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:
> 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:
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?
Every Christian, Jew, and Muslim (over 50% of the world population) have the same two “bottleneck” stories in their traditions and religious texts. I find it hard to believe that the idea is foreign to most people, maybe just most people you interact with.
It's a single creation and flood story from a single Middle Eastern culture
Just because it spread across half the world by the later military and commercial success of its practicioners doesnt mean the "distant history" aspect of its mythology has any more basis in reality than gods manipulating lightning, the divinity of cats or tree nymphs (or indeed the same religious tradition's emphasis on creation as a six day process). Especially since a couple birthing children and a flood are near-universally experienced concepts that don't really have that much in common with tribal migrations and non-flood near-extinction events many millenia earlier.
this reaction here reminds me of a party in Denmark where I made a comment about the concept of a genetic eve having been found and one party goer got very indignant and explained how humans came from Africa, in short I don't think the person you're replying to said anything about the flood myth being true, they just said that the concept of a genetic bottleneck is actually pretty widespread throughout the world and many people would be familiar with the idea even if not actually believing in the story that gave them that idea.
I can't divine exactly what the OP meant, but it's a pretty common argument amongst nonbelievers that ancient religious myths (especially the Flood, also present in a handful of non-abrahamic traditions) were somehow inspired by even older oral traditions of stuff that actually happened in their dim and distant past (as opposed to the flooding they experience on a regular basis). It appears I'm not the only person that perceived that was being implied.
Regardless, I don't think "genetic bottlenecks scientists believe exist in the human evolutionary tree" and "religious stories that may or may not be interpreted literally" has much conceptual overlap, either in terms of modern people's awareness of modern bottleneck theories or in terms of links between prehistoric events and mythology which became popular much later.
I think they overlap. The assumption the stories are based on older events doesn’t have to be correct, it still makes for a familiarity with the idea. I wouldn’t mind chatting with you about this at a party. :)
Sure but I think that what was pointed by the parent post is that many people are very acquainted with the concept of human population going through a bottleneck.
Just because you learnt it in a fairy tale doesn’t mean you didn’t understand a concept.
hundreds of thousands of people have passed this information across generations, and you an individual can say "it means the same as complete fiction" .. It is hubris on your part in some real way.
It seems to me that the comment suggested (either intentionally or not) that the same event has been recorded independently in the mythologies of a few separate religions, to which the reply was that these religions have only been split from each other long after these stories have been written down, so in this regard they all should count as just a single religion.
While I’m not as familiar with Islam as the other two, my understanding is its oral history diverged long before there was any written Jewish history. So while they do have a common origin, its split was about 350 years prior to any written Jewish history and about 1800 years before Christianity.
It sounds like you actually know nothing about any of these religions!
Judaism obviously claims its story is continuous from the beginning of creation, but the timeline in its own narrative suggests approximately 7000 BC. At first this was oral tradition, but estimates as for when it was written down range from 900 BC to about 450BC.
As far as Christians are concerned, the last Jewish books chronologically were Ezra and Nehemiah, written approximately 400 BC. After the period recorded in this book, the Jews were waiting for their Messiah to arrive.
Christianity per se didn't start until after Jesus' death around (around 32 AD), and the first books were written between about 40AD and 70AD. But obviously, Christianity didn't even start until many centuries after the Jewish tradition was recorded in written form, because it needed Jesus to have been born first.
The selection of which books make up the bible today was decided upon by the Council of Nicea in the late 4th century AD, and is mostly unchanged to this day, although some religious groups also include some other books, collectively called the Apochrypha, in their bibles. Some argue these aren't important, others argue they are, but whatever in the 4th century, the leaders of the church from all around the world met up several times to choose to selection of books they felt were most important for people to know. It was mostly limited because paper was expensive then, and they wanted the minimal set that contained everything considered essential to Christianity.
The Jews continued writing and considered some books important after that point, but essentially 400 BC was the last significant event even in their canon.
Islam is much later than this, and certainly much later than Christianity. As I said above, the bible in its current form was decided on in the 4th century AD and the prophet Muhammad wasn't born until the 6th century AD. Most people date Islam to 610, which is when Muhammad recorded his first revelation. You can even see Islamic teaching that references Christianity - initially positive, recognising Jesus as a prophet from God, and later more combative when Islam was largely ignored by Christians as being unnecessary.
I've read more cynical interpretations that Muhammad was hoping to ally with Christians to avoid persecution, and when they all largely ignored everything he was saying, then he decided they too were infidels who oppose the will of God, and later parts of the Quran are distinctly anti-Christian in contrast to the earlier parts.
Muhammad also re-framed old Jewish stories (accepted as true by both Jews and Christians) in a way that tried to discredit their traditions, but paint Islam more favourably. The most contentious of these is regarding Abraham and Isaac - in the Jewish tradition, he and his wife Sarah had been childless for many decades after God had promised him that his children would have many children and become many nations. Finally had a son, and God asked him to sacrifice his firstborn as a test of his faith in God to provide another son. When God saw that he would be willing to obey him and perform the sacrifice, God tells him to stop, reaffirmed his promise to bless all nations through his son, and provided a substitute animal for the sacrifice. This is all in Genesis 22. The Islamic tradition, on the other hand, re-frames this as Abraham going crazy for some reason, trying to kill his only son after decades of being childless, and God having to stop in to stop him from murdering the son he'd been longing for for decades.
So, far from divergent history long before any written Jewish history, it's the complete opposite - Jewish history largely ends in 400 BC still waiting its Messiah; Christianity claims to be about that Messiah and covers the period from about 3 BC to around 40 AD, and was largely finished being recorded around 70 AD; Islam claims to have yet more revelation recorded between around 610 AD and 650 AD. If it wasn't for the fact that the previous believers didn't agree with the new revelations each time, you could consider them to be linear and not divergent at all, rather continuing from where the previous tradition finished.
I think you are taking a too strong stance on interpretation of those stories by holy books. What stood out to me is the case of Islam twisting Abraham story. Perhaps they were not trying to shame jewish version, but were displeased with depiction of god as "playing games" and chose to present him as "wise observer that intervenes". Just wanted to provide an extra look, but if you have some more proof/info on that interpretation (I am not knowledgeable on the subject) I would love to hear.
Hypothetically speaking, and I'm putting an emphasis on the "hypothetical" part, you could have two individuals starting a new population of arbitrary size, without ill-effects of inbreeding.
There is only one requirement. And one caveat. The requirement is that both individuals need to be free of genetic defects in their alleles, so that no matter how many generations down you go you never end up with two defective alleles in the same descendant. That is impossible in practice. Eventually you would get some diversity from random mutation and at that point you would be back to "normal" state of affairs.
The caveat is disease resistance. All of their descendants would have the same immune system. If one gets sick, they all do. Any infection will spread like wildfire, if it spreads. And nothing short of total quarantine would stop it.
There an amazing number of coincidences that have led to human life existing. I only know of the anthropic principle greatest hits from physics including The Moon, plate tectonics, distance from sun, etc but I assume there are more from the natural world of evolution.
So I wouldn’t be surprised to hear that the bottleneck population also wiped their bottoms with leaves from a tree that grows only in natural uranium ore, thereby artificially boosting their genetic diversity as well as putting pressure on them to reproduce frequently and often before they reach their radiologically reduced life expectancy of 25.
All of this in light of the very literal form of survivorship bias.
Try a few billion or trillion planets to get the conditions JUST right and there will probably be at least one getting it right. Inhabited by folks who wonder why it was their planet that had everything going for it.
Even back with Leibniz, arguing this is the 'best of all possible worlds' because it is the one we exist in that god provided. It's circular, or calls for some mysticism or parallel universes.
This seems like such a contradiction with Christians. They just do lot of hand-waving and ignore it.
Then went and read the Bible and what did I find, there were other people at the time of Adam and Eve. The Bible actually discusses the other humans that were living in other lands At The Same Time As Adam and Eve. Totally blown away.
So then, why do Christians today completely believe that God Created Adam And Even and they were the very first humans and thus Evolution is Wrong. How can you argue that Evolution is wrong, because of Adam and Eve, when right in the Bible it discusses the other groups of humans?
> I don't like to be harsh about a paper, but the fanfare around this one makes it necessary to respond.
> There are many ways to go wrong when inferring past events from genomic data; the datasets are large and noisy, and computational methods get complicated.
> Thus it's essential to demonstrate clearly that your results are not an artefact of data processing or methodology, or the consequence of overfitting to a particular aspect of the data. Simulations are a vital tool for this, and they need to show that your results are robust..
> to alternative scenarios that violate the assumptions of your model. They also need to show that the observed data are indeed consistent with the model you have inferred. Sadly, it's not clear that these requirements have been met in the paper published in Science.
It could mean more than that, or maybe not. Velikovsky had the interesting hypothesis that you could compare this histories of different traditions to see if they synchronize.
For example, joshua stopping the sun for three days, which would have been in the evening (you’d stop the sun at sunset, not at noon)… so you can look a Chinese history where it was dark for three days, or aztec history where the sun was about to rise.
He does play fast and loose with his source material (based on the ones I’m familiar with) but I think the general idea is interesting…
Written words are deemed more valid than Spoken words.
So tweets are true, but what someone just spoke to me is not-true.
Better to take stance that all communication is fallible and has noise.
Plato 'wrote' about 'Atlantis'. Written means true?
A lot of Roman Historians, like Livy, etc... Embellished or were Propaganda, or even pumped up travel guides.
Where some Oral Traditions put a great deal of emphasis on memorization and can be just as good at passing information, even if the information is also wrong.
They both have fallibilities.
The Telephone effect exists in Oral.
But in Written, it is wildly miss-interpreted.
But, if across continents, cultures, methods of communication, there are flood myths everywhere. It is ok to wonder if they are based on some common occurrence. Can we put money on an exact date and cause based on some myth? Maybe not, but we can't ignore them either.
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.
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.
> Even if most Western men don’t take multiple wives, men tend to father children with more females than females do with males, a practice called “effective polygamy”.
Maybe I'm oversensitive to men's issues, but I feel western society is very biased against men, to the point that this bias overrides basic logic.
No, "men" cannot father children with more females than females do with males, but SOME (highly successful) men father children with more women whereas MORE men are left childless than women.
But God forbid we don't portray ALL men as pigs trying to father children with as many women as possible whereas women are helpless victims to this process.
While it sounds extraordinary it's a commonly held view. Not in the sense that men (overall) are structurally oppressed but there are various places where males are disadvantaged. (Note : I am not supporting this notion, just reporting what is a popular view).
Why all the disclaimers?
Unless, you know, all the knee-jerk reactions about talking about any mens issue have very serious, negative consequences in the modern world.
Experience that it's useful to be clear what you're advocating vs explaining. Not particularly serious consequences but it's irritating when you come back to a post where you say "Holocaust deniers believe X" and find multiple people have read that as "I love Hitler". (Only a slight exaggeration). That's less of an issue here than elsewhere but one develops habits.
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.
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
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 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.
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
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
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]"
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.
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.
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.
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.
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.
That’s an interesting point about the dependence of likelihood on the outcome.
However, a counter-argument is that if you win a lottery 250 times, it would be reasonable to conclude that the lottery is biased in your favor. If you lost a bet on a coin toss picking tails 250 times in a row, you’d assume the coin is biased.
In that case, every toss with the same outcome informs you of the bias.
So does an outcome really say nothing of the chance for that outcome?
In a similar way, our survival might say that a chance for extinction was sufficiently low each year/month/day/period. The longer we survive, the more confidently we can say that the possibility of survival was high and extinction — low.
If you knew the number of attempts, the outcome would say something of the probability.
So to your last paragraph, yes, we can say something about the odds of survival any given period, because we see many periods.
But we see only one instance of our survival, and we inherently need to be here to see it, so our survival in general for the whole period tells us nothing of how likely (few events reducing our chances) or unlikely (many such events) our survival was in the past, because no matter how unlikely we wouldn't be here to discuss the probability if we didn't survive, and unlikely things do happen.
Yes, if you look at survival as one instance, it does become difficult to say anything about the likelihood based on the outcome.
But I think it's too easy to dismiss this as survivorship bias. There are also other selection biases, which might explain the higher chances of survival of a species if an alive species is selected.
There's also the multiverse theory, or more locally, something we could call "multi-environment". It does make sense that if we were here at all, we would most likely be in an environment where we were most likely to survive. Imagine 20 planets, or 20 timelines, where some make our survival nearly impossible, some - very difficult, and some - relatively easy and likely. We'd probably find ourselves alive on a planet or in a timeline where it was relatively easy and likely.
I just read a bit more on this and it looks like the debate for whether human survival implies the low risk of extinction in the past is ongoing with good arguments on each sides. So I think I'll leave it up to more academic people than me to debate this, but thanks for your thoughts.
Whether or not there are other instances of long term survival, without having access to them, they can't form a basis for our probability calculations, so the point remains that our single survival is insufficient to use as a basis for the probability of events in our past.
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/