Human ancestors may have almost died out after ancient population crash

Almost 99% of all human ancestors may have been wiped out around 930,000 years ago, a new paper has claimed.

The new research, published in the journal Science, used DNA from living people to suggest that humans went through a bottleneck, an event where populations shrink drastically. The paper estimates that as few as 1,300 humans were left for a period of around 120,000 years.

While the exact causes aren't certain, the near-extinction has been blamed on Africa’s climate getting much colder and drier.

Dr Yi-Hsuan Pan, who co-authored the research, says, ‘The novel finding opens a new field in human evolution by raising many new questions.’

‘Where did these individuals live? How did they overcome catastrophic climate change? And did natural selection during the bottleneck affect their evolution? All this remains to be answered.’

While other scientists have welcomed the research, they have questions over just how severe this bottleneck was.

Professor Chris Stringer, an expert in human evolution from the Natural History Museum who reviewed the paper, says, ‘During the period of the bottleneck, there are a number of sites that record evidence of human occupation. This could mean that there wasn’t a bottleneck, but could equally mean it only had a localised impact on part of the human population.’

‘While there are a lot of uncertainties around this proposed bottleneck, it raises some interesting ideas and demonstrates the need for more fossils from this point in human evolution to answer fundamental questions about our origins.’

How was the human bottleneck discovered?

Evolution is full of bottlenecks, and the history of humanity is no different. Disease, natural disasters and climate change can all drive species to the edge of extinction, forcing them to adapt or die.

Not all bottlenecks are as violent, however, and perhaps the most notable bottleneck in human history is an example of this. When our species, Homo sapiens, left Africa, only a small group of the entire population went on this migration.

At a genetic level, this means that only a fraction of the Homo sapiens gene pool was brought along for the journey. When examining the DNA of living people, the signature of this bottleneck can be seen in the genetics of people with non-African heritage.

The bottleneck discovered in the current research happened hundreds of thousands of years before this 'Out of Africa' migration. It was identified using a methodology developed by the researchers known as FitCoal, which analysed the genomes of almost 3,200 people from populations inside and outside Africa.

While the mathematics involved in the process are quite complicated, FitCoal is based on the simple idea that all of our DNA and the genes it contains have been inherited from our ancestors over hundreds of thousands of years.

As these genes are traced back through time, they will merge back into older versions that they evolved out of and eventually coalesce into a common ancestor. This process is affected by the size of populations, allowing researchers to assess how this has changed over time.

‘Large populations can contain more genetic variation than small ones, so you can use the coalescence of genes to assess how diverse a population was at a certain point in time,’ Chris says.

The scientists estimate that there would have only been an effective population size of around 1,280 individuals between 930,000 and 813,000 years ago, suggesting the presence of a bottleneck. While that doesn’t mean this was the entire population, only this number successfully bred and passed on their genes to the next generation.

Such a low population size would have posed problems for humans, making it more likely that they would become extinct.

Lead author Dr Wangjie Hu says, ’We first found hints of something really interesting happening in human population size at this time about five years ago, but the real “wow” moment came after we multi-checked our findings using FitCoal.’

‘We realized we had discovered something big about human history and that there's a lot more to uncover.’

What could the bottleneck reveal?

If the bottleneck is confirmed, it could help to answer one of the biggest questions in human evolution today - its timing. Following the origins of Homo erectus about two million years ago, a variety of other species evolved. However, when and in what order they did this is a matter of debate.

The proposed bottleneck lies right in the middle of the period when these human species are thought to have first appeared. It may even have been responsible for triggering speciation, potentially as a result of changes in human genetics.

‘As the authors of the bottleneck study point out, ancestral hominins had 48 chromosomes, the same as chimpanzees and gorillas,’ Chris says. ‘At some stage, probably around the time of the proposed bottleneck, two of these fused to become our modern chromosome two, leaving modern humans with 46 chromosomes.’

‘While it may have had minimal impact, it’s also possible that this change limited interbreeding with other populations, contributing to them becoming a new species.’

As Denisovans and Neanderthals also have 46 chromosomes, it suggests that this fusion must have taken place before they split from the ancestors of our species. This latest study offers a new line of inquiry for scientists investigating when the common ancestors of our three species lived, as if both Neanderthals and Denisovans show evidence of the bottleneck, then we know the split must have happened after 813,000 years ago. 

Identifying the common ancestor itself, however, remains difficult. There is a relative lack of fossil evidence from the time when the bottleneck is thought to have taken place.

Based on fossils from Africa, the researchers suggest that Homo heidelbergensis could be a potential candidate, but other scientists aren't so sure. Fossils of another species, Homo antecessor, have also been dated to this period, while an even older species, Homo erectus, was also still alive.

The presence of many these fossils from all over the world imply that the effects of the bottleneck may have been limited, and if the effects weren’t as widespread it also means the proposed impact of climate was probably more localised.

‘A climate transition took place about 900,000 years ago, which saw cold periods become longer and more intense,’ Chris says. ‘However, if the impacts of this were severe globally, it’s a surprise we don’t find more of a gap everywhere in the record.’

Aside from fossils, the nature of the analysis also meant it had to make a number of assumptions which may not reflect reality. While the authors believe their simulations show that these factors don’t affect their conclusions, the estimated population size during the bottleneck is so low that it's uncertain how humans could have survived.

To address these concerns, discovering more fossils will be crucial to give us a better picture of this period in our evolution.

‘The more sites that can be well dated to this time, then the less likely it is that the bottleneck was such a severe event,’ Chris says. ‘Alternatively, if we find more fossil sites from before and after the bottleneck, but not during it, then it becomes more probable.’

‘Better dating our existing sites will also help with this, as estimates for some sites stretch across hundreds of thousands of years.’

With FitCoal now freely available for other scientists to use, the authors hope that further research will support their conclusions, and open up new avenues to explore.

Professor Li Haipeng, a co-author on the paper, says, ‘These findings are just the start. Future goals with this knowledge aim to paint a more complete picture of human evolution during this Early to Middle Pleistocene transition period, which will in turn continue to unravel the mystery that is early human ancestry and evolution.’