North Africa in Genetics and History

detailed map of African and Middle Eastern ethnicities in Haaks et al’s dataset

North Africa is an often misunderstood region in human genetics. Since it is in Africa, people often assume that it contains the same variety of people referenced in terms like “African Americans,” “black Africans,” or even just “Africans.” In reality, the African content contains members of all three of the great human clades–Sub-Saharan Africans in the south, Polynesians (Asian clade) in Madagascar, and Caucasians in the north.

The North African Middle Stone Age and its place in recent human evolution provides an overview of the first 275,000 years of humanity’s history in the region(300,000-25,000 years ago, more or less), including the development of symbolic culture and early human dispersal. Unfortunately the paper is paywalled.

Throughout most of human history, the Sahara–not the Mediterranean or Red seas–has been the biggest local impediment to human migration–thus North Africans are much closer, genetically, to their neighbors in Europe and the Middle East than their neighbors across the desert (and before the domestication of the camel, about 3,000 years ago, the Sahara was even harder to cross.)

But from time to time, global weather patterns change and the Sahara becomes a garden: the Green Sahara. The last time we had a Green Sahara was about 9-7,000 years ago; during this time, people lived, hunted, fished, herded and perhaps farmed throughout areas that are today nearly uninhabited wastes.

The Peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages sheds light on how the Green (and subsequently brown) Sahara affected the spread (and separation) of African groups into northern and sub-Saharan:

In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. … We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase. …

Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.

In other words, modern North Africans have some maternal (female) Sub-Saharan DNA that arrived recently via the Islamic slave trade, but most of their Sub-Saharan Y-DNA (male) is much older, hailing from the last time the Sahara was easy to cross.

Note that not much DNA is shared across the Sahara:

After the African humid period, the climatic conditions became rapidly hyper-arid and the Green Sahara was replaced by the desert, which acted as a strong geographic barrier against human movements between northern and sub-Saharan Africa.

A consequence of this is that there is a strong differentiation in the Y chromosome haplogroup composition between the northern and sub-Saharan regions of the African continent. In the northern area, the predominant Y lineages are J-M267 and E-M81, with the former being linked to the Neolithic expansion in the Near East and the latter reaching frequencies as high as 80 % in some north-western populations as a consequence of a very recent local demographic expansion [810]. On the contrary, sub-Saharan Africa is characterised by a completely different genetic landscape, with lineages within E-M2 and haplogroup B comprising most of the Y chromosomes. In most regions of sub-Saharan Africa, the observed haplogroup distribution has been linked to the recent (~ 3 kya) demic diffusion of Bantu agriculturalists, which brought E-M2 sub-clades from central Africa to the East and to the South [1117]. On the contrary, the sub-Saharan distribution of B-M150 seems to have more ancient origins, since its internal lineages are present in both Bantu farmers and non-Bantu hunter-gatherers and coalesce long before the Bantu expansion [1820].

In spite of their genetic differentiation, however, northern and sub-Saharan Africa share at least four patrilineages at different frequencies, namely A3-M13, E-M2, E-M78 and R-V88.

A recent article in Nature, “Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81),” tells some of North Africa’s fascinating story:

Here, by using whole Y chromosome sequences, we intend to shed some light on the historical and demographic processes that modelled the genetic landscape of North Africa. Previous studies suggested that the strategic location of North Africa, separated from Europe by the Mediterranean Sea, from the rest of the African continent by the Sahara Desert and limited to the East by the Arabian Peninsula, has shaped the genetic complexity of current North Africans15,16,17. Early modern humans arrived in North Africa 190–140 kya (thousand years ago)18, and several cultures settled in the area before the Holocene. In fact, a previous study by Henn et al.19 identified a gradient of likely autochthonous North African ancestry, probably derived from an ancient “back-to-Africa” gene flow prior to the Holocene (12 kya). In historic times, North Africa has been populated successively by different groups, including Phoenicians, Romans, Vandals and Byzantines. The most important human settlement in North Africa was conducted by the Arabs by the end of the 7th century. Recent studies have demonstrated the complexity of human migrations in the area, resulting from an amalgam of ancestral components in North African groups15,20.

According to the article, E-M81 is dominant in Northwest Africa and absent almost everywhere else in the world.

The authors tested various men across north Africa in order to draw up a phylogenic tree of the branching of E-M183:

The distribution of each subhaplogroup within E-M183 can be observed in Table 1 and Fig. 2. Indeed, different populations present different subhaplogroup compositions. For example, whereas in Morocco almost all subhaplogorups are present, Western Sahara shows a very homogeneous pattern with only E-SM001 and E-Z5009 being represented. A similar picture to that of Western Sahara is shown by the Reguibates from Algeria, which contrast sharply with the Algerians from Oran, which showed a high diversity of haplogroups. It is also worth to notice that a slightly different pattern could be appreciated in coastal populations when compared with more inland territories (Western Sahara, Algerian Reguibates).

Overall, the authors found that the haplotypes were “strikingly similar” to each other and showed little geographic structure besides the coastal/inland differences:

As proposed by Larmuseau et al.25, the scenario that better explains Y-STR haplotype similarity within a particular haplogroup is a recent and rapid radiation of subhaplogroups. Although the dating of this lineage has been controversial, with dates proposed ranging from Paleolithic to Neolithic and to more recent times17,22,28, our results suggested that the origin of E-M183 is much more recent than was previously thought. … In addition to the recent radiation suggested by the high haplotype resemblance, the pattern showed by E-M183 imply that subhaplogroups originated within a relatively short time period, in a burst similar to those happening in many Y-chromosome haplogroups23.

In other words, someone went a-conquering.

Alternatively, given the high frequency of E-M183 in the Maghreb, a local origin of E-M183 in NW Africa could be envisaged, which would fit the clear pattern of longitudinal isolation by distance reported in genome-wide studies15,20. Moreover, the presence of autochthonous North African E-M81 lineages in the indigenous population of the Canary Islands, strongly points to North Africa as the most probable origin of the Guanche ancestors29. This, together with the fact that the oldest indigenous inviduals have been dated 2210 ± 60 ya, supports a local origin of E-M183 in NW Africa. Within this scenario, it is also worth to mention that the paternal lineage of an early Neolithic Moroccan individual appeared to be distantly related to the typically North African E-M81 haplogroup30, suggesting again a NW African origin of E-M183. A local origin of E-M183 in NW Africa > 2200 ya is supported by our TMRCA estimates, which can be taken as 2,000–3,000, depending on the data, methods, and mutation rates used.

However, the authors also note that they can’t rule out a Middle Eastern origin for the haplogroup since their study simply doesn’t include genomes from Middle Eastern individuals. They rule out a spread during the Neolithic expansion (too early) but not the Islamic expansion (“an extensive, male-biased Near Eastern admixture event is registered ~1300 ya, coincidental with the Arab expansion20.”) Alternatively, they suggest E-M183 might have expanded near the end of the third Punic War. Sure, Carthage (in Tunisia) was defeated by the Romans, but the era was otherwise one of great North African wealth and prosperity.

 

Interesting papers! My hat’s off to the authors. I hope you enjoyed them and get a chance to RTWT.

6 thoughts on “North Africa in Genetics and History

  1. Thank you for retweeting these earlier. (Uh, that *was* you, wasn’t it?)

    I came here to uh…reply to a tweet. Since I’m bad at being concise. And also don’t have a twitter account (so after their recent change, I can’t read others’ conversations anymore; woe is me ;)). There are no more open posts–does that mean you’d rather we didn’t do this? If so, I won’t do it again.

    Here’s what I wrote this time:

    Since you were tweeting about the term “mansplaining”…yeah, “mansplaining” is not a concept I typically use either; AFAIK it belongs to the next generation.

    Once online I was accused of “mansplaining” by someone who didn’t know I’m a woman. And I *was* talking down to her–because we had a large age difference. I’m not sure whether I started out talking down to her because she was so young, or whether she said something that suggested she lacked information or that struck me as “overemotional” and I reacted by telling myself “forgive her, she’s young,” which may have showed through as talking down.

    And maybe it wasn’t just that I was talking down to her; maybe the impression I was getting, that she didn’t understand $thing so I needed to explain it to her, really was inaccurate.

    *But* by reacting to this by calling it “mansplaining,” she, intentionally or not, triggered an online mob. She in effect declared war. It’s a shame, because I think for people experiencing this kind of miscommunication–where they seem to be getting pigeonholed as “idiot who doesn’t know $thing” when actually they totally do know $thing–for some of them, “splaining” is the most mentally accessible concept they have to recognize that situation. In which case, they’re not trying to declare war, they’re just trying to say they’re being misinterpreted.

    Another time online, I was the one “pigeonholed as ‘idiot who doesn’t know $thing’ when actually I knew more about $thing than they did.”

    From my POV: They made a blog post that made clear a glaring gap in their knowledge. Since they routinely say very rude things to their commenters, I tried to be extra polite in my efforts to share that knowledge. But everything I said, they interpreted in the “stupidest” possible way–that is, the way that best fit “commenter is an idiot,” even if it didn’t fit my actual words very well–rather than the most likely way, the way that best fit my actual words. When it came to communication, they were not a team player. ;)

    It didn’t occur to me to accuse them of “mansplaining,” but I did lose my temper and say a couple mildly rude things, which inspired them to announce they were never speaking to me again. IOW, just like the person who accused me of mansplaining, I did not solve the miscommunication but instead said something which put paid to any possibility of continuing conversation.

    I’m not sure what started the problem. From my POV they were just stuck firmly in a model of me as something like a 14-year-old and *nothing I tried* could break out of that. Culture clash can certainly cause such a thing: Maybe what I considered polite lack of self-promotion, they heard as “States no credentials, therefore has none, is idiot,” or similar. (Or maybe they were just used to always dealing with 14-year-olds.)

    But since it never became clear to me what *had* caused it…well, that’s exactly the kind of thing that, when it happens face to face, it’s common for a member of a stereotyped group to chalk it up to that stereotype. “Someone had me pigeonholed as an idiot and couldn’t break out of it no matter what I tried”–if I don’t know why, and I do know there *is* a stereotype, I’m very likely to assume it’s “because I’m a woman (or black or etc.).” (Because if there is a stereotype, then sometimes that *is* why.)

    If so, that suggests the obvious remedy of “OK everyone, let’s all pay less attention to stereotypes”…except…well, I’m about to go into my stereotypes speech. This is long enough already, maybe some other time.

    BTW: You retweeted a link to Harvard Magazine’s review of Tom Nichols’ “The Death of Expertise.” It quotes him: “I was trying to tell people, ‘Look, trust me, I’m a Russia guy; there’s a Russian hand behind this.'” […] Finally one day, someone said to him, “‘Tom, I don’t think you understand Russia. Let me explain Russia to you.’ This was a person who didn’t know where Russia was three months earlier.”

    Looks like he’s been “splained” to as well.

    OTOH, I don’t think he’s as expert as he thinks he is. And that’s one of the big issues with the “splaining” experience: When both sides think they know better, who really does and can we prove it? (Or are they more likely to be “the blind men and the elephant”?)

    Like

    • Every post is an open post!
      I just haven’t had the spare time to post labeled open posts.

      Ironically, one of the big questions in political science is “Why didn’t political scientists predict the fall of the Soviet Union?” (And further, why did some Soviet countries collapse and others, like Cuba, persist?) The actions of other people–much less entire countries full of them–are notoriously difficult to predict. (If we could predict other countries easily, we’d have a lot fewer wars.)

      “Mansplaining” properly belongs in the category of “things I don’t understand.” Maybe there are dynamics going on that I’m not privy to because of age, location, job, thought process, or just luck. But I have my theories:
      1. The world is full of people. Some of them will ‘splain things to you. Some of them are dumb or incorrect people who overestimate how much they know and will try to ‘splain things to people who actually do know more than they do. Some are jerks. Some are just really bad at checking whether the other person knows something already or not.

      My mother, for example, is always ‘splaining things to me. If I saw men regularly ‘splaining like my mom splains, I’d be a raging feminist.

      Most people just chalk this behavior up to “sometimes people are annoying.” Feminists, however, have a particular dynamic/lens they see the world through, where men (ie, the patriarchy) are the cause of their oppression. This inspires men to try to explain that they aren’t, and inspires feminists to see any explanations from men as part of the patriarchy’s insidious plan to keep them down.

      Unfortunately, feminism (usually) doesn’t judge the utility of facts based on truth, but on their support for feminist theories. (All ideologies probably engage in this, to some extent.) Since in feminism, “men” are the enemy, things men do or try to say get specially singled out as “the actions of the enemy.” Plus, since most of the obvious, large scale sources of average group performance differences have already been addressed, feminists believe there must be some very subtle things going on in society to blame, like “People think group x is dumb, therefore they treat group x like they are dumb, therefore group x gets denied jobs and makes less money.”

      But if you don’t start with the assumption that men are the enemy, then you just get a statistical question: do men explain things to women who already know those things more often than women do? I’ve never seen any data one way or another on the matter.

      Even in the Tweet that annoyed me and jump-started this whole conversation, the original tweeter didn’t actually say “I already knew this.” They actually said, (I may be misquoting slightly) “If I want to know it, I can look it up on Google.” Which actually implies that they *didn’t* know the information they were being told.

      Which gets to my second, less kind and much more vague theory.

      As a schoolchild, I obviously didn’t have a whole lot of friends and struggled to interact with my classmates. For practical reasons, my interactions were mostly with other girls, so I can’t judge boys either way, but it sure seemed like there was a variety of girls who were almost hostile to information. Maybe they weren’t “dumb,” exactly. Maybe their logic skills were fine. But they were hostile to knowledge, and trying to share some interesting thing you’d learned with them only resulted in scorn.

      Of course these people were more popular than me, though that isn’t saying much. But if you combine this attitude with an intense popularity drive, in which people see everything as either a bid for popularity or to decrease someone else’s social standing, then “people who are trying to share information” are easily transformed into “people who are trying to make me look dumb,” and if the person involved actually does know less stuff than the people around them, then they’re going to encounter a lot of people who are supposedly trying to make them look dumb.

      Since this is not how I naturally think, this is a dynamic I am largely blind to aside from being on the receiving end of other people’s hostility.

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      • >Feminists, however, have a particular dynamic/lens they see the world through, where men (ie, the patriarchy) are the cause of their oppression. This inspires men to try to explain that they aren’t, and inspires feminists to see any explanations from men as part of the patriarchy’s insidious plan to keep them down.

        That’s not what “the patriarchy” means. Or meant, anyway. It meant: For generations the people in charge were men, and so they instinctively always looked at social problems from the POV of the men involved and failed to adequately consider the POV of the women (often even when they kinda tried–because understanding others is hard), and this caused their leadership to be unintentionally biased in favor of men. That system of laws and customs that evolved over those generations under male leadership, that is “the patriarchy.”

        The term “the patriarchy,” and anthropomorphizing discussion of it, was metaphorical. Just like James Lovelock’s “Gaia hypothesis.” Unfortunately, just like Lovelock’s Gaia hypothesis, later on less thoughtful people came along and took it literally, to ridiculous effect.

        >do men explain things to women who already know those things more often than women do? I’ve never seen any data one way or another on the matter.

        Deborah Tannen and Elizabeth Aries had some speech data. Tannen’s the one who pioneered the “unintentional mismatch of speaking styles” explanation. From The Economist’s writeup:

        But Ms Tannen says “the reason is not—as it seems to many women—that men are bums who seek to deny women authority.” Instead, she says, “the inequality of the treatment results not simply from the men’s behavior alone but from the differences in men’s and women’s styles.” […]

        And if Ms Tannen’s differing goals play even a partial role in the outcome, we would expect exactly the outcome we see. A man lays down a marker by mentioning something he knows, an opening bid in establishing his status. A woman acknowledges the man’s point, hoping that she will in turn be expected to share and a connection will be made. The man takes this as if it were offered by someone who thinks like him: a sign of submission to his higher status. And so on goes the mansplaining. This is not every man, every woman, every conversation, but it clearly happens a lot….

        Both boys and girls should be taught that there are several purposes to talking with others. To exchange information, to achieve status and to achieve connection are goals of almost any conversation. If one party to a chat expects an equal exchange and the other is having a competition, things get asymmetrical—and frustrating.

        Or as Tannen memorably put it, “Playful sparring can be a knockout blow to someone whose fists aren’t raised to fight.”

        >They actually said, (I may be misquoting slightly) “If I want to know it, I can look it up on Google.” Which actually implies that they *didn’t* know the information they were being told.

        I’d take that to mean, “That’s irrelevant,” “Who are you to give me this information?” or both.

        Like,
        1. Factoid offered
        2. Don’t see its relevance
        3. Must be a status move then.

        (IMX when men have this reaction they call me “emasculating,” and that’s why I’ve developed the habit of dismissing all complaints about (figurative) “emasculation.” Oh and when I was a kid and adults had this reaction they called me “arrogant,” and that’s why I never take claims that someone’s “arrogant” on faith; for years I just didn’t believe “arrogance” was even a real thing at all.)

        >For practical reasons, my interactions were mostly with other girls, so I can’t judge boys either way, but it sure seemed like there was a variety of girls who were almost hostile to information. Maybe they weren’t “dumb,” exactly. Maybe their logic skills were fine. But they were hostile to knowledge, and trying to share some interesting thing you’d learned with them only resulted in scorn.

        Have some Hollingworth:

        [A] seven-year-old boy with [a ratio] IQ of 178…was not sent to school until the age of seven because of his advanced interest in reading. At seven, however, the compulsory attendance law took effect and the child was placed in the third grade at school. After about four weeks of attendance, he came home from school weeping bitterly. “Oh Grandmother, Grandmother,” he cried, “they don’t know what’s *good*! They just *won’t* read!”

        The fact came to light that he had taken book after book to school–all his favorites from his grandfather’s library–and had tried to show the other third-grade pupils what treasures these were, but the boys and girls only resisted his efforts, made fun of him, threw the treasures on the floor, and finally pulled his hair.

        Boys do it too. (BTW, I ran this by several male family members who also all asserted unprompted that both boys and girls did/do this.)

        (BTW2, I was mostly friends with boys for similar reasons to your “trans” theory: Boys were willing to chalk my differences up to my being a girl, rather than the truth that I was just weird. ;) And my friends were weird too–three of my friends were “sissy/crybaby” boys, one was “the scholarship boy.” It was the older nerd dynamic, the one I’ve used “Revenge of the Nerds” as an example of in the past, rather than the modern one where “sissy” and “fabulous” boys (like RotN’s Lamar) are considered not as much a part of the “nerd” group.)

        >But if you combine this attitude with an intense popularity drive, in which people see everything as either a bid for popularity or to decrease someone else’s social standing, then “people who are trying to share information” are easily transformed into “people who are trying to make me look dumb,” and if the person involved actually does know less stuff than the people around them, then they’re going to encounter a lot of people who are supposedly trying to make them look dumb.

        But this assumes that those other people will be constantly sharing their knowledge, which doesn’t strike me as likely. Most people react to “hostility to information” by ceasing to share it with that person. “I’ll respect their apparent wishes,” and/or “Why should I help them if they’re going to be mean about it?” and/or “Might as well give them enough rope to hang themselves with.”

        >Since this is not how I naturally think, this is a dynamic I am largely blind to aside from being on the receiving end of other people’s hostility.

        “Noticing status games” is my weak point too. (Socionics–the version of Jungian type analysis that developed behind the Iron Curtain at the same time as Myers-Briggs in the West–says this is *typically* the weak point of INTJs, and I’ve seen no reason to disagree.) Most people use status games the way dogs use “play fighting,” to establish who would beat whom in a “serious” fight over politics or principle; since I don’t “play fight,” they don’t expect me to ever fight for real, and are very surprised when I do. Makes my real fights harder than they’d have had to be.

        My experience also agrees with Tannen’s research: Men tend to focus more on this kind of “status game”–one-upmanship, play-fighting–and women tend to focus more on affiliation. Men are more sensitive to being put down (“emasculated” by someone else’s information), women are more sensitive to being rejected (such as by my cold, cruel introverted and thinking nature ;)). I’m being very general here because I agree with Tannen that these are cultures. Even people whose natures don’t really fit these attitudes have been somewhat enculturated into them. (The cultures probably grew out of the personality traits of the “typical” members of each gender, but they’ve taken on a life of their own / it’s a vicious circle / however you want to put it.)

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      • So here’s a question: why doesn’t this dynamic happen to me?
        I mean, my mother ‘splains, yes. She’ll sit and explain things I researched in depth ten years ago for 20 minutes without letting me get a word in edgewise (and if I try, she’ll complain that I’m “interrupting.”) (I am really not trying to turn this into a thing about my mom; she’s jut the only person I know who does this.) (Full disclosure: I’m pretty sure I interrupt my husband more than he interrupts me.)

        Now, maybe I’ve just been lucky. Back when I was employed, maybe I just had great coworkers (it’s true, they were lovely people.) I don’t talk to many non-relative men in real life, and the men I hung out with in college were nice folks, too.

        I’ve encountered lots of mean people, of both genders, but just not a lot of people who offer me random factoids or try to explain things to me. (Or if they do, I haven’t noticed.)

        So I see several possibilities:
        1. I’ve just been lucky. Random chance.
        2. It’s a corporate dynamic and if I had a corporate job, I’d encounter it all the time.
        3. It involves social dynamics I’m blind to.
        4. Men only mansplain to people whose opinions they disagree with, and I tend to have opinions they agree with.
        5. Feminist perspective makes women perceive “mansplaining” where the rest of us just perceive “annoying person.”
        6. Dumb people get ‘splained to.

        EG: https://mobile.twitter.com/razibkhan/status/980150225053601792/photo/1
        Like Reich is an actual geneticist who knows population genetics… but these people are going to ‘splain genetics to him. But since Reich’s male, this isn’t mansplaining, it’s just part of the give-and-take of how people argue their points.

        (I know that’s not how patriarchy was originally defined, but that’s how people often use it (see: intersectionality). If people see the world through a particular lens that says “this group is responsible for your problems” then they are more likely to interpret various phenomena through that lens.)

        Similarly, if someone argued that I don’t understand genetics, I’d assume that either: 1. They’re right and I’ve misunderstood something 2. I’m right and they’re mistaken, or 3. They dislike a conclusion based on the genetics and are therefore attacking the genetics. I don’t assume “they think I’m dumb because I’m female.”

        Even people who seem overall to think that women are dumb (who are pretty thick about these parts) don’t seem inclined to mansplain things to me, which suggests that the phenomenon actually isn’t due to men just thinking women are dumb.

        (I agree that most people react to hostility to information by ceasing to share information, but since this is the internet, you can keep encountering new people.)

        Then there are the corporate possibilities, which I really can’t comment on.
        Thanks for the interesting links.

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