African skeleton throws light on our origins

The DNA of an African skeleton, belonging to a man who lived over 2000 years ago in the southernmost tip of Africa, has thrown light on humanity’s earliest common genetic ancestry. The skeleton’s DNA profile is one of the oldest in genetic terms found to date, in a region where modern humans are believed to have originated roughly 200,000 years ago.

The skeleton was discovered by archaeologist Professor Andrew Smith, from the University of Cape Town, at St Helena Bay in 2010 - very close to the site where 117,000-year-old human footprints had been found. He contacted Professor Vanessa Hayes, an expert in African genomes who currently heads the Laboratory for Human Comparative and Prostate Cancer Genomics at Sydney’s Garvan Institute of Medical Research.

The 1.5 m-tall skeleton was examined by Professor Alan Morris from the University of Cape Town, who “used his skills in forensics and murder cases to assemble a profile of the man behind the St Helena skeleton”, said Professor Hayes. A bony growth in the man’s ear canal, known as ‘surfer’s ear’, suggested that he spent some time diving for food in the cold coastal waters; shells carbon-dated to the same period, and found near his grave, confirmed his seafood diet. Osteoarthritis and tooth wear placed him in his fifties.

“Alan helped establish that this man was a marine hunter-gatherer - in contrast to the contemporary inland hunter-gatherers from the Kalahari Desert,” said Professor Hayes. “We were very curious to know how this man related to them.”

The researchers sought to sequence the man’s maternal DNA, or ‘mitochondrial DNA’, to provide clues to early modern human prehistory and evolution. Mitochondrial DNA provided the first evidence that we all come from Africa and helps us map a figurative genetic tree, all branches deriving from a common ‘Mitochondrial Eve’.

Due to the acidity of the soil within the region, acquiring DNA from skeletons has proven problematic. But working with the laboratory of paleogeneticist Professor Svante Pääbo, at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, the team generated a complete mitochondrial genome, using DNA extracted from a tooth and a rib.

The findings provide genomic evidence that this man, as well as other indigenous coastal dwellers like him, was closely related to Mitochondrial Eve. Professor Hayes noted that the man “pre-dates migration into the region, which took place around 2000 years ago when pastoralists made their way down the coast from Angola, bringing herds of sheep”.

“We could demonstrate that our marine hunter-gatherer carried a different maternal lineage to these early migrants - containing a DNA variant that we have never seen before,” she said.

The work underlines the significance of southern African archaeological remains in defining human origins - an area of study which Professor Hayes is hoping will inform genomic research and medicine worldwide.

“One of the biggest issues at present is that no-one is assembling genomes from scratch - in other words, when someone is sequenced, their genome is not pieced together as is,” she said.

“Instead, sections of the sequenced genome are mapped to a reference genome. Largely biased by European contribution, the current reference is poorly representative of indigenous peoples globally.

“If we want a good reference, we have to go back to our early human origins.

“In this study, I believe we may have found an individual from a lineage that broke off early in modern human evolution and remained geographically isolated. That would contribute significantly to refining the human reference genome.”

The study has been published in the journal Genome Biology and Evolution.