The skeleton of a man who walked the earth 2,330 years ago in the southernmost tip of Africa tells us about ourselves as humans, and sheds some crucial light on our earliest common genetic ancestry.
What can DNA from the skeleton of a man who lived 2,330 years ago in the south of Africa possibly tell us about ourselves as humans? Well, quite a lot when his DNA profile is one of the ‘earliest diverged’, oldest in general terms, found to-date in a part of the world where modern humans are thought to have originated approximately 200,000 years ago.
The man’s maternal DNA, otherwise known as ‘mitochondrial DNA’, was sequenced to obtain a better understanding of early modern human prehistory and evolution. Mitochondrial DNA offered the first evidence that we all originate from Africa, and helps us map a figurative genetic tree, all branches originating from a common ‘Mitochondrial Eve’.
When archaeologist professor Andrew Smith, of the University of Cape Town, discovered the skeleton at St. Helena Bay in 2010, very close to the site where 117,000-year-old human footprints were discovered, labeled “Eve’s footprints”, he made contact with Professor Vanessa Hayes, a world-renowned expert in African genomes.
Hayes was a Professor of Genomic Medicine at the J. Craig Venter Institute in San Diego, California at the time. Now, Hayes heads the Laboratory for Human Comparative and Prostate Cancer Genomics at Sydney’s Garvan Institute of Medical Research.
Professor Alan Morris, of the University of Cape Town, examined the complete 1.5 metre tall skeleton. As a biological anthropologist, Morris indicated that the man was a ‘marine forager’. This was due to a bony growth in his earth canal, suggesting that he spent some time diving for food in the cold coastal waters, while shells carbon-dated to the same period, discovered near his grave, confirmed a seafood diet. Osteoarthritis and tooth wear suggested he was in his fifties.
Because of the acidity of the soil in the region, collecting DNA from skeletons was problematic. Therefore, the Hayes team worked with the world’s leading laboratory in ancient DNA research, specifically that of palaeogenticist Professor Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who successfully sequenced a Neanderthal.
The team generated a complete mitochondrial genome, using DNA extracted from a tooth and rib. The findings offered genomic evidence that this man, from a lineage presumed to be extinct, as well as other indigenous coastal dwellers similar to him, were the most closely related to the ‘Mitochondrial Eve’.
The study outlines the importance of southern African archaeological remains in defining human origins, and is now published in the journal Biology and Evolution online.
“We were thrilled that archaeologist Andrew Smith understood the importance of not touching the skeleton when he found it, and so did not contaminate its DNA with modern human DNA,” said Professor Hayes.
“I approached Svante Pääbo because his lab is the best in the world at DNA extraction from ancient bones. This skeleton was very precious and we needed to make sure the samples were in safe hands.”
“Alan Morris undertook some incredible detective work. He used his skills in forensics and murder cases to assemble a profile of the man behind the St. Helena skeleton.”
“Alan helped establish that this man was a marine hunter-gatherer- in contrast to the contemporary inland hunter-gatherers from the Kalahari dessert. We were very curious to know how this man related to them.”
“We also know that this man pre-dates migration to the region, which took place around 2,000 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.”
“Because of this, the study gives a baseline against which prehistoric herders at the Cape can now be compared.”
While very interested in African lineages, and how they interact with each other, Professor Hayes is especially interested in Africa informing genomic research and medicine across the globe.
“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.”
“None of us that walk on this planet now are pure anything, we are all mixtures. For example, 1-4% of Eurasians even carry Neanderthal DNA.”
“We need more genomes that don’t have extensive admixture. In other words, we need to reduce the noise.”
“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.”
Contributing Source: Garvan Institute
Header Image Source: WikiPedia
