human genomes (see the Perspective by Ashton and Stringer). The model detected a reduction in the population size of our ancestors from about 100,000 to about 1000 individuals, which persisted for about 100,000 years. The decline appears to have coincided with both major climate change and subsequent speciation events. —Sacha Vignieri

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.
RELATED PERSPECTIVE
Did our ancestors nearly die out?
BY NICK ASHTON, CHRIS STRINGER


 

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