Early humans living about one million years ago were extremely close to extinction. Evidence from a novel genetic approach, one that probes ancient DNA regions, suggests that the population of early human species back then, including Homo erectus, H. ergaster and archaic H. sapiens, was 55,500 individuals, tops.

Lynn Jorde, a human geneticist at the University of Utah, and his colleagues came to this conclusion after scanning two completely sequenced modern human genomes for a type of mobile element called Alu sequences, which are short snippets of DNA that move between regions of the genome. They shift with such low frequency that their presence in a region suggests that it is quite ancient. Because older Alu-containing portions have had time to accumulate more mutations, the team could also estimate the age of a region.

The scientists then compared the sequences in these old regions with the overall diversity in the two genomes to come up with an ancient census figure of 55,500. (Population geneticists actually calculate the so-called effective population size, which is an indicator of genetic diversity and is generally much lower than absolute population numbers; in this case, the effective population of humanity 1.2 million years ago was 18,500, which Jorde used to estimate the total population number.) The findings appear online in the January 19 Proceedings of the National Academy of Sciences USA.

The small number is surprising because, according to the fossil record, members of our Homo genus were spreading across Africa, Asia and Europe, suggesting that the hominin numbers should be expanding, Jorde says. A major setback must have occurred back then, he thinks, as devastating as a purported super­volcano thought to have nearly annihilated humans 70,000 years ago. “We’ve gone through these cycles where we’ve had large population size but also where our population has been very, very small,” he observes.