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svnt · 2 years 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/

attractivechaos · 2 years 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

svnt · 2 years 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?

Deleted Comment

somenameforme · 2 years 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_Geng...

svnt · 2 years ago
There is a pretty good accounting for polygamy in the genetic history of humans as well.

https://www.newscientist.com/article/dn14817-polygamy-left-i...

Mitochondrial DNA, which most people understand to be inherited entirely along the female line, is believed to point back to some single individual female “Eve” 100kya.

jjk166 · 2 years ago
That would look very different genetically from a population bottleneck.

There are two factors at play: inheritance and mutation. If you had a large population of genetically similar individuals, you'd expect after a few gereations many parallel lineages each with their own distinct mutations.

Imagine everyone starts out with a gene that looks like AAAAAAAA; some lines would wind up with AACAAAAA while others wind up with AAAACAAA. In later generations you might see a gene like GACCATTA which came from that first group, whereas a gene like TTAACACG which came from the second (note the position of the C).

Alternatively, if you have a small population, mutations are going to accumulate in series. Perhaps you start out with some AAAAAAAA and some TTTTTTTT variants, in later generations you'd expect to find versions of the gene like AATCAGAT and AAACAGAAT which descend from the first line and TTTCAGTC and TGTCAGTT which descend from the second. The lineages' distinctness is conserved, but they both spent a lot of time developing mutations before they radiated.

Time estimates can get a little wonky because we don't really know what the mutation rate was at any given point in the past; we can kind of calibrate by sequencing genes of fossil specimens but there are only so many specimens of sufficient quality, and they only tell us which mutations had already occurred by that point in time. But the sequence of events is much clearer.

daliusd · 2 years 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
jacquesm · 2 years ago
Let's hope there won't be another one.
tedunangst · 2 years ago
Sign up now to be one of the 1280 survivors allowed to live after we nuke the planet to stop AGI.
jokoon · 2 years ago
Which is why humans are very sensitive to interbreeding
roncesvalles · 2 years 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.
daliusd · 2 years ago
That’s not the case everywhere IMHO. E.g. marrying cousins is kind of norm in some countries
clnq · 2 years 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?

thaumasiotes · 2 years 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.

sam0x17 · 2 years ago
At minimum you need a breeding pair to keep the population going. That's a whole lot less than 1200, so from that macro perspective, I'd say it's fairly hard to wipe most things out, especially the things that have made it this far, just like it's hard for me to completely get rid of the duckweed that keeps growing in my fish tank. Even if I pluck out all the visible duckweed, there's always one or two in the filter that re-seed the population and within a few days the whole surface is covered again. Most life is a little bit like this, to the point where I don't think it's very improbable for a species to have bottlenecks. For a species to make it, surviving bottlenecks has to be a defining feature, and for the most part we are exposed to species that make it.
kqr · 2 years ago
If you have a fair coin, and then you toss it ten times and it lands ten heads in a row, that result is no longer unlikely -- it has a probability (in whatever sense that word is now meaningful) of 100 %.

You can only judge hypotheses more or less likely in relation to each other. When you have multiple hypotheses that all explain the current situation, one may be more likely to have happened in the past than another. So if all you know is that on the first 20 tosses half were heads, you might say it's less likely the sequence was ten heads followed by ten tails, than some mix of heads and tails.

But of course, the difficult part is judging whether two hypotheses explain the same outcome. That's often somewhat subjective when it comes to historical analyses like these.

maxerickson · 2 years ago
Acceptance of the bottleneck is based on the lack of variation in human DNA.

Statistics rather than intuition.

vidarh · 2 years ago
Once you've won the lottery, the odds of you having won the lottery is 1 no matter how small they were before the draw.

So, no, in other words, you can't draw that conclusion. Consider that in any instance where bottlenecks led to extinction we couldn't be here to discuss it, and so the only possibilities is that we won the lottery, whatever the odds were.

svnt · 2 years ago
Correct. We are an unlikely species, as far as we can tell, for a number of reasons.
gumby · 2 years ago
And, according to the article, it's not just lucky that we survived that, but that very bottleneck could have itself produced H. Hiedelbergensis, and thus H. Sapiens Sapiens.

Which also implies that while one remote group could have shrunk to a colony of about 1,300 hominids and leading to us, elsewhere other species of humans could have survived just fine for longer, later dying out due to other exogenous pressure, perhaps from our closer ancestors.

I have read that the world's cheetah are so genetically similar that they appear to have suffered two population bottlenecks, the recent one being only 10-12Ky ago in which the population might have shrunk as low as 30-40 cheetahs.

bglazer · 2 years ago
Fun fact about cheetahs is that they’re so interrelated that any cheetah can accept a skin graft from nearly any other cheetah. They’re so similar that their immune system can’t recognize that the transplanted skin is from a different individual
taneq · 2 years ago
If that's true then maybe we could graft whole cheetahs together to form Cheetah Voltron.
jacquesm · 2 years ago
Irish Wolfhounds have been brought back through outbreeding, I wonder if the same would hold for them.
sidewndr46 · 2 years ago
Got a source for that? It sounds fascinating
titzer · 2 years ago
> might have shrunk as low as 30-40 cheetahs

Or, at one point a mutation, or a group of mutations, gave rise to a small number of super-cheetahs that interbred, and those cheetahs completely out-competed all other cheetahs.

adrian_b · 2 years ago
There is no "Or, ".

The bottleneck consists in the fact that the present cheetahs are the descendants of a group of 30-40 cheetahs that have lived at a certain time.

There are multiple possible explanations for why the bottleneck happened.

There might have been a climate change or another abiotic cause that has killed the other cheetahs, there might have been a disease that has killed the other cheetahs, their prey might have disappeared, another predator, like lions or hyenas might have killed most of them, and so on.

Among the possible causes, both in this case and in the case of humans, there is also the possibility that there has been, as you say, some mutation that has given to a small group an unusually important advantage, allowing them to outcompete any other cheetahs, so in time only their descendants have survived while the descendants of any other cheetahs have disappeared.

In the case of cheetahs, such a cause for the apparent bottleneck seems much less likely than in the case of humans, because it is hard to imagine a decisive advantage of the mutated cheetahs. Something like one extra meter per second in maximum speed does not seem to give enough advantage over competing predators.

gumby · 2 years ago
Or, more likely, at one point a mutation, or a group of mutations, gave rise to a small number of super-cheetahs that interbred, and those cheetahs completely out-competed all other cheetahs until the remaining standard cheetahs, that had been enslaved rebelled under the cheetah Spartacus, overwhelming and eradicating the super-cheetahs using the super-cheetah's own aircraft and other weapons, though even in victory leaving only a small number of normal ones to continue the species.

Ockham's razor says my scenario is more likely.

beowulfey · 2 years ago
What are you describing is one possible explanation for how a bottleneck happened, but your scenario would still result in a genetic bottleneck.
kirubakaran · 2 years ago
That explains why cheetahs never prosper
xnx · 2 years ago
I'm not qualified to say anything about the science, but every since reading about the theory described in "When the Sea Saved Humanity" (https://www.scientificamerican.com/article/when-the-sea-save...), something about the idea of a small band of humans holed holding on to survival near the southern tip of Africa has captivated me.
dontwearitout · 2 years ago
Thanks for sharing, that was a great read. I've always really been fascinated by the aquatic ape hypothesis (https://en.wikipedia.org/wiki/Aquatic_ape_hypothesis), even if it's not widely accepted as fact.
jacquesm · 2 years ago
I always thought that was a nice fiction but without some serious evidence to back it up it will likely remain so. You'd expect at a minimum either some fossils with unique properties or maybe even a descendant alive today since apes are still here as well on the land. Absent both it looked like someone had a neat idea and attempted to rewrite history to match the idea based on cherry picked data, rather than that a piece of evidence was discovered that didn't match the view up to that point requiring a re-thinking of how we got here.

The accepted explanation seems to be - by far - the simpler of the two.

autokad · 2 years ago
I never bought into the aquatic ape theory. besides the fact that its not backed up at all by fossil record, we are built runners, not swimmers. Furthermore, we are built to be vertically oriented, which is horrible for swimming. its one of the reasons why humans don't make natural swimmers.
nl · 2 years ago
Speaking of way-out theories, I always thought the (almost certainly wrong) ape-pig hybrid origin of humans was an interesting theory: https://skeptics.stackexchange.com/questions/34279/are-human...
frozenport · 2 years ago
I'd argue they didn't have too much humanity, or at least what differentiates us from Chimpanzees.
chrisco255 · 2 years ago
Most certainly they did by then. About 1.8 million years ago is when the hand axe (handheld stone axes used as weapons and for cutting) was first developed, and fire control was developed by 1.5 million years ago by earlier hominids.
psychphysic · 2 years ago
The article suggests control of fire is what lead to recovery of the population. So indeed quite a different time.
ahauxuueei · 2 years ago
By that time we had mastered fire by probably a million years already.
c420 · 2 years ago
Mastery of fire has entered the chat.
Aardwolf · 2 years ago
It's pretty crazy to think about this: if a generation would be 25 years on average, only 5 million individuals lived during those 100k years. But today, 100k years in the future sounds like a 100x longer time than what would already be unimaginable science fiction...
aap_ · 2 years ago
Imagine this: watch two years of the life of every human alive today. You'll need more time than the age of the universe (as far as we know).
tw1984 · 2 years ago
so we human beings just spent 1.5x of the age of the universe fighting covid-19. sad!
titzer · 2 years ago
No, it doesn't mean that. The bottleneck doesn't say anything about how many people were alive then, just how many contributed DNA surviving until present day. There could have been millions of individuals whose offspring eventually ended up as genetic dead ends and we'd never know, except for fossils.
taneq · 2 years ago
Would we get the same result from a few millennia of a tribal social structure where only the chief gets to impregnate the women?
guiambros · 2 years ago
> ...if a generation would be 25 years on average, only 5 million individuals lived during those 100k years.

Related: roughly 8% of people who have ever lived are still alive today [1]. And in one year we have 25x more children born than homo sapiens in those first hundreds of thousands of years (140M/yr vs. a few millions).

[1] https://www.techopian.com/eight-per-cent-of-people-who-have-...

leafmeal · 2 years ago
Crazy to think about! Minor correction: 5 million reproduced, presumably more lived but died young, etc. but you point still stands
kzrdude · 2 years ago
That perspective - is why we can say that we live in a very busy world right now. So much human life going on at the same time in this moment. A lot more than compared with 100k, 10k, 1k and 100 years ago.
calimoro78 · 2 years ago
Fair to say most of humankind’s time then has been spent staring at small digital screens.
T-A · 2 years ago
The paper places the bottleneck "between around 930,000 and 813,000 years ago" and has it lasting "for about 117,000 years" [1]. This overlaps with the bottleneck found back in 2017 (also by genetic analysis) in early Neanderthal and Denisovan populations [2][3]:

Approximately 750,000 years ago, according to Rogers, the forerunners of Neanderthals and Denisovans left the ancestors of modern humans behind in Africa to make their way across Eurasia’s expansive territory. Once on their own, something nearly wiped them out entirely; the genetic data shows the population passed through a severe bottleneck, never observed in previous studies.

[1] https://www.science.org/doi/10.1126/science.abq7487

[2] https://www.pnas.org/doi/full/10.1073/pnas.1706426114

[3] https://www.quantamagazine.org/genetics-spills-secrets-from-...

Edit: typos, the bane of my existence.

red_trumpet · 2 years ago
Should be "back in 2017" ;)
T-A · 2 years ago
Thanks, beat me to it.
titzer · 2 years ago
Headline is misleading. The existence of a population bottleneck of approximately 1200 individuals does not imply that humans almost went extinct. It doesn't say anything about the size of the population before or after that bottleneck. In fact, it doesn't even say anything about the size of the population at that time. It just means that those 1200 individuals are the only ones that have contributed genes to the gene pool that survives today. There could have been other human populations that did not pass on their genetic material to modern humans, but were the same species as those who did. In fact, there could have been a lot of them. There were many different hominid species alive at that time, and humans were in competition with them. We have no idea of their relative number. It could have been millions for all we know.

Absent any other evidence, a population bottleneck (derived through studies of live human DNA) suggests nothing about the population at the time, or over time.

Survivor bias.

daveguy · 2 years ago
Yes. The number of breeding pairs present at one time could have coincided with a large population of human-like creatures that went extinct.

The key point in your phrasing is: "There were many different hominid species alive at that time, and humans were in competition with them."

If humpback whales eventually become extinct and blue whales eventually dominate global ecosystems we aren't going to say that means blue whales didn't experience a near extinction because "hey! plenty of whale-critters".

A minimal number of breeding pairs is the definition of near-extinction. To imply otherwise is misleading.

Homo-sapiens is not the same as Homo-neanderthalensis.

titzer · 2 years ago
Even then, there could have been many breeding pairs of humans that were alive and operating and their descendants just did not survive until today. As I wrote in my comment, it doesn't actually say that the population was 1280 individuals, just that some 1280 individual subset of the population passed on their genetic material to us. The descendants of the rest could have died out at any point between now and that time.
saalweachter · 2 years ago
It's pretty trivial to fabricate a thought experiment where the genetic record looks one way and the historical record another.

Let's imagine we've got a thousand islands a million years ago, each with a thousand proto-humans living on them.

These islands live in peace and tranquility, with people occasionally swimming from one island to another to trade or visit or start a new life.

Then one year, one island decides it's had enough of peace and tranquility. It cuts off contact with all the other islands. From this point on, everyone born on that island is a descendant of only the thousand people living on that island, instead of intermingling with the neighboring islands over time, but there's still a million people.

Then, one generation, they go to war. They swim to a neighboring island, kill everyone there, and take it over, and then divide themselves between the two islands. The population drops from 1 million to 999,000. Over time, they expand to fill the two islands, and the population rises back to 1 million.

A hundred years later, they decide they need another island, so they swim to a third island, kill everyone there, and repeat.

Bit by bit, over the course of a hundred thousand years, the descendants of the original xenophobic island swim to each of the other thousand islands, kill everyone there, and repopulate.

In the genetic record, you have a bottleneck -- everyone descends from this small starting population. In the historic record, you just have a gradual pattern of migration and genocide. At no point does the population drop much below the original million; at no point does the population of pre-humans "almost go extinct".

borissk · 2 years ago
This bottleneck occurred before the split between "us" and neanderthals - so if this small population didn't survive there wouldn't be not only modern humans, but neanderthals as well.
asdff · 2 years ago
The number is also referring to effective population size vs the true population size which is larger. For reference the effective population size today is estimated to be between 10,000-20,000 individuals.

https://bionumbers.hms.harvard.edu/bionumber.aspx?s=n&v=0&id...

dang · 2 years ago
(We've replaced the article title with its subtitle, which is more specific.)
borissk · 2 years ago
IMHO you're only partially correct. The population of our ancestors was larger before and after the bottleneck. And it's a very important event, no doubt modern human genetics and behavior is influenced by it.
lainga · 2 years ago
The romantic optimist in me will keep some hope out that that sort of thing was the Great Filter which felled so many of our unseen galactic neighbours.
api · 2 years ago
The Great Filter is really just an arbitrary speculation since we don't know most of the parameters in the Drake equation with any certainty.

It's also a fallacy to assume that a great filter, if it exists, must be a single discrete climactic test or have a single explanation. It could be that there exists on average a continuous low probability of an event or evolutionary path that rules out advanced intelligence in a given biosphere.

Let's say that the yearly probability of such a terminal event or path is about 0.00000002%. Over 500 million years this would amount to a 99% chance of failing the great filter.

If this is true it would mean that we're almost there, very likely to succeed, but also very likely pretty alone at least in our galaxy since there won't be that many advanced intelligences around.

The difference though is that unlike the discrete great filter hypothesis there is no single apocalyptic event to fear. It's a small probability spread over aeons.

This is just to show that we don't know the answer to the Fermi paradox at all. There's no testable or scientific answer at least. Only way to really know is to go out there and look around.

borissk · 2 years ago
There may be 99% chance of failing the great filter in the 500M years before an industrial evolution and 99.99999999% chance of failing it in the 10K years past. Humankind invented nuclear weapons and had a lot of luck that they are hard to make and so far only 2 were used in anger. There's a good chance that with the progress of AI, nanotech, CRISPR very powerful weapons will become available to groups like ISIS - greatly decreasing humankind's chances of survival.
krick · 2 years ago
How do you actually get a number like that? What are the computations, simplified? Is it a coincidence that 1280 = 2⁷ * 10? (I mean, it makes me wonder if it isn't basically a result of using some sort of a decision tree splitting some set by 2 or something, and 10 is perhaps just some hard-coded into the model assumption — which it most probably isn't, of course, I'm just wondering: what is that number?)
Shrezzing · 2 years ago
>Is it a coincidence that 1280 = 2⁷ * 10?

1280 is the nearest threshold we can estimate to, for the reason you've describe. In the OP's title it suggests "exactly 1280", while the original published piece in Science[1] uses the phrase "around 1280".

[1]https://www.science.org/doi/10.1126/science.abq7487