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When scientists first started to figure out how to extract DNA from ancient skeletons, their success was met with astonishment. One minute, scientists were fishing Richard III’s genes from his royal bones, and the next they were showing off DNA retrieved from 5,000-year-old Incan mummies.

The idea that DNA could survive for thousands of years — let alone be reassembled into an entire genome — seemed little short of miraculous.

Despite the field’s rapid advances in recent years, though, ancient DNA is still hard to find and hard to make sense of. Potential errors lurk around every corner. Even little oversights can cause big headaches.

Andrea Manica, a geneticist at the University of Cambridge, appreciates this fact all too well. A head-turning study by his team turned out to have a fundamental flaw that erased some of its most provocative conclusions.

In October, Dr. Manica and his colleagues reconstructed the first ancient human genome ever found in Africa, retrieved from the skeleton of a man who lived in Ethiopia 4,500 years ago.

Ancient DNA experts...