9 ms·

Out of Africa's midlife crisis

100 points by nkurz 5y ago

rayiner 5y ago
I subscribe to Razib’s substack. His writing style is a little weird and scattered, but he writes a lot about how this area of science is rapidly changing, and has good coverage of new hominid fossil discoveries.
- PaulHoule 5y ago
  Yep, my take was that the content of this article is brilliant but there is something annoying about the writing at the paragraph level that needs work.
- valarauko 5y ago
  I've been reading Razib for close to 20 years, and he's never been a great, or even a very good writer. He more than makes up for it with how prolific he is, and I appreciate how frank he is with his theories.
nkurz 5y ago
I thought this was an interesting article. Summarizing from my very-non-expert POV, he's dividing the world into three groups: a small number (less than 1 million) original African inhabitants; a larger number (about a billion) sub-Saharan Africans who broke off about 100,000 years ago; and then the rest-of-the-world (who went though a tight bottleneck less than 100,000 years ago) about the time they left Africa. The surprising part is that measured genetic diversity within the small group of original Africans is greater than that of rest-of-the-world. Counter to intuition that skin tone is a strong indicator of relatedness, a Swede and an Andaman Islander probably have more common genetics than two members of different tribes who both live in the Kalahari desert in Namibia. I'm confused though by his comments about "our species’ one-time amazing levels of genetic diversity." Overall, he seems to be espousing the idea that "diversity" is something we once had lots of, but have lost over time. Is this true? Did the the different tribes of African Bushmen start out as genetically distinct as they are today, or did they start from a common population and diverge over the last 200,000 years? Were those who left Africa always distinct from those who stayed, or did they change through selection (and interbreeding with Neanderthals and Denisovans) over time?
- AlotOfReading 5y ago
  As a general rule, species start out with fairly high levels of diversity from natural processes of evolution. What happened with the out-of-Africa population is what's known as the founder effect. A small population leaves and becomes reproductively isolated. Whatever diversity can be found in their descendents is largely limited to the diversity that was present in the founding population. One thing that should be made very clear is that ancient population structures generally don't map neatly to modern cultures or languages. It's best to treat modern terms as labels of convenience.
  - dorfsmay 5y ago
    Do we have any idea about the size of the original population, the size of the group which left for Europe, the size of the group's who migrated to central/west Africa? I had heard that there were several waves of migration towards Europe, do we have a better estimate about this? Wouldn't multiple waves over time provide more diversity?
    - davisYC 5y ago
      you can infer sizes from genetic diversity ('effective pop') for the out of africa group i've seen sizes from 100 to 10,000. i used 1,000 to 10,000 as a likely moderate number, and the range also points to the census size being larger we can assume that conditional on the size of OoA the other groups were way larger (10x or more). otoh, the main thing i did not explore is that i am now believing that africans themselves especially agriculturalists are 'compounds' of various bottlenecked groups (why west africans are closer to eurasians than they are to khoisan)
      - AlotOfReading 5y ago
        It's worth noting that effective population size != actual population size. The former is simply a lower bound on it. If the population is structured enough and in the right ways, the actual size can be orders of magnitude higher. This has been an issue with several supposed bottlenecks within African populations.
bsanr2 5y ago
On an extremely tangential note: I wish we would stop using the term, "Sub-Saharan." The semantic quandaries should be obvious, but it also subscribes to a curious linguistic glitch of putting the North and South into a hierarchy that only exists if you are rather incurious about the ambiguity of geographic perspective (see: the infamous "upside down" Gall-Peters projection for some mind-blowey fun). I would personally prefer something like "SOS (South-of-Sahara) Africa," or perhaps even something as provocative as "Africa Major" (riffing on Asia Minor and referring to the fact that that part of the continent is, in fact, a majority of its landmass).
- fallingknife 5y ago
  Nobody in their right mind actually thinks placement towards the top of a map actually denotes some kind of hierarchy.
  - api 5y ago
    There is no top of the map since there is no objective frame of reference in space. The axis on which the Earth spins relative to its orbit is a point of orientation but which side is the "top" is arbitrary.
    - fallingknife 5y ago
      Yes, everybody knows that, and if someone asks me where Greenland is on a map, I will say "at the top" like a normal person.
      - api 5y ago
        You don't reference the galactic orientation by reference to the nearest superclusters? Pleb.
        nerfbatplz 5y ago
        The enemy's gate is down
dalbasal 5y ago
For me, it's easier to understand these ideas by adopting a "lumper" mentality to human history. IE, Neanderthals, Denisovans, late Erectus & other archaics were just populations of humans. Sections on a large map of human diversity. On another section were, for example, that small subpopulation accounting for most modern human genetics. Near that little section were other subpopulations that even a "splitter" would call Sapiens. Just because they're Sapiens and we're Sapiens doesn't mean that they left more genetic legacy than Neanderthal subpopulations. I do have some questions though... "If you don’t have Sub-Saharan African ancestry, all of your ancestry (aside from your differential rates of Neanderthal/Denisovan ancestry) goes back to the same 1,000-10,000 humans that split off from other Africans." No introgression with other Sapien populations? We know that Sapiens existed outside of Sub-Saharan Africa long before that bottleneck. Are all additions to that genetic stock from other species? Also, what's the relationship between genetically isolated and genetically diverse? Most of our ancestors went through single a bottleneck 60kya-120kya, with non africans going through at least one more. Theirs did not go through that bottleneck or a seperate one. Coincidence, or is it part of the story somehow?
- valarauko 5y ago
  > No introgression with other Sapien populations? Perhaps indirectly. As he addresses later in the text, it's possible that Denisovans in South East Asia encountered Homo erectus and interbred with them. The Denisovans appear to have more population structure as compared to Neanderthals, and introgression from H. erectus might explain some of it. Considering that South East Asia and Papua New Guinea has the highest Denisovan introgression in modern humans, it's possible that some of that H. erectus ancestry ended up in those of us from East of the Indus. For what it's worth, I have seen other studies pop up from time to time that claim to have found introgression from some unknown ghost sapien population, but these outliers usually go away by tweaking the parameters.
  - dalbasal 5y ago
    Interesting. What I meant though was introgression with closer groups. IE there clearly were surviving populations that didn't go through the major sapien funnels. Their descendants are in the "very diverse" group. Obviously there was, is and will be "introgression" with them. Were there other such groups, in or out of sub-saharan africa... whos genes we carry?
TimonKnigge 5y ago
I'm curious if this genetic diversity is just something that shows up as a number on a computer, or does it translate into something phenotypically* visible? Also, how much of, say, our medical/biological knowledge actually only applies to the descendants of the bottleneck mentioned in the post? I understand the "very diverse" in the article have better things to do than be subjected to researchers, but reading the article I can't help but be curious what this genetic diversity means in practice? *) not necessarily visually
imbnwa 5y ago
Related https://www.discovermagazine.com/planet-earth/how-africa-became-black https://www.discovermagazine.com/planet-earth/how-africa-bec...

100 points by nkurz 5y ago

I subscribe to Razib’s substack. His writing style is a little weird and scattered, but he writes a lot about how this area of science is rapidly changing, and has good coverage of new hominid fossil discoveries.

PaulHoule 5y ago
Yep, my take was that the content of this article is brilliant but there is something annoying about the writing at the paragraph level that needs work.
valarauko 5y ago
I've been reading Razib for close to 20 years, and he's never been a great, or even a very good writer. He more than makes up for it with how prolific he is, and I appreciate how frank he is with his theories.

nkurz 5y ago

I thought this was an interesting article. Summarizing from my very-non-expert POV, he's dividing the world into three groups: a small number (less than 1 million) original African inhabitants; a larger number (about a billion) sub-Saharan Africans who broke off about 100,000 years ago; and then the rest-of-the-world (who went though a tight bottleneck less than 100,000 years ago) about the time they left Africa. The surprising part is that measured genetic diversity within the small group of original Africans is greater than that of rest-of-the-world. Counter to intuition that skin tone is a strong indicator of relatedness, a Swede and an Andaman Islander probably have more common genetics than two members of different tribes who both live in the Kalahari desert in Namibia. I'm confused though by his comments about "our species’ one-time amazing levels of genetic diversity." Overall, he seems to be espousing the idea that "diversity" is something we once had lots of, but have lost over time. Is this true? Did the the different tribes of African Bushmen start out as genetically distinct as they are today, or did they start from a common population and diverge over the last 200,000 years? Were those who left Africa always distinct from those who stayed, or did they change through selection (and interbreeding with Neanderthals and Denisovans) over time?

AlotOfReading 5y ago
As a general rule, species start out with fairly high levels of diversity from natural processes of evolution. What happened with the out-of-Africa population is what's known as the founder effect. A small population leaves and becomes reproductively isolated. Whatever diversity can be found in their descendents is largely limited to the diversity that was present in the founding population. One thing that should be made very clear is that ancient population structures generally don't map neatly to modern cultures or languages. It's best to treat modern terms as labels of convenience.
- dorfsmay 5y ago
  Do we have any idea about the size of the original population, the size of the group which left for Europe, the size of the group's who migrated to central/west Africa? I had heard that there were several waves of migration towards Europe, do we have a better estimate about this? Wouldn't multiple waves over time provide more diversity?
  - davisYC 5y ago
    you can infer sizes from genetic diversity ('effective pop') for the out of africa group i've seen sizes from 100 to 10,000. i used 1,000 to 10,000 as a likely moderate number, and the range also points to the census size being larger we can assume that conditional on the size of OoA the other groups were way larger (10x or more). otoh, the main thing i did not explore is that i am now believing that africans themselves especially agriculturalists are 'compounds' of various bottlenecked groups (why west africans are closer to eurasians than they are to khoisan)
    - AlotOfReading 5y ago
      It's worth noting that effective population size != actual population size. The former is simply a lower bound on it. If the population is structured enough and in the right ways, the actual size can be orders of magnitude higher. This has been an issue with several supposed bottlenecks within African populations.

bsanr2 5y ago

On an extremely tangential note: I wish we would stop using the term, "Sub-Saharan." The semantic quandaries should be obvious, but it also subscribes to a curious linguistic glitch of putting the North and South into a hierarchy that only exists if you are rather incurious about the ambiguity of geographic perspective (see: the infamous "upside down" Gall-Peters projection for some mind-blowey fun). I would personally prefer something like "SOS (South-of-Sahara) Africa," or perhaps even something as provocative as "Africa Major" (riffing on Asia Minor and referring to the fact that that part of the continent is, in fact, a majority of its landmass).

fallingknife 5y ago
Nobody in their right mind actually thinks placement towards the top of a map actually denotes some kind of hierarchy.
- api 5y ago
  There is no top of the map since there is no objective frame of reference in space. The axis on which the Earth spins relative to its orbit is a point of orientation but which side is the "top" is arbitrary.
  - fallingknife 5y ago
    Yes, everybody knows that, and if someone asks me where Greenland is on a map, I will say "at the top" like a normal person.
    - api 5y ago
      You don't reference the galactic orientation by reference to the nearest superclusters? Pleb.
      - nerfbatplz 5y ago
        The enemy's gate is down

dalbasal 5y ago

For me, it's easier to understand these ideas by adopting a "lumper" mentality to human history. IE, Neanderthals, Denisovans, late Erectus & other archaics were just populations of humans. Sections on a large map of human diversity. On another section were, for example, that small subpopulation accounting for most modern human genetics. Near that little section were other subpopulations that even a "splitter" would call Sapiens. Just because they're Sapiens and we're Sapiens doesn't mean that they left more genetic legacy than Neanderthal subpopulations. I do have some questions though... "If you don’t have Sub-Saharan African ancestry, all of your ancestry (aside from your differential rates of Neanderthal/Denisovan ancestry) goes back to the same 1,000-10,000 humans that split off from other Africans." No introgression with other Sapien populations? We know that Sapiens existed outside of Sub-Saharan Africa long before that bottleneck. Are all additions to that genetic stock from other species? Also, what's the relationship between genetically isolated and genetically diverse? Most of our ancestors went through single a bottleneck 60kya-120kya, with non africans going through at least one more. Theirs did not go through that bottleneck or a seperate one. Coincidence, or is it part of the story somehow?

valarauko 5y ago
> No introgression with other Sapien populations? Perhaps indirectly. As he addresses later in the text, it's possible that Denisovans in South East Asia encountered Homo erectus and interbred with them. The Denisovans appear to have more population structure as compared to Neanderthals, and introgression from H. erectus might explain some of it. Considering that South East Asia and Papua New Guinea has the highest Denisovan introgression in modern humans, it's possible that some of that H. erectus ancestry ended up in those of us from East of the Indus. For what it's worth, I have seen other studies pop up from time to time that claim to have found introgression from some unknown ghost sapien population, but these outliers usually go away by tweaking the parameters.
- dalbasal 5y ago
  Interesting. What I meant though was introgression with closer groups. IE there clearly were surviving populations that didn't go through the major sapien funnels. Their descendants are in the "very diverse" group. Obviously there was, is and will be "introgression" with them. Were there other such groups, in or out of sub-saharan africa... whos genes we carry?

TimonKnigge 5y ago

I'm curious if this genetic diversity is just something that shows up as a number on a computer, or does it translate into something phenotypically* visible? Also, how much of, say, our medical/biological knowledge actually only applies to the descendants of the bottleneck mentioned in the post? I understand the "very diverse" in the article have better things to do than be subjected to researchers, but reading the article I can't help but be curious what this genetic diversity means in practice? *) not necessarily visually

imbnwa 5y ago

Related https://www.discovermagazine.com/planet-earth/how-africa-became-black https://www.discovermagazine.com/planet-earth/how-africa-bec...