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Early human ancestors came close to eradication in a severe evolutionary bottleneck between 800,000 and 900,000 years ago, according to scientists.

A genomics analysis of more than 3,000 living people suggested that our ancestors’ total population plummeted to about 1,280 breeding individuals for about 117,000 years. Scientists believe that an extreme climate event could have led to the bottleneck that came close to wiping out our ancestral line.

“The numbers that emerge from our study correspond to those of species that are currently at risk of extinction,” said Prof Giorgio Manzi, an anthropologist at Sapienza University of Rome and a senior author of the research.

However, Manzi and his colleagues believe that the existential pressures of the bottleneck could have triggered the emergence of a new species, Homo heidelbergensis, which some believe is the shared ancestor of modern humans and our cousins, the Neanderthals and Denisovans. Homo sapiens are thought to have emerged about 300,000 years ago.

“It was lucky [that we survived], but … we know from evolutionary biology that the emergence of a new species can happen in small, isolated populations,” said Manzi.

Prof Chris Stringer, the head of human origins at the Natural History Museum in London, who was not involved in the research, said: “It’s an extraordinary length of time. It’s remarkable that we did get through at all. For a population of that size, you just need one bad climate event, an epidemic, a volcanic eruption and you’re gone.”

The decline appears to coincide with significant changes in global climate that turned glaciations into long-term events, a decrease in sea surface temperatures, and a possible long period of drought in Africa and Eurasia. The team behind the work said the time window also coincides with a relatively empty period on the fossil record.

“We know that between about 900,000 and 600,000 years ago, the fossil record in Africa is very scarce, if not almost absent, while both before and after we have a greater number of fossil evidence,” said Manzi. “The same can be said for Eurasia: for example, in Europe we have a species known as Homo antecessor around 800,000 years ago and then nothing for about 200,000 years.”

However, Stringer said there was not convincing evidence for a global “blank” in the fossil record of early humans, raising the possibility that whatever caused the bottleneck was a more local phenomenon. “Maybe this bottleneck population was stuck in some area of Africa surrounded by desert,” he said.

The paper, published in the journal Science, analysed genomic sequences from 3,154 people alive today, from 10 African and 40 non-African populations. By looking at the different versions of genes across a population, it is possible to roughly date when specific genes first emerged – the more time that has elapsed, the more chance for different variants of a gene to crop up. By estimating the frequency with which genes have emerged over time, scientists can gain insights into how ancestral populations grew and shrank over time.

The analysis found evidence for the bottleneck in all the African populations, but only a weak signal of the event was detected in the 40 non-African populations. This is probably due to the ancestors of those of non-African heritage having in effect undergone a more recent population bottleneck during the out-of-Africa migration, which would be expected to mask the earlier event.

The timing roughly coincides with when the last shared ancestor with Neanderthals and another ancient human species, the Denisovans, are believed to have roamed the Earth. Scientists now want to look at whether genetic samples from these ancient cousins share evidence of the same bottleneck, which could give new insights into when, where and why the species diverged.

Hannah Devlin is the Guardian's science correspondent, having previously been science editor of the Times. She has a PhD in biomedical imaging from the University of Oxford. Hannah also presents the Science Weekly podcast.

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