Did Humans Nearly Go Extinct?

Humans are strikingly similar to one another genetically. Two chimpanzees from neighbouring forests in central Africa can differ more than two people from opposite sides of the planet. For decades, that low diversity has invited a dramatic explanation: at some point, our ancestors were reduced to a very small population and squeezed through a bottleneck.

Two candidate catastrophes have dominated the debate. One is a supervolcano. The other is a long, slow crisis nearly a million years ago. Here is how each claim holds up.

Toba: the biggest eruption in two million years

About 74,000 years ago, the Toba volcano on Sumatra erupted with a force unmatched in the last two million years. It ejected on the order of 2,800 cubic kilometres of material — thousands of times more than Mount St Helens in 1980. Lake Toba, 100 kilometres long, fills the collapsed caldera today. Ash fell as far away as India, where layers several metres thick survive, and fine glass shards reached southern Africa.

In 1998 the anthropologist Stanley Ambrose connected the eruption to the genetic evidence. His Toba catastrophe hypothesis proposed that years of volcanic winter and a millennium of cold killed most humans, leaving perhaps a few thousand to 10,000 survivors, and that later human populations diversified rapidly from this remnant.

Why the Toba catastrophe has faded

The hypothesis made a testable prediction: if you find the Toba ash layer at an archaeological site, human activity should crash above it. When archaeologists found such sites, it didn’t.

Jwalapuram, India

Michael Petraglia’s team found stone tools directly below and above the Toba ash in southern India, made in similar ways on both sides. Whoever lived there came through the eruption, at least locally.

Pinnacle Point, South Africa

In 2018, Eugene Smith and colleagues identified microscopic Toba glass shards in sediments at Pinnacle Point 5-6 on the south coast of South Africa, 9,000 kilometres from the volcano. The human occupation not only continued through the eruption layer; it intensified.

Shinfa-Metema 1, Ethiopia

In 2024, John Kappelman’s team found Toba shards at a riverside site in northwest Ethiopia. People there seem to have adapted to drier conditions after the eruption by fishing in shrinking seasonal pools and following rivers — “blue highways” that may even have helped carry people out of Africa.

Lake Malawi

Sediment cores from Lake Malawi, which trap Toba ash, show no major cooling or vegetation collapse in East Africa after the eruption.

Toba was a genuine global event. It simply does not appear to have been an extinction-level one for our species.

The genetic side of the argument

Part of Toba’s original appeal came from a misunderstood number. Geneticists often estimate human effective population size at around 10,000. That does not mean only 10,000 people were alive. Effective size is a long-term average that reflects how much genetic variation a population keeps; a species spread across a continent in many small, loosely connected groups can have millions of individuals over time and still have a low effective size.

So low diversity is evidence of a smallish, structured ancestral population over a long time — not necessarily of one sudden near-extinction event.

The 900,000-year-old bottleneck

In 2023 Wangjie Hu, Haipeng Li and colleagues published a far more startling claim in Science. Using a new method called FitCoal, which reconstructs past population sizes from patterns of variation in modern genomes, they analysed 3,154 genomes from 50 populations. They concluded that our ancestors crashed from around 100,000 breeding individuals to about 1,280, starting roughly 930,000 years ago, and stayed at that level for some 117,000 years.

The timing is intriguing. It overlaps the Mid-Pleistocene Transition, when glacial cycles lengthened and intensified, and it coincides with a notable gap in the African and Eurasian hominin fossil record. The authors also suggested the squeeze might relate to the fusion of two ancestral chromosomes into human chromosome 2, and to the origin of the lineage that later split into Neanderthals, Denisovans and us.

Why many geneticists are unconvinced

Several independent teams have pushed back:

• Other methods don’t see it. Widely used techniques such as PSMC and Relate, applied to the same kind of data, do not detect a severe crash at that time.
• Simulations can mislead it. A 2024 critique argued that FitCoal can infer a spurious bottleneck from population histories that never had one, depending on assumptions.
• Population structure mimics bottlenecks. If ancestral humans lived in partly separated groups that later merged, genetic signals can look like a population crash without one happening.
• It is hard to reconcile with the map. Hominins were widespread in Africa and Eurasia at the time. A total of 1,280 breeding adults for 117,000 years would require most of those groups to contribute nothing to us.

The claim has not been refuted, but it has not been confirmed either. The honest position is that it is a serious hypothesis with serious objections.

The bottlenecks we are sure of

Real, well-documented bottlenecks exist, just on a smaller scale. The small groups that left Africa roughly 60,000–50,000 years ago carried only part of Africa’s variation, which is why African populations remain the most genetically diverse on Earth. The first people into the Americas passed through a further founder bottleneck. And late Neanderthals had extremely low diversity, with long runs of identical DNA in some individuals — a sign of small, inbred groups on a path to extinction.

What it means

Our species may never have come within a whisker of vanishing in a single catastrophe. The more likely story is quieter: a population that was small, scattered and patchily connected for hundreds of thousands of years, surviving climate swings through flexibility rather than luck. That is less cinematic than a supervolcano — and arguably more impressive.