With Ancient Human DNA, Africa’s Deep History Is Coming to Light

By Bridget Alex | February 8, 2019 3:00 pm
ancient african dna

Ancient DNA can reveal much about the genetic history of Africa because it predate major events like slavery and colonialism, which upended African populations and territories. (Credit: Zita/shutterstock)

In 2010, extraordinary circumstances allowed geneticists to reconstruct the first full genome of an ancient human: the DNA came from a hairball, frozen 4,000 years in Greenland soil. Since then, methods have improved so much in cost and efficiency that individual papers now report genomic data from hundreds of dead people (here, here, here). Ancient DNA (aDNA) has now been published from well over 2,000 human ancestors, stretching as far back as 430,000 years ago.

But around 70 percent of those sequences are from Eurasia, where cold temperatures favor DNA preservation and considerable archaeological research has occurred. For researchers interested in the genetic history of Europe and Asia, there are plenty of excavated skeletons, sitting in museums and other collections, and there’s a good chance those bones hold appreciable DNA.

The situation is different in Africa — the place where Homo sapiens originated some 300,000 years ago and has continued diversifying ever since. Despite Africa’s prominence in the human story, so far only 30 ancient genomes between 300 and 15,000 years old have been published from the continent.

Part of the reason is methodological and environmental: Hot, humid conditions destroy DNA in human remains, long before geneticists attempt to extract it. However, in 2015 scientists showed that aDNA preservation can be 100-fold higher in the petrous — dense bone surrounding the inner ear — than other skeletal parts. In 2018, researchers used this bone to recover the oldest African genomes yet, from 15,000-year-old skeletons excavated from a cave in Morocco.

It’s unlikely geneticists will capture much older African DNA than that. So, the petrous find is a “game changer,” not a miracle maker. But bones between 5,000 and 15,000 years old — surrounding the start of the Holocene, our current geologic epoch — can reveal much about the genetic history of Africa. That’s because they predate major events that upended African populations and territories. These include the slave trade and colonialism. Earlier still, there were major migrations within Africa linked to the spread of herders and farmers, starting around 5,000 years ago.

“What we see is this huge amount of noise from the past 5,000 years,” says Elizabeth Sawchuk, an archaeologist who works in East Africa.

DNA from Holocene remains would allow researchers to peer beyond this noise, to glimpse the genetic map of Africa prior to agriculture and historical migrations. And now, it’s technologically possible.

Yet there’s reason to pause, as ancient DNA studies receive criticism. Archaeologists and historians accuse geneticists of making sweeping claims based solely on DNA data, without considering the centuries of evidence and scholarship accumulated by other fields. Ethical concerns have also been raised about taking skeletal samples out of Africa and into Western laboratories for the destructive process of genetic sequencing. Moreover, the results may fuel ancestry claims over territories or cultural heritage, and therefore affect living people who did not consent to the research.

In this context, some scientists are proceeding with caution, and a number of African aDNA projects are underway. One of the largest is led by Sawchuk, archaeologist Mary Prendergast and geneticist David Reich, who runs the aDNA laboratory at Harvard Medical School.

Discover talked to Sawchuk, a post-doctoral researcher at Stony Brook University, about the potential risks and rewards of African aDNA.

Why is African aDNA important?

It’s where our species evolved, where we’ve been the longest. And as a consequence, Africa has the highest genetic diversity of anywhere else on the planet. It potentially is going to tell us the most about our species, but it’s an area that we know the least about.

Why is that?

Largely because of underfunded research. Africa is very expensive to go to. The continent is humongous. Areas are inaccessible for geographical, environmental and political reasons. As a result there are fewer skeletons and archaeological sites identified for this huge area and huge period of time. [Also aDNA] preservation is bad because high heat, humidity and water destroy the organic content of bones. Getting aDNA out of this continent was regarded to be something we would all love to do, but nobody could do.

Now that it’s technologically feasible, why should researchers be cautious?

Human remains are the only direct link we have to the past. We have far fewer skeletons in Africa than other parts of the world, so every skeleton is incredibly precious. That puts a really big burden on these genetics projects in terms of how much material they’re sampling, how many sites they’re sampling, if they’re sampling all of the sites.

There’s a fundamental tension: You don’t know which skeletons and sites will have aDNA preserved, so you just have to try them all. But if we try them all now, in 5 years, 10 years, 15 years, 50 years, the science might be completely different, and we may have limited ourselves in the future. So it’s a tight line to walk.

What are some concerns of present-day Africans?

Across a continent as big of Africa, [countries] with individual, imposed colonial histories have very different ways of approaching their own national heritage. Transporting material outside of Africa to a clean room — so we can minimize contamination and maximize the chance of getting a sequence — that kind of parallels a lot of the colonial justifications for removing artifacts out of their countries of origin to better funded European or American institutions. So there needs to be a lot of sensitivity about how human remains are approached, sampled, processed, and eventually returned.

How has your project been responsive to these concerns and other criticisms of aDNA research?

It’s taken a lot longer compared to other genetic projects to start — to get the permissions, to really get everybody on board, and to do this right. It just takes time, face-time. People who can go there, propose this research, bring on African collaborators in a senior role, and then do this project going forward together.

Many of the criticisms of other DNA projects are that it’s DNA first, Anthropology second. This was really an Anthropology first project. It’s driven by questions that myself and many other anthropologists have been asking for decades, but integrating this new line of evidence, DNA.

It’s absolutely really exciting that we might have this new line of evidence, but DNA will not be the magic key to all of these answers. It’s not to the exclusion of decades and hundreds of years of pottery studies, ancient tool studies, landscape archaeology, ethnographies. These are all just pieces of a puzzle that we need to put together. This is always going to have to be an interdisciplinary effort, where we work with other types of scientists and we work with local communities.

This is so exciting. We just have to make sure that we do it right, right now.

What have you found so far?

We’ve sampled from institutions in Tanzania and Zambia and Kenya. This will be one of the largest African DNA studies to date when it comes out. It’s blown my mind. I hope it will blow many other peoples’ minds.

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  • CharleyX

    What’s the big deal about in doing research in the Dark Continent? They are as crooked as Mexicans. Crookeder? (LOL) Just hand over the loot and you’re good!

    • Occasional-Cortex

      It’s like building a new telescope on a sacred mountain in Hawaii. Give the self appointed social justice types enough money and the gods are suddenly appeased.

      • OWilson

        Or putting a pipeline, stringing a telephone wire across “ancient sacred grounds’ on a reservation!

        No problem with Casino though! :)

    • Tony Kuria

      Why the hate towards Africans, people who have done nothing wrong to you. You must be a very lonely and miserable human being.

      • http://www.mazepath.com/uncleal/EquivPrinFail.pdf Uncle Al

        www(.)fourmilab(.)ch/documents/reading_list/images/population_forecast.png
        … Africa is civilizations’ obscenity.

        • 7eggert

          That’s what happens if you focus on keeping children alive while leaving adults alone and don’t care for education. Children – a lot of children since many would die – are the traditional security for old age.

          But don’t worry, the lack of food will make sure they don’t breed to much. We just need a way to make them not migrate. Also we should neither stop keeping African children alive nor start caring for education and birth control.

      • CharleyX

        I haven’t been to Africa but know several people who spent years there. What I said is true according to them.

        • http://www.mazepath.com/uncleal/EquivPrinFail.pdf Uncle Al

          Pesdient Kennedy’s Peace Corpse accomplished two goals:

          … 1) 30 years of not teaching Africans how to dig slit latrines, and
          … 2) Cross-breeding with White girls by rape.

          • CharleyX

            I think it wore off. According to my pals, they are still just spear chunkers but with AK-47s now.

        • OWilson

          My friend worked in Nigeria putting up electrical transmission lines.

          They put them up in the daytime, and by next morning they had largely disappeared. It went on for a long time, and nobody seemed to care!

        • Erik Bosma

          You will always find what you look for.

          • CharleyX

            Please. That makes me sound like a Democrat.

    • bicfj

      BIGOT !!!

      • CharleyX

        You can’t handle the truth!

  • http://www.mazepath.com/uncleal/EquivPrinFail.pdf Uncle Al

    Post-1500 AD Europe scourged the Earth – and well it should have – aggrandizing valuables and crushing the locals and their puny gods. The only indigenous exception was the Māori Aotearoa. When Captain Cook arrived, the native response was “We will eat you.” And they did. Things worked out for both sides. The Māori genome is the hot button of humanity.

    Ethical concerns” LMFAO, re Spain and South America, Belgium and the Belgian Congo; Democratic Republic of the Congo. Peoples Democratic Republic of Korea, Yemen, Lao, Algeria, Ethiopia, Malaya, Kenya….

    • OWilson

      Slavery was the way the work force of the ancient world was organized. Mesopotamia, Persia, Egypt, Greece, Rome, Africa, India, China, and in good old pre-Columbian Americas. It still exists in a hundred countries today, according to the U.N.

      A good slave was valuable, and was treated generally no worse than a servant in today;s Vatican Palace, and and the mansions of the political and celeb mansions of the rich and famous! Fed well, clothed, bathed and housed.

      I believe it was the white man, who legislated an end to most of it! :)

      • bicfj

        Wrong. The white man INDUSTRIALIZED slavery in the plantations that were the corporations of the day.

        • OWilson

          We have inner city plantations today, run by progressives to farm votes!

          Run by whites and blacks!

          • http://www.mazepath.com/uncleal/EquivPrinFail.pdf Uncle Al

            Every great civilization had slaves. The accomplished like luxury. Folks whose only value is a strong back need employment.

            Every great civilization forgets how it was earned. It compassionately frees its slaves. It then succumbs to the mobs’ unlimited appetites.

            French farmers are exploited but satisfied with their lot – that is not historically unattractive. Their Socialist government – to dialectically save the world for the vigorish – turned the screws, majorly screwing the large agrarian community.

            www(.)youtube(.)com/watch?v=UgqVCJpRqWQ&t=0m52s
            … When you carry a firearm against wolves you are primed to turn it against Paris.

    • Erik Bosma

      Oh, so that’s where the word ‘cook’ originated.

  • gimpi1

    Ok, this is the most horrible thread ever… did no one read the post? Is no one interested on the anthropology or archeological information? Is everything just a platform for people to spew whatever toxic trash bubbled to the top of the tank recently? Ick… I’m going to break out the brain bleach.

    • Jennifer A. Nolan

      It’s because humans first evolved from apish-looking ancestors in the savannas, and because black Africans have the most prognathous skulls in our species, that this hoarded intellectual trash keeps spilling out of the white American closet. Black Africans “look more like apes” than any other broad ethnic category, so they must be the most apelike in their behavioral and mental lives. (Never mind that apes themselves are quite sensitive and complex beings.) These people haven’t read any Leo Igwe or Chinua Achebe, or listened to any Nelson Mandela speeches.

      • Erik Bosma

        Humans don’t look like apes; apes and humans look like a last common ancestor of all of us. I can’t believe that you can say that black people “look more like apes”. You must hang out with a very limited variety of people. I’ve known scads of Europeans who look more brutish than many of the black people I know. Geez…

        • Jennifer A. Nolan

          I’m sorry I pushed your buttons with this comment; I did put the “looks more like apes” part in scare quotes for a reason: because I don’t think African humans look apish, either. It’s just an old piece of racial stereotyping, something that was inflicted on East Asians and even Irish immigrants, back in the 19th and early 20th centuries. It’s a load of humbug; that’s exactly what I was trying to say.

    • saymwah

      There are a few regular trolls on this site who feel the need to proselytize their racism and sexism at the most tangential mention of race or gender.

    • Mike Richardson

      This is unfortunately true. A fascinating article discussing the issues with preserving DNA in Africa, and why this DNA is important to scientists seeking to learn about our earliest ancestors. But instead of a discussion of these issues, we get bigots issuing generalized racist statements about Africans, Mexicans, Native Americans, etc. So much for these folks following the Golden Rule.

      • OWilson

        The worst form of prejudice and yes, racism, is the inherant superiority shown by so called “progressive” whites who believe they are privileged by no more than their skin color.

        They demand special sensitivity, social, political, and material “help” for those they feel less “fortunate” because of their skin color. This predisposition is a dangerous racist view of humanity.

        In fact, there are cultural, rather than racial, differences between societies, some, laudable, some deplorable, and all humanity has been guilty, and still is, of the most agregious behavior to others, regardless of skin color. See both World Wars and the Cold War.

        To excuse, and show special “sensitivity” to some racial groups over others, is an implicit admission of racial prejudice. The prejudice of low expectaions. They may “feel” good about their Affirmative Action efforts, but it smacks of an attitude of skin color superiority.

        Obama and Oprah, don’t need your condescention, thank you! :)

        We routinely dig up skeletons, and loot burials and tombs which have been laid down with the most inticate ceremonial care, without a thought, for scientific research, Vikings, Romans, Anglo Saxons, but a certain “sensitivity” must be shown to “certain” indigenous groups, who happen to have different skin color.

        I choose to live in a black society, and the only racial problem I see is this superior condescending attitude of whites, towards blacks. There’s always this narcisistic feel good need to “help” them.

        We are all god’s chillun, no better or worse than the next person.

        Ancient DNA is DNA. Go at it, equally, and try to subdue your own prejudices!

        • saymwah

          Jesus H. It’s the indigeneous groups themselves who object to Western scientists digging up graves and removing the remains and artifacts, and it’s the indigenous groups who want them returned. And none of this has anything to do with affirmative action or the War on Poverty. You RWNJs are really pieces of ignorant, ill-informed “work.”

          • Mike Richardson

            Notice how quick they project and deflect, rather than self reflect on their own behavior. Some of it may simply be trolling, but unfortunately, I think with many of them these are actual statements of belief. 😞

          • OWilson

            Thanks for the infantile name calling! :)

            Let’s define “Indigeneous peoples”

            “The United Nations Permanent Forum on Indigenous Issues has developed an understanding of the term based on the following:

            Self-identification as indigenous peoples at the individual level and accepted by the community as their member.
            Historical continuity with pre-colonial and/or pre-settler societies
            Strong link to territories and surrounding natural resources
            Distinct social, economic or political systems
            Distinct language, culture and beliefs
            Form non-dominant groups of society
            Resolve to maintain and reproduce their ancestral environments and systems as distinctive peoples and communities”

            A vague definition of ancient populations who seek “special status” in even modern democratic states.

            Used as Identity Politics to seek and add “special rights” to those rights already granted to each citizen under the law!

            Rights, in a Democracy, is a zero sum game. Special Rights for one group diminishes the rights of others.

            Religion, gender, skin color are other bases of Identity Politics. No more than tribalism exploited by cynical politicians, seeking to divide an conquer a population.

            Today it has great political momentum, and where it ends, remains to be seen!

            We may get a clue from the current battle going on in your Democratic Party between white, and black, anti-semitic muslims, Jews, and males and females, young and old.

            Hopefully they will be able to unite their tribal “tent” before presenting a worthy Presidential Candidate to the people! :)

          • Mike Richardson

            I think your comments here just help support all of those conclusions. As for deluded, you might want to look in a mirror. 😉

        • Mike Richardson

          And that long-winded rant does nothing to change the fact that you and others here have made blatantly racist statements against particular groups. You, specifically, go after Native Americans for some reason, though your comment about “inner city plantations” shows you have room for other prejudices. Stop trying to gaslight others, and work on improving your own reprehensible behavior!

          • OWilson

            Not here, Mikey!

            Keep your trolling where it belongs! Those left wing trolling blogs!

            This is a science blog.

            We are talking about “Ethical concerns (that) have also been raised about taking skeletal samples out of Africa and into Western laboratories for the destructive process of genetic sequencing” by the usual suspects! :)

          • Mike Richardson

            Oh now you want to call off the trolling you started with your own comments here? And were the comments made under the “OWilson” username in “left wing trolling blogs” a different person? Give me a break. I should’ve known better than to expect you to act like an adult and apologize for your own horrid words, just in this comment thread alone. That kind of self awareness and ability to learn from your mistakes just isn’t in you.

            As for the topic of this article, you’ve yet to express any opinion or provide any topical anecdote, so drop the holier-than-thou act. It’s just another futile effort to deflect from your initial remarks.

          • OWilson

            Have a nice day, Mikey!

          • OWilson

            Well, Mikey, when you start to “act lke an adult”, and you apologise for your “closet fascist”, “alcoholic”, “racist”, “mental incompetent”, “senile”, who’s family should have me “committed to a sanitarium”, along with my “duped wife”, on these science blogs, I may apologise for jokingly referring to your former U.S. Presdient “Obanana” (with smiley you left out) on a left wing political blog!, Where the names they call Trump and his family, I couldn’t even repeat here! :)

            Deal?

            Lol

          • Mike Richardson

            Well, Ol’Wilson, I’ll offer an apology the same vein that you appear to be attempting in that barely coherent stream of consciousness above:

            I apologize for “jokingly” questioning your mental state and/or sobriety, and for any offense you took at those joking comments. 😀 Look, see the smiley!

            I wouldn’t want you to continue acting the martyr despite your own behavior, since obviously only other people should be held accountable for comments made in the past, and not yourself for remarks you made yesterday and today. Nice of you to bring up the President, though, who seems to share your behavioral traits in that regard. Now have a nice day yourself!

          • OWilson

            You too, Mikey!

            Don’t forget to turn out the lights!

            Lol

        • Olarotimi Onayemi

          Thank you.
          I can’t add more to thecynicism and idiocy inherent in scientists and they won’t let people without EU and US passports in their faculties and research

    • http://www.mazepath.com/uncleal/EquivPrinFail.pdf Uncle Al

      Democrat Socialist President Johnson’s 1965 “Great Society,” eventually diverted a $trillion/year to Welfare alone. It converted the desperately poor 4% of the population into the professionally poor 30% of the population. American Coloreds are back in Africa and the Spanish New World – as is the Untied States.

      Alaric is banging on the border. The mob is eager to admit him.

      • gimpi1

        You, sir, are a foolish, vicious liar. I can’t imagine how unpleasant it must be to be stuck in a tiny, filthy place like your mind. I would pity you, except you have refused ample opportunities to grow up. You deserve yourself.

        • http://www.mazepath.com/uncleal/EquivPrinFail.pdf Uncle Al

          Your doctors, dentists, lawyers, CPAs…how many of them are DESERVING? Mine are Jewish and Asian. I reap the bounties of my empirical knowledge.

    • Jennifer A. Nolan

      Just took a fresh look at this thread (2/10/19, 4:42 pm). A couple of guys have improved it somewhat, but the bigots are shooting their efforts down. Too bad!! Where can I find some of that brain bleach?

      • gimpi1

        Right now, I’m going with a Tariquet XO Armagnac. It’s a pleasant way to clean out the synapses, and they used to give brandy for shock… right? I certainly found this thread a bit of a shock.

        • Jennifer A. Nolan

          Me, too! And you should see the comments on the New Republic on uexpress — wait a minute — no, you shouldn’t!

  • AJacobs

    Is anyone concerned with the meaning behind the article? Quite honestly the science and anthropology is the reason I read the article. I thought I might find some educated comments of people that shared the same interest.

  • Mike

    Interesting article.
    Can’t recommend the comments.

  • Olarotimi Onayemi

    That 15000 year old a DNA is not important and never will be for anything spelt ‘human’.

    Why do you people ignore the poverty, misery and death in Africa and what bothers you is removing and returning an ancient… what did you call it?

    • http://www.mazepath.com/uncleal/EquivPrinFail.pdf Uncle Al

      poverty, misery and death in Africa” are sub-Saharan culture, ditto China, Russia and Ireland. African historic population was hard by 80 million (Germany). Current population is 1.3 billion and rising – the whole of it dependent upon massive external charity (harvesting a cut of the cashflow).

      www(.)fourmilab(.)ch/documents/reading_list/images/population_forecast.png
      … You were indoctrinated not educated.

  • peterjohn936

    There are places in Africa where it is dry like the deserts, the mountains and the high plateaus. You should be able to find old DNA in the burials in Egypt, the Sudan, and Ethiopia.

    Then there are modern Africans themselves. Their DNA should in many ways reflect their ancestors’ DNA.

    • http://www.mazepath.com/uncleal/EquivPrinFail.pdf Uncle Al

      The Sahara was Rome’s breadbasket. Africa transforms every opportunity of potential wealth into irremediable disaster. The one exception was slave trade to the New World. This was marginalized by Southern mechanization plus Irish and Eastern European migration to the US (the Northern slave trade)..

      One would do well to search out every cave for its undisturbed contents.

      • peterjohn936

        The Sahara was never Rome’s bread basket. What you are talking about is mostly what is now Tunisia. Africans never transform anything into a disaster. The disaster came from Europe. Please don’t mistake a small blip in history, about a century, to be the entire sum of history. We are no where near the end of the game so we can count up and decide who is winner.

  • wfk3

    These are really interesting ideas the author puts forward. As highly as I regard DNA analysis, the future has to be composed of many integrated disciplines. I wish people would throw out all the “racial” anger talk.

  • StanChaz

    Someone should tell some of these poor lost, racist, bigoted commentators that this is not Breitbart –nor Trump’s twitter account.

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