Humanity’s Ancestors Nearly Died Out, Genetic Study Suggests

No place on the planet has escaped the influence of Homo sapiens, from the rainforests cleared for farms to microplastic-laced deep oceans to climate-altered jet streams. Last November, the world population reached 8 billion.

But as omnipresent as humans may be today, a team of scientists now claims that our species came very close to never appearing at all.

Researchers in China have found evidence suggesting that 930,000 years ago, the ancestors of modern humans suffered a massive population crash. They point to a drastic change to the climate that occurred around that time as the cause.

Our ancestors remained at low numbers — fewer than 1,280 breeding individuals — during a period known as a bottleneck. It lasted for over 100,000 years before the population rebounded.

“About 98.7 percent of human ancestors were lost at the beginning of the bottleneck, thus threatening our ancestors with extinction,” the scientists wrote. Their study was published on Thursday in the journal Science.

If the research holds up, it will have provocative implications. It raises the possibility that a climate-driven bottleneck helped split early humans into two evolutionary lineages — one that eventually gave rise to Neanderthals, the other to modern humans.

But outside experts said they were skeptical of the novel statistical methods that the researchers used for the study. “It is a bit like inferring the size of a stone that falls into the middle of the large lake from only the ripples that arrive at the shore some minutes later,” said Stephan Schiffels, a population geneticist at Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

For decades now, scientists have reconstructed the history of our species by analyzing the genes of living people. The studies all take advantage of the same basic facts of our biology: every baby is born with dozens of new genetic mutations, and some of those mutations can be handed down over thousands or even millions of years.

By comparing genetic variations in DNA, scientists can trace people’s ancestry to ancient populations that lived in different parts of the world, moved around and interbred. They can even infer the size of those populations at different times in history.

These studies have gotten more sophisticated as DNA sequencing technology has grown more powerful. Today, scientists can compare the entire genomes of people from different populations.

Every human genome contains over 3 billion genetic letters of DNA, each of which has been passed down for thousands or millions of years — creating a vast record of our history. To read that history, researchers now use increasingly powerful computers that can carry out the vast numbers of calculations required for more realistic models of human evolution.

Haipeng Li, an evolutionary genomics researcher at Chinese Academy of Sciences in Shanghai, and his colleagues spent over a decade creating their own method for reconstructing evolution.

The researchers named the method FitCoal (short for Fast Infinitesimal Time Coalescent). FitCoal lets scientists cut up history into fine slices of time, allowing them to create a model of a million years of evolution divided into periods of months.

“It is a tool we created to figure out the history of different groups of living things, from humans to plants,” Dr. Li said.

At first he and his colleagues focused on animals like fruit flies. But once enough genetic data from our own species had been sequenced, they turned to the history of humans, comparing the genomes of 3,154 people from 50 populations around the world.

The researchers explored various models in order to find one that best explains today’s genetic diversity among humans. They ended up with a scenario that included a near-extinction event among our ancestors 930,000 years ago.

“We realized we had discovered something big about human history,” said Wangjie Hu, a computational biologist at the Icahn School of Medicine at Mount Sinai in New York and an author of the study.

Before the bottleneck, the scientists concluded, the population of our ancestors included about 98,000 breeding individuals. It then shrank to fewer than 1,280 and stayed that small for 117,000 years. Then the population rebounded.

Dr. Hu and his colleagues argue in their paper that this bottleneck is consistent with the fossil record of our human ancestors.

Our branch of the evolutionary tree split from that of other apes about seven million years ago in Africa. Our ancestors had evolved to be tall and big-brained in Africa by about a million years ago. Afterward, some of those early humans spread out to Europe and Asia, evolving into Neanderthals and their cousins, the Denisovans.

Our own lineage continued to evolve into modern humans in Africa.

After decades of fossil hunting, the record of ancient human relatives remains relatively scarce in Africa in the period between 950,000 and 650,000 years ago. The new study offers a potential explanation: there just weren’t enough people to leave behind many remains, Dr. Hu said.

Brenna Henn, a geneticist at the University of California, Davis, who was not involved in the new study, said that a bottleneck was “one plausible interpretation.” But today’s genetic diversity might have been produced by a different evolutionary history, she added.

For example, humans might have diverged into separate populations then come together again. “It would be more powerful to test alternative models,” Dr. Henn said.

Dr. Hu and his colleagues propose that a global climate shift produced the population crash 930,000 years ago. They point to geological evidence that the planet became colder and drier right around the time of their proposed bottleneck. Those conditions may have made it harder for our human ancestors to find food.

But Nick Ashton, an archaeologist at the British Museum, noted that a number of remains of ancient human relatives dating to the time of the bottleneck have been found outside Africa.

If a worldwide disaster caused the human population in Africa to collapse, he said, then it should have made human relatives rarer elsewhere in the world.

“The number of sites in Africa and Eurasia that date to this period suggests that it only affected a limited population, who may have been ancestors of modern humans,” he said.

Dr. Li and his colleagues also drew attention to the fact that modern humans appear to have split from Neanderthals and Denisovans after their proposed population crash. They speculate that the two events are related.

The researchers noted that most apes have 24 pairs of chromosomes. Humans have only 23, thanks to the fusion of two sets. After the crash, the scientists suggest, a fused set of chromosomes may have arisen and spread through the tiny population.

“All humans with 24 pairs of chromosomes became extinct, while only the small isolated population with 23 pairs of chromosomes fortunately survived and passed down from generation to generation,” said Ziqian Hao, a bioinformatics researcher at Shandong First Medical University and an author of the study.

But Dr. Schiffels isn’t buying the story of the bottleneck quite yet: “The finding is very surprising indeed, and I think the more surprising the claim, the better the evidence should be.”