At some point in the deep past, humans may have come frighteningly close to disappearing altogether. Here’s what we know, according to research.
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According to genetic evidence published in a 2023 study from Science, our ancestors experienced an extreme population bottleneck around 900,000 years ago. This means just over a thousand breeding individuals persisted for more than 100,000 years. If true, this would’ve been one of the most severe population crashes ever inferred for a large mammal. In fact, a crash as severe as this could have potentially erased the human lineage before it truly began.
The idea has captured public imagination because it reframes our evolution. Most would assume, given our success, that it’s been a steady ascent, rather than a narrow escape. Yet, as with any extraordinary scientific claim, it has also sparked intense debate.
Many now wonder whether or not this was really a near-extinction event — or if what we’re actually seeing is a mirage created by the limits of genetic inference. The truth of the matter lies at the intersection of genomics, climate change and the deep uncertainties of reconstructing life nearly a million years in the past.
Here’s a breakdown of what we know, according to research.
A Bottleneck Hidden In Human DNA
This story started with modern human genomes rather than fossils. In the 2023 study, a team of researchers analyzed genetic data from more than 3,000 present-day individuals across both African and non-African populations. Notably, they employed a newly developed statistical method called FitCoal (Fast Infinitesimal Time Coalescent Process). With this, they were able to reconstruct changes in ancestral population size far deeper in time than most previous methods would’ve allowed.
The results showed that, between roughly 930,000 and 813,000 years ago, the effective human population size appeared to have plunged down to around 1,280 individuals — a decline of more than 98% from earlier levels. To greater surprise, the findings suggest that this bottleneck persisted for over 100,000 years, which is an uncommonly long time for such a severe demographic collapse.
In evolutionary terms, this means that humans were on the verge of extinction.
An important distinction to note, however, is that effective population size is not the same thing as the total population, or headcount. Instead, it refers to the number of individuals contributing genes to the next generation: people who were able to successfully breed. But even accounting for this distinction, that inferred population is still extraordinarily small for a species that has since proliferated across the globe.
Genetics alone doesn’t explain why exactly this bottleneck occurred. That said, it likely isn’t a coincidence that the timing matches up with a period of profound environmental upheaval: the Early–Middle Pleistocene Transition.
During this period, around one million years ago, the Earth’s climate system was changing dramatically. This shift was especially influential on glacial cycles, which became longer, colder and much more extreme. Ice sheets expanded and sea levels dropped; in turn, ecosystems across Africa and Eurasia were repeatedly disrupted.
For early human ancestors (most likely members of the genus Homo predating Homo heidelbergensis), these changes would have been devastating. Food sources would have been scarce and their habitats were likely fragmented, which would’ve made survival especially difficult.
The authors of the study argue that this prolonged environmental stress may explain why human populations remained at dangerously low levels for tens of thousands of years. It’s also argued that this is why they weren’t able to rebound as quickly as many species do after short-term crashes. And if these findings are correct, then this bottleneck may have shaped the entire trajectory of human evolution.
How Humans Hit The Genetic Reset Button
One of the most intriguing implications of the proposed bottleneck is the role it may have played in human speciation. Specifically, the bottleneck’s timing seemingly aligns with when the fossil record becomes markedly sparse and ambiguous, and is only later followed by the emergence of more recognizable human forms.
Some speculate that this population crash could have served as a genetic “reset,” in the sense that it may have reduced diversity and set the stage for later evolutionary innovations.
What’s particularly notable is that this bottleneck also coincides with estimates for when humans may have lost one pair of ancestral chromosomes. That is, the point in time where we shifted from having 48 chromosomes, like other great apes, to the 46 chromosomes that we have today.
Although this chromosomal fusion alone did not make us human, it would’ve made it much easier for a small, isolated population to exhibit genetic changes that could successfully spread and become fixed.
One important question many have asked in the wake of the 2023 study is: If we actually did nearly go extinct, then why did it take us so long to find out about it? This is a valid question, the answer to which lies in the limits of traditional demographic models.
Most earlier methods have shown little reliability in inferring population sizes beyond a few hundred thousand years. This is because genetic signals from long ago can become blurred by mutation, recombination and later population expansions — especially the explosive growth of humans over the past 50,000 years. FitCoal was designed to overcome some of these limitations by modeling the genealogical process at much finer time scales.
In simpler terms, rather than averaging over long periods, FitCoal attempts to capture rapid changes in population size, even those buried deep in evolutionary history. This is the methodological advance that made it possible for the 2023 study to detect a signal that previous analyses may have missed.
However, new tools also bring new risks.
Did Humans Really Face Near-Extinction?
Not all geneticists are convinced that the 900,000-year bottleneck reflects a real demographic catastrophe. In a subsequent 2024 study published in the journal Genetics, other researchers argued that the signal discovered in the 2023 study could have been a statistical artifact: a pattern created by assumptions in the model, rather than a bona fide population crash.
One key concern that supports this critique is population structure. Early humans were not a single, well-mixed population, as they likely existed in fragmented groups across Africa, with limited gene flow between them. If a structure like this were indeed ignored, FitCoal could have mistakenly inferred a sharp decline in population size.
Another issue is introgression, or gene flow from archaic hominin groups. As further 2025 research from Molecular Biology and Evolution argues, mixing between diverging populations can distort estimates of effective population size, which would make it appear smaller than it really was. Critics also point out that fossil evidence doesn’t unequivocally suggest a near-extinction event at this time, although the fossil record itself is notoriously incomplete.
In other words, even if the genetic signal is real, we still can’t be 100% certain as to what it really means.
So, did humanity really almost vanish 900,000 years ago? The most honest answer is: possibly, but we don’t know for sure. The 2023 Science study presents one of the strongest genetic cases ever made for an ancient human bottleneck.
On one hand, it was methodologically sophisticated, statistically rigorous and largely consistent with major climatic disruptions in Earth’s history. But on the other hand, the claims made push demographic inference to its limits. Small modeling assumptions can have large effects when reconstructing events that occurred nearly a million years ago.
Why This Matters To Us Humans Today
If humanity survived a near-extinction event, then our existence today is the product of extraordinary contingency. It would mean that our intelligence, culture and technology were not as inevitable as we believe, but rather that they’re mere possibilities that survived a bottleneck few species escape.
On top of this, it also reframes our resilience as a species. Humans did not emerge because we were invincible, but because small populations adapted, endured and eventually expanded when conditions allowed.
But, most importantly, even if near extinction isn’t what the exact reality was at the time — which no one truly knows yet — what’s nevertheless clear is that early human populations were far more fragile than once thought. Whether they dwindled to a few thousand individuals or merely endured prolonged hardship, it’s still a reminder for us to approach human evolution with humility, as it probably wasn’t as smooth an ascent as we’d think.
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