5 ms·

The idea of (at least one) population bottleneck in the evolutionary history of humans is fairly widely accepted. I haven't reviewed the paper or methods but ge

by svnt 3y ago

The idea of (at least one) population bottleneck in the evolutionary history of humans is fairly widely accepted. I haven't reviewed the paper or methods but generally their results fit the range of expectations of many in the field. This new paper is interesting in that they developed a new method in population genomics specifically to attempt to pin down all of: the time, the duration, and the size of the population. There are many earlier papers describing different methods for arriving at similar conclusions. The below paper used similar genetic signatures from bottleneck events such as the loss of rare alleles. Their methods were different. It explains one such process fairly well and is available to read: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842629/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842629/

jokoon 3y ago
Which is why humans are very sensitive to interbreeding
- roncesvalles 3y ago
  By sensitive to interbreeding do you mean that's the reason why humans can't have offspring with other apes? Curious to know how this is implied by a genomic bottleneck.
  - trane_project 3y ago
    I think they meant incest. If we already did our share of it in the distant past, then fun with your cousin leads to a baby with a pig's tail. Or at least it did for the Buendía family: https://en.wikipedia.org/wiki/One_Hundred_Years_of_Solitude https://en.wikipedia.org/wiki/One_Hundred_Years_of_Solitude
- daliusd 3y ago
  That’s not the case everywhere IMHO. E.g. marrying cousins is kind of norm in some countries
  - joe__f 3y ago
    I've read that it was encouraged in ancient Egypt
    - Auracle 3y ago
      Ancient? "As of 2016, about 40% of marriages in Egypt were between cousins." https://upload.wikimedia.org/wikipedia/commons/7/7b/Global_prevalence_of_consanguinity.svg https://upload.wikimedia.org/wikipedia/commons/7/7b/Global_p... https://en.wikipedia.org/wiki/Cousin_marriage_in_the_Middle_East https://en.wikipedia.org/wiki/Cousin_marriage_in_the_Middle_...
      - fireant 3y ago
        First time hearing about this. I'm surprised the whole region isn't massively degenerated after centuries of traditional incest. The numbers are pretty staggering
        Auracle 3y ago
        I've heard it argued that it could be the reason the middle east is the way it is now as opposed to the world's hub of scientific discoveries and great culture that is used to be. However, that's racist-adjacent so I doubt there's any actual research or scientific basis for it. They certainly have much higher rates of genetic diseases. As noted in that Wikipedia article: "While babies of Pakistani heritage accounted for roughly 3.4% of all births in the UK (2005), "they had 30% of all British children with recessive disorders and a higher rate of infant mortality," according to research done by the BBC.[46]"
jacquesm 3y ago
Let's hope there won't be another one.
- tedunangst 3y ago
  Sign up now to be one of the 1280 survivors allowed to live after we nuke the planet to stop AGI.
  - jacquesm 3y ago
    You forgot the link ;) And it just had to be 1280... at least they will all have one column each on the demographics graph of my old monitor.
    - actionfromafar 3y ago
      Only eligible candidates see the link.
attractivechaos 3y ago
> There are many earlier papers describing different methods for arriving at similar conclusions. The paper under your link is claiming a recent second bottleneck (in addition to the out-of-Africa one at ~60kya) but the Science paper is claiming an ancient bottleneck at ~900kya. These are very different conclusions. Note that the method in the Science paper is unable to find this second bottleneck directly in non-Africans. The authors have to fix recent population sizes to find it. This doesn't sound right. The new method is also inconsistent with earlier established methods (disclaimer: one of them is mine) which the authors don't have an adequate explanation to. More discussions at: https://twitter.com/aylwyn_scally/status/1697344429135135018 https://twitter.com/aylwyn_scally/status/1697344429135135018
- svnt 3y ago
  They are very different times, yes, but the idea of a human population bottleneck at all in my experience is foreign to most people outside of the evolutionary anthropology/archaeology/etc fields. Is there more discussion at your link or just the single dismissal post? Maybe I need to log in?
  - mistrial9 3y ago
    except, multiple tribal groups have oral history about that
    - rpearl 3y ago
      that is not evidence of a historical fact
      - ClumsyPilot 3y ago
        much of accepted hidtory is not a provable fact. We have just people's word, written or not
      - h0l0cube 3y ago
        It could be classified as a very unreliable tertiary source
clnq 3y ago
Why is the bottleneck idea widely accepted? It seems to my non-academic brain that each bottleneck would make an ongoing population less likely, as it is an opportunity for the population to die out. So it seems like us having this chat today is evidence that there weren’t too many bottleneck events. The more we would have had, the less likely it would be that humans would have survived until today. 0 bottleneck events seem most likely though that lens, 1 - less likely, 2 - even less, and so on. Right?
- svnt 3y ago
  Correct. We are an unlikely species, as far as we can tell, for a number of reasons.
- thaumasiotes 3y ago
  As far as I understand it, the bottleneck idea is based on a back-calculation of "effective population size" in the past from existing genetic diversity in the present. (This is definitely the case in the article, which specifies "the population of breeding individuals".) There are a couple of things that tend to be miscommunicated: 1. An effective population size of N means an actual population size that is significantly larger; children too young to reproduce, adults too old to reproduce, and nerds too awkward to reproduce are all not counted in effective population size. 2. If a group gets demographically wiped out at time T, their ancestors at time T-1000 vanish from the effective population at time T-1000, even though those same ancestors were part of the effective population at time T-1000 if you did the same calculation at time T-200. (This is true to the extent that the vanishing ancestors don't also have other descendants in groups that survive. But the effect is quite significant - the effective size of the pre-Cherokee population in the year 1000 was much larger in the year 1450 than the same quantity, the effective size of the pre-1450-Cherokee population in the year 1000, is today. Was there a bottleneck? Sure; Amerinds in the region of the United States got wiped out. How long did that process take? When did it happen? We know a lot about the shape of the population over the relevant time period - is it something we're comfortable calling a "bottleneck"?) So we might estimate our group of 1300 effective individuals as reflecting maybe 430 men of reproductive age, 870 women of reproductive age, plus 220 more women of reproductive age who fail to reproduce, 650 more men of reproductive age who fail to reproduce, and a few thousand children and elders not of reproductive age. And if this group later loses a war, their population could be a lot higher than that.
somenameforme 3y ago
What's the argument against the seemingly obvious possibility of instead of it being a bottleneck, it was the result of a dominant group? So for the contemporary example, something like 8% of Asian men are related to Genghis Khan [1]. And that's in a very recent time frame, and in a world that was already much more spread out than the ones in the distant past. It seems that if there was a group that was particularly dominant (killing competitors, spreading their own genes far and wide), as were their offspring and so on, then it could easily lead to a scenario that would look like a bottleneck due to a surge of a very limited number of individuals taking over a disproportionate dominance of the human gene pool. It seems this would look near identical to a bottleneck, even if it wasn't. [1] - https://en.wikipedia.org/wiki/Family_and_descendants_of_Genghis_Khan#DNA_evidence https://en.wikipedia.org/wiki/Family_and_descendants_of_Geng...
- daliusd 3y ago
  Killing competitors means competitors are dead. Thus bottleneck. How many competitors that group could have killed? Up to 1000 - maybe, 10000 - that would be very interesting. 2000 is still bottleneck
  - somenameforme 3y ago
    Killing was an extremely very poor choice of words on my part, as this certainly doesn't have to involve death. Take South Korea as a contemporary example with their publicized 0.7 fertility rate. That trends towards extinction at an exponential pace. But now imagine there was another group within South Korea that started going the opposite direction and just having massive numbers of children. You could even create an equilibrium level (probably more theoretic than practical at the population levels in modern times, but not necessarily in ancient) where this group's fertility trends up end perfectly balancing against the rest of South Korea's low fertility trends, such that the population doesn't even meaningfully change, or maybe even increases, yet the DNA pool ends up near to 100% controlled by a tiny minority. I'm curious if and how this would look different (from a long distant DNA analysis) from the suggestion that suddenly all of South Korea just mysteriously died and these were the only people left.

by svnt 3y ago

jokoon 3y ago

Which is why humans are very sensitive to interbreeding

roncesvalles 3y ago
By sensitive to interbreeding do you mean that's the reason why humans can't have offspring with other apes? Curious to know how this is implied by a genomic bottleneck.
- trane_project 3y ago
  I think they meant incest. If we already did our share of it in the distant past, then fun with your cousin leads to a baby with a pig's tail. Or at least it did for the Buendía family: https://en.wikipedia.org/wiki/One_Hundred_Years_of_Solitude https://en.wikipedia.org/wiki/One_Hundred_Years_of_Solitude
daliusd 3y ago
That’s not the case everywhere IMHO. E.g. marrying cousins is kind of norm in some countries
- joe__f 3y ago
  I've read that it was encouraged in ancient Egypt
  - Auracle 3y ago
    Ancient? "As of 2016, about 40% of marriages in Egypt were between cousins." https://upload.wikimedia.org/wikipedia/commons/7/7b/Global_prevalence_of_consanguinity.svg https://upload.wikimedia.org/wikipedia/commons/7/7b/Global_p... https://en.wikipedia.org/wiki/Cousin_marriage_in_the_Middle_East https://en.wikipedia.org/wiki/Cousin_marriage_in_the_Middle_...
    - fireant 3y ago
      First time hearing about this. I'm surprised the whole region isn't massively degenerated after centuries of traditional incest. The numbers are pretty staggering
      - Auracle 3y ago
        I've heard it argued that it could be the reason the middle east is the way it is now as opposed to the world's hub of scientific discoveries and great culture that is used to be. However, that's racist-adjacent so I doubt there's any actual research or scientific basis for it. They certainly have much higher rates of genetic diseases. As noted in that Wikipedia article: "While babies of Pakistani heritage accounted for roughly 3.4% of all births in the UK (2005), "they had 30% of all British children with recessive disorders and a higher rate of infant mortality," according to research done by the BBC.[46]"

jacquesm 3y ago

Let's hope there won't be another one.

tedunangst 3y ago
Sign up now to be one of the 1280 survivors allowed to live after we nuke the planet to stop AGI.
- jacquesm 3y ago
  You forgot the link ;) And it just had to be 1280... at least they will all have one column each on the demographics graph of my old monitor.
  - actionfromafar 3y ago
    Only eligible candidates see the link.

attractivechaos 3y ago

> There are many earlier papers describing different methods for arriving at similar conclusions. The paper under your link is claiming a recent second bottleneck (in addition to the out-of-Africa one at ~60kya) but the Science paper is claiming an ancient bottleneck at ~900kya. These are very different conclusions. Note that the method in the Science paper is unable to find this second bottleneck directly in non-Africans. The authors have to fix recent population sizes to find it. This doesn't sound right. The new method is also inconsistent with earlier established methods (disclaimer: one of them is mine) which the authors don't have an adequate explanation to. More discussions at: https://twitter.com/aylwyn_scally/status/1697344429135135018 https://twitter.com/aylwyn_scally/status/1697344429135135018

svnt 3y ago
They are very different times, yes, but the idea of a human population bottleneck at all in my experience is foreign to most people outside of the evolutionary anthropology/archaeology/etc fields. Is there more discussion at your link or just the single dismissal post? Maybe I need to log in?
- mistrial9 3y ago
  except, multiple tribal groups have oral history about that
  - rpearl 3y ago
    that is not evidence of a historical fact
    - ClumsyPilot 3y ago
      much of accepted hidtory is not a provable fact. We have just people's word, written or not
    - h0l0cube 3y ago
      It could be classified as a very unreliable tertiary source

clnq 3y ago

Why is the bottleneck idea widely accepted? It seems to my non-academic brain that each bottleneck would make an ongoing population less likely, as it is an opportunity for the population to die out. So it seems like us having this chat today is evidence that there weren’t too many bottleneck events. The more we would have had, the less likely it would be that humans would have survived until today. 0 bottleneck events seem most likely though that lens, 1 - less likely, 2 - even less, and so on. Right?

svnt 3y ago
Correct. We are an unlikely species, as far as we can tell, for a number of reasons.
thaumasiotes 3y ago
As far as I understand it, the bottleneck idea is based on a back-calculation of "effective population size" in the past from existing genetic diversity in the present. (This is definitely the case in the article, which specifies "the population of breeding individuals".) There are a couple of things that tend to be miscommunicated: 1. An effective population size of N means an actual population size that is significantly larger; children too young to reproduce, adults too old to reproduce, and nerds too awkward to reproduce are all not counted in effective population size. 2. If a group gets demographically wiped out at time T, their ancestors at time T-1000 vanish from the effective population at time T-1000, even though those same ancestors were part of the effective population at time T-1000 if you did the same calculation at time T-200. (This is true to the extent that the vanishing ancestors don't also have other descendants in groups that survive. But the effect is quite significant - the effective size of the pre-Cherokee population in the year 1000 was much larger in the year 1450 than the same quantity, the effective size of the pre-1450-Cherokee population in the year 1000, is today. Was there a bottleneck? Sure; Amerinds in the region of the United States got wiped out. How long did that process take? When did it happen? We know a lot about the shape of the population over the relevant time period - is it something we're comfortable calling a "bottleneck"?) So we might estimate our group of 1300 effective individuals as reflecting maybe 430 men of reproductive age, 870 women of reproductive age, plus 220 more women of reproductive age who fail to reproduce, 650 more men of reproductive age who fail to reproduce, and a few thousand children and elders not of reproductive age. And if this group later loses a war, their population could be a lot higher than that.

somenameforme 3y ago

What's the argument against the seemingly obvious possibility of instead of it being a bottleneck, it was the result of a dominant group? So for the contemporary example, something like 8% of Asian men are related to Genghis Khan [1]. And that's in a very recent time frame, and in a world that was already much more spread out than the ones in the distant past. It seems that if there was a group that was particularly dominant (killing competitors, spreading their own genes far and wide), as were their offspring and so on, then it could easily lead to a scenario that would look like a bottleneck due to a surge of a very limited number of individuals taking over a disproportionate dominance of the human gene pool. It seems this would look near identical to a bottleneck, even if it wasn't. [1] - https://en.wikipedia.org/wiki/Family_and_descendants_of_Genghis_Khan#DNA_evidence https://en.wikipedia.org/wiki/Family_and_descendants_of_Geng...

daliusd 3y ago
Killing competitors means competitors are dead. Thus bottleneck. How many competitors that group could have killed? Up to 1000 - maybe, 10000 - that would be very interesting. 2000 is still bottleneck
- somenameforme 3y ago
  Killing was an extremely very poor choice of words on my part, as this certainly doesn't have to involve death. Take South Korea as a contemporary example with their publicized 0.7 fertility rate. That trends towards extinction at an exponential pace. But now imagine there was another group within South Korea that started going the opposite direction and just having massive numbers of children. You could even create an equilibrium level (probably more theoretic than practical at the population levels in modern times, but not necessarily in ancient) where this group's fertility trends up end perfectly balancing against the rest of South Korea's low fertility trends, such that the population doesn't even meaningfully change, or maybe even increases, yet the DNA pool ends up near to 100% controlled by a tiny minority. I'm curious if and how this would look different (from a long distant DNA analysis) from the suggestion that suddenly all of South Korea just mysteriously died and these were the only people left.