The skeleton of a man who lived more than 2300 years ago and foraged food from the ocean off southern Africa belonged to an ancient group of modern humans now presumed extinct, an Australian-led study has found.
When archaeologists discovered the complete skeleton in St Helena Bay in 2010, they feared the region's acidic soils would have destroyed its DNA.
But an international team led by Sydney geneticist Vanessa Hayes was able to generate a complete mitochondrial genome of the man, using material extracted from a tooth and a rib.
Mitochondrial DNA contains information passed from mother to child, and from this the team learned that the man was a member of the earliest ethnic group of humans to diverge from the maternal common ancestor all humans share.
Professor Hayes, an expert in African genomes, said everyone living on Earth today shared a common maternal ancestor, an ancestral "Mitochondrial Eve", who lived in Africa about 200,000 years ago.
"From Eve, this [individual] comes from the earliest branch, which diverged around 150,000 to 170,000 years ago," said Professor Hayes, the head of the Laboratory for Human Comparative and Prostate Cancer Genomics at the Garvan Institute of Medical Research.
The discovery will likely reignite debate about the region in Africa where the first modern humans arose.
"If you're an archaeologist you may say it's in east Africa because the oldest archaeological finds, which date to 195,000 years ago, are found in the Omar Valley," Professor Hayes said.
"But genetic data tells us that the earliest diverged human lineages are found in southern Africa."
The man's skeleton suggests he stood about 1.5 metres tall, and was about 50 years old when he died.
Detective work by University of Cape Town anthropologist Alan Morris established the man was a hunter-gatherer who foraged for food in the ocean. A bone growth in his inner ear suggests he had surfer's ear, a common condition among people who spent a lot of time in cold water.
"His teeth were in immaculate condition, telling us he was a hunter-gatherer, because there is no natural sugar in the diet of the hunter-gatherers," Professor Hayes said.
In 2010 Professor Hayes sequenced the genomes of four Kalahari Desert bushmen from Africa, which showed that the hunter-gatherer bushmen of southern Africa have remained isolated from other populations for about 100,000 years.
While this group were around at the same time as the St Helena Bay man and other coastal dwellers like him, the two groups remained isolated from each other. Genetic studies of modern Kalahari bushmen show they do not share the man's unique mutations.
Because of this, the researchers presume the St Helena man's ethnic group is now extinct. Their findings have been published in the scientific journal Genome Biology and Evolution.
