An ‘ancestral bottleneck’ took out nearly 99 percent of the human population 
800,000 years ago

Only 1,280 breeding individuals may have existed at this dramatic era of human 
history.

BY LAURA BAISAS | AUG 31, 2023
https://www.popsci.com/science/human-population-pleistocene/


A team of scientists from the United States, Italy, and China may have finally 
explained a large gap in the African and Eurasian fossil record.

According to a model in a study published August 31 in the journal Science, the 
population of human ancestors crashed between 800,000 and 900,000 years ago.

They estimate that there were only 1,280 breeding individuals alive during this 
transition between the early and middle Pleistocene.

About 98.7 percent of the ancestral population was lost at the beginning of 
this ancestral bottleneck that lasted for roughly 117,000 years, according to 
the study.


During the Late Pleistocene, modern humans spread outside of the African 
continents and other human species like Neanderthals began to go extinct. The 
Australian continent and the Americas also saw humans for the first time and 
the climate was generally cold. This era is best known for its massive ice 
sheets and glaciers that shifted around the planet and shaped many of the 
landforms we see on Earth today..

In this study, the team used a new method called fast infinitesimal time 
coalescent process (FitCoal), as a way to determine ancient demographic 
inferences with modern-day human genomic sequences from 3,154 people.

“The fact that FitCoal can detect the ancient severe bottleneck with even a few 
sequences represents a breakthrough,” study co-author and University of Texas 
Health Science Center at Houston theoretical population geneticist Yun-Xin FU 
said in a statement.

FitCoal helped the team calculate what this ancient loss of life and genetic 
diversity looked like utilizing present-day genome sequences from 10 African 
and 40 non-African populations.

“The gap in the African and Eurasian fossil records can be explained by this 
bottleneck in the Early Stone Age chronologically,” study co-author and 
Sapienza University anthropologist Giorgio Manzi said in a statement.  “It 
coincides with this proposed time period of significant loss of fossil 
evidence.”

Some of the potential reasons behind this population drop are mostly related to 
extremes in climate. Temperatures changed, severe droughts persisted, and food 
sources may have dwindled as animals like mammoths, mastodons, and giant sloths 
went extinct. According to the study, an estimated 65.85 percent of current 
genetic diversity may have been lost due to this bottleneck. The loss in 
genetic diversity prolonged a period of minimal numbers of humans who could 
successfully breed and was a major threat to the species.

However, this bottleneck also may have contributed to a speciation event, which 
happens when two or more species are created from a single lineage. During this 
speciation event, two ancestral chromosomes may have converged to form what is 
now chromosome 2 in modern humans. Chromosome 2 is the second largest human 
chromosome, and spans about 243 million building blocks of DNA base pairs. 
Understanding this split helped the team pinpoint what could be the last common 
ancestor for the Denisovans, Neanderthals, and Homo sapiens (modern humans).

“The novel finding opens a new field in human evolution because it evokes many 
questions, such as the places where these individuals lived, how they overcame 
the catastrophic climate changes, and whether natural selection during the 
bottleneck has accelerated the evolution of human brain,” co-author and East 
China Normal University evolutionary and functional genomics expert Yi-Hsuan 
PAN said in a statement.

In future studies, researchers could continue to find answers to how such a 
small population persisted in the face of climate adversity. It’s possible that 
learning to control fire and a climate that began to shift to be more 
hospitable to human life may have contributed to the rapid human population 
increase about 813,000 years ago.

“These findings are just the start,” study co-author and Shanghai Institute of 
Nutrition and Health theoretical population geneticist and computational 
biologist LI Haipeng said in a statement. “Future goals with this knowledge aim 
to paint a more complete picture of human evolution during this Early to Middle 
Pleistocene transition period, which will in turn continue to unravel the 
mystery that is early human ancestry and evolution.”


Laura Baisas is a science news writer, covering a wide variety of subjects, but 
she is particularly fascinated by all things aquatic, paleontology, 
nanotechnology, and exploring how science influences daily life. Laura is a 
proud former resident of the New Jersey shore, a competitive swimmer, and a 
fierce defender of the Oxford comma.

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