Ancient human genome from southern Africa throws light on our origins

September 29, 2014, Garvan Institute of Medical Research
Professor Vanessa Hayes in the field. Credit: Chris Bennett photography

What can DNA from the skeleton of a man who lived 2,330 years ago in the southernmost tip of Africa tell us about ourselves as humans? A great deal when his DNA profile is one of the 'earliest diverged' – oldest in genetic terms – found to-date in a region where modern humans are believed to have originated roughly 200,000 years ago.

The man's maternal DNA, or 'mitochondrial DNA', was sequenced to provide clues to early 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'.

When archaeologist Professor Andrew Smith from 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 had been found – dubbed "Eve's footprints" – he contacted Professor Vanessa Hayes, a world-renowned expert in African genomes.

At the time, Hayes was Professor of Genomic Medicine at the J. Craig Venter Institute in San Diego, California. She now heads the Laboratory for Human Comparative and Prostate Cancer Genomics at Sydney's Garvan Institute of Medical Research.

The complete 1.5 metre tall skeleton was examined by Professor Alan Morris, from the University of Cape Town. A biological anthropologist, Morris showed that the man was a 'marine forager'. A bony growth in his ear canal, known as 'surfer's ear', suggested that he spent some time diving for food in the cold coastal waters, while 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.

Due to the acidity of the soil within the region, acquiring DNA from skeletons has proven problematic. The Hayes team therefore worked with the world's leading laboratory in ancient DNA research, namely that of paleogeneticist Professor Svante Pääbo at the Max Planck Institute for Evolutionary Anthropolgy in Leipzig, Germany, who successfully sequenced a Neanderthal.

The team generated a complete , using DNA extracted from a tooth and a rib. The findings provided genomic evidence that this man, from a lineage now presumed extinct, as well as other indigenous coastal dwellers like him, were the most closely related to 'Mitochondrial Eve'.

The study underlines the significance of southern African archaeological remains in defining human origins, and is published in the journal Genome Biology and Evolution, now 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 sample was 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 into 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 historic herders at the Cape can now be compared."

While interested in African lineages, and how they interact with each other, Professor Hayes is especially keen for Africa to 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."

"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."

Explore further: Separating Neandertal DNA from modern human contamination

More information: Paper - gbe.oxfordjournals.org/content … /gbe.evu202.full.pdf

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Jeffhans1
5 / 5 (3) Sep 29, 2014
"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"

Europeans and Asians have 1 to 4% of their DNA from Neanderthals. Your statement suggests only 1 to 4 % of those people have legacy DNA and 96 to 99% have no Neanderthal DNA. http://en.wikiped...n_humans shows that there were at least 3 branches of humanity to survive long enough to contribute DNA to some people living today.
Shootist
1.8 / 5 (5) Sep 29, 2014
3 branches? H. Sapiens Sapiens, H. Sapiens Neanderthalis, H. Sapiens Denisovian, H. Erectus, H. Sapiens flourienses and an H. Sapiens unnamed (human subspecies existed ~13 KYA in Australia) also co-existed with modern humans . . . . did we not breed?
Shootist
2.5 / 5 (8) Sep 29, 2014
Ancient human genome from southern Africa throws light on our origins


I've read this essay again and again and I see nothing that sheds light on anything.
gdot
5 / 5 (1) Sep 30, 2014
The story did not mention that Africans, Africans Americans, and Puerto Ricans have little to no Neanderthal DNA. Personally speaking I have 0.6% Neanderthal DNA.
cinnamonape
not rated yet Sep 30, 2014
So is this a pre-mtEve branch of mt DNA (i.e. pre-E* or E0). If it simply is part of the subsequent E1 or E2 clades then it's not really all that important.

But if it actually precedes mt-Eve then I can see it being of interest. It would suggest that there were branches that didn't go extinct from genetic drift until fairly recently. However it's also more than likely that this line wasn't entirely isolated. The mtDNA is only one of many possible contributions to the genome and simply because this female lineage died out does not mean that this individual or group did not interbreed with others in the region.
Captain Stumpy
4.2 / 5 (5) Sep 30, 2014
Ancient human genome from southern Africa throws light on our origins


I've read this essay again and again and I see nothing that sheds light on anything.
@shooty AND Verkle
that is because you have religious blinders on and refuse to acknowledge science.

when that happens, you might just behold the various wonders that you should have seen all along...
Returners
1 / 5 (3) Oct 02, 2014
"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."


Doesn't that reflect incompetence on geneticists part?

I've suggested doing a true human genetic survey years ago, and she's saying they still haven't done that?

What the hell do they get paid for?

It takes 40 to 100 samples from a POPULATION in order to develop statistical relevance.

Discovering genes never before seen is always relevant, but in this case it doesn't tell you much, because apparently those genes are now extinct.

You need DNA from every racial and ethnic group, and preferably the 40 purest-blooded, but not directly related people you can find.

Native Americans? Let's not lump them all together, find at least 2 or 3 tribes from N. America and again from s. America, including those groups who are still indigenous and living in the rainforest.
Returners
1 / 5 (3) Oct 02, 2014
that is because you have religious blinders on and refuse to acknowledge science.

when that happens, you might just behold the various wonders that you should have seen all along...


The article shed's light on just how incomplete the "mapping" of the human genome is. They talk about ancient DNA, and the findings refute their own claim, because in this case the "new" genes are apparently extinct, or else they haven't done their homework in establishing a proper modern baseline (which she admitted).

So that claim that all modern humans share 98% of their DNA? It's clearly unsubstantiated, because they admit they've never actually sequenced enough people to know that.

In fact, all they've done is "gene referencing", not true gene mapping of different race and ethnicities, which means they've basically not been compiling a true genetic record of tested subjects at all.

What they've done is bordering on scientifically useless.
Returners
1 / 5 (2) Oct 02, 2014
there are at least 7 major distinct groups descended from north American natives:
Aztec, Mayan, Pueblo, Navajo, Cherokee, Mohawk(less discussed N. England/canadian region), and Eskimo.

Latin America is highly inter-bred with descendants from Aztec and Mayan, so you'll need even more 100 to 1000 FULLY MAPPED genomes, and cross-reference those against a massive baseline of FULLY MAPPED European Spanish genomes to remove the European signature as much as possible.

Same with S. American natives and Spaniards

Africa? Has the most different sub-races and ethnic groups of any continent, including re-mixing of freed western slaves as well, some of which may have been interbred with whites. Need to map at least a couple hundred genomes from every nation, and in some cases much more than that.

Overall, I'd say a proper baseline of each sub-race would require about 1000 to 1500 total fully mapped genomes per continent; A minimum of 40 to 100 per sub-race.
Returners
1 / 5 (2) Oct 02, 2014
Mitochondrial DNA can't be passed on by a man, so it would seem it should be about twice as likely to go extinct as most nuclear DNA.

If a woman's mitochondrial DNA develops a novel, useful mutation, but she dies before giving birth to another female, or her daughter dies, or one of them is barren, etc, then the gene doesn't get passed on.

I suppose the same could be said for any particular mutant variant of the Y-chromosome in men, since it is only passed on by the man.

Perhaps this is a stabilizing mechanism, or perhaps sperm just aren't large enough to carry "male" mitochondria to contribute to the new cell. Maybe it takes too much energy, and decreases the success of male nuclear DNA, so it isn't present for that reason.

Let's not forget humans are our own worst enemy.
War, genocide, and murder go a long way to removing entire genetic families from the population, particularly males: typically women were kept and raped, or forced into marriages.
Straw_Cat
not rated yet Oct 04, 2014
It appears as though we need to set up a modern advanced genetics research lab in Africa somewhere, and another in South America. To help "to reduce the noise" as one quote in the article points out.

I'll chip in $10 or $20 to help pay for it...

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