Our Human Ancestors Almost Extinct 900,000 Years Ago, Genetics Suggests

For 75 years the Doomsday Clock has been a powerful metaphor, representing how close humanity is to annihilation from threats such as nuclear weapons. Currently set at 90 seconds to midnight, the clock suggests we are closer to disaster today than at any time since it began in 1947.

But if the doomsday warning system was around 900,000 years ago, it would have been estimated that there was only one second left before midnight signaled the end of mankind. Exciting new genetic research shows that our ancestors dwindled to only 1,280 people at the time, and nearly died out long before modern humans existed.

The study, published Thursday in the Science, analyzed the genetic lines of 3,154 modern humans to trace their traits back and show the population patterns that most likely produced their existing genomes. Wangjie Hu, of the Chinese Academy of Sciences, and his colleagues suggest that between 813,000 and 930,000 years ago the early humans that would eventually give rise to our species, Wise man, and experience what geneticists call “the problem.” For unknown reasons, perhaps the harsh environmental conditions, their numbers dropped dramatically to the point where our lineage was on the brink of extinction. Based on estimates from that study, about 98.7 percent of our human ancestors were wiped out.

Paleontologist Chris Stringer, of the Natural History Museum in London, says: “The estimated population of our ancestral lineage is small, and that problem lasted remarkably long, if done correctly.” “If this problem were to happen, it would certainly bring our ancestors closer to extinction.”

Geneticists suggest that the bottleneck may have resulted in increased inbreeding and the subsequent loss of genetic diversity that has continued to this day. They also think that the bottleneck may have given rise to a remarkable new hominin species. The bottleneck timeline is consistent with existing genetic estimates that rely on the same time when a new hominin appeared that may have been the last ancestor of the three large-brained Pleistocene species: Neanderthals, Denisovans and us.

University of Wisconsin-Madison population geneticist Aaron Ragsdale, who was not involved in the research, says the study raises very interesting questions about human evolution at a time when both genetic and fossil data are scarce. “I’m eager to see if their results can be replicated using other methods,” Ragsdale said.

Population fluctuations, even those hundreds of thousands of years ago, leave signatures that can be identified in the genomic sequences of modern humans. To analyze them, a group of researchers led by Chinese geneticists developed a new tool called FitCoal. The researchers used this tool on more than 3,000 live individuals from 10 African and 40 non-African populations. FitCoal’s calculations tracked the population’s number of genetic changes and their likelihood of occurring over time to arrive at estimates of population sizes at different times in evolutionary history.

“Our results suggest that a severe bottleneck brought ancestral populations close to extinction and completely restored the genetic diversity of modern populations,” the authors wrote in the study.

Ragsdale wasn’t sure the situation was that bad. He says: “I think it is far from reaching a conclusion with these results that people’s ancestors were on the verge of extinction. The actual population size is often larger than “breeding” methods such as providing FitCoal, he notes. The advice of a young population over several generations can be reduced in very short periods of time with reduced numbers, he added.

What could have caused the decline? The answers are not found in genetic data, but scientists do know that time saw dramatic changes in Earth’s environment. The middle Pleistocene transition was a time of climate change – including a sharp global cooling about 900,000 years ago that saw the growth of ice, colder oceans, droughts and heavy rains. The wildlife of Africa and Eurasia changed dramatically during this time.

Many studies have shown how climate and environmental change have helped drive major changes in human evolution. But it doesn’t seem like time produced a global population decline among the various hominin species on the planet that weren’t our direct ancestors.

Nick Ashton, a Paleolithic archaeologist at the British Museum who was not involved in the study, notes that many archaeological sites in Africa and Eurasia go through the proposed bottleneck period. That means that any human crash affected only a limited group, probably in Africa, which may have been the ancestors of modern humans. “Looking for the causes of the proposed barrier will be fruitful, whether it is regional drought, volcanoes or other environmental factors,” he said.

Amazingly, studies show that our ancestors were able to survive in very small numbers for a very long time—an estimated 120,000 years. But when conditions again became suitable for human habitation, whether through beneficial climate change or, as the authors point out, technological advances such as human control of fire, our ancestors quickly bounced back. Around 813,000 years ago, all ten Africans in the study appeared to have increased by an average of 20 times.

The Museum of Natural History’s Stringer notes that, like other methods of population reconstruction, FitCoal relies on some assumptions and simplifications such as rates of change. Since the authors have made FitCoal available to researchers, he adds, its accuracy will be further tested, and researchers can use it to investigate populations with other genomes such as those of Neanderthals and Denisovans.

The authors of the study suggest this long period during which our ancestors survived in such small numbers may have led to the emergence of an entirely new species that could be the last ancestor of modern humans and our close relatives the Neanderthals and Denisovans. Ashton says this idea fits genetic evidence that shows the common ancestor of these species lived as recently as 500,000 to 700,000 years ago. “But there are other possible changes,” he said.

For example, fossil studies, tracking morphological changes such as skull and tooth shape, suggested that the lines had already diverged before any bottle, which means that Neanderthals and Denisovans would have avoided its effects.

The estimated bottleneck period is too old to produce any ancient DNA—at least with modern methods. The oldest hominin DNA found is only 400,000 years old. In Africa, the origin of humanity, the climate made the preservation of ancient DNA very difficult.

Artifacts on the ground, such as stone tools and bones, are also difficult to find, but many sites exist from this key period in time. Further examination of skulls and bones found in various parts of eastern and southern Africa, China, Indonesia and Spain may help scientists determine if the changes seen in our bones are consistent with those suggested by genetic models. Ashton says: “The genetic hypothesis should be thoroughly tested on fossil and human skeletal evidence. “This is best achieved through a more thorough dating of current and potential new locations over the proposed period.”