Ancient DNA reveals pervasive directional selection across West Eurasia [pdf]

Posted by Metacelsus 1 day ago

Comments

Comment by vintermann 1 day ago

The dataset excites me more than the fairly vague conclusion that some SNPs possibly linked to traits were selected for (or hitched along to genes which were selected for). Genetic archaeology is just so much more exciting than this.

But I bet there will be a ton more of that too, thanks to the high quality dataset.

Comment by timmg 1 day ago

> the fairly vague conclusion that some SNPs possibly linked to traits were selected for

Interesting. I find that part of the paper the most exciting. We always knew selection would happen for valuable traits. But seeing demonstrations of it in the timelines we have is pretty important.

Comment by asdff 1 day ago

Makes you wonder what is being selected for currently.

Comment by rossdavidh 1 day ago

One of the authors of this paper, David Reich, has written a book called "Who We Are and How We Got Here", which is worth reading. My thoughts on it: https://www.goodreads.com/review/show/2605841954

Comment by e40 12 hours ago

Create an account to read? No thanks.

Comment by falaki 1 day ago

Absolutely worth reading.

Comment by Metacelsus 1 day ago

See also the press release: https://hms.harvard.edu/news/massive-ancient-dna-study-revea...

This study covers about 10,000 years of recent human evolution in Europe and West Asia.

From the abstract:

>in the past ten millennia, we find that many hundreds of alleles have been affected by strong directional selection. We also document one-standard-deviation changes on the scale of modern variation in combinations of alleles that today predict complex traits. This includes decreases in predicted body fat and schizophrenia, and increases in measures of cognitive performance. These effects were measured in industrialized societies, and it remains unclear how these relate to phenotypes that were adaptive in the past. We estimate selection coefficients at 9.7 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.

Comment by bcjdjsndon 1 day ago

How did they decide what made a trait adaptive?

Comment by MarkusQ 1 day ago

The didn't decide, they observed; consistent directional pressure over thousands of years is strong evidence that an allele is being selected for.

Comment by bcjdjsndon 1 day ago

So if it survives it's fit, if it's fit it survives? The old tautology

Comment by pegasus 1 day ago

Evolution is survival of the fittest. That's not a tautology, it actually says something, namely that the traits which survive and thus propagate tend to be the ones that enable some form of adaptation to its living conditions to the individual. The paper lists a bunch of examples:

  - lactose tolerance
  - immunity and disease resistance
  - lighter skin at northern latitudes
  - metabolism and vitamin D processing changes in response to changes in diet after the rise of agriculture

All these traits go beyond just increasing the odds of survival, they improve the life of the individual directly. I.e. they confer fitness. Individuals carrying those traits will, on average, in that ecosystem they are inhabiting, be more healthy than those who don't.

Comment by bcjdjsndon 10 hours ago

> All these traits go beyond just increasing the odds of survival, they improve the life of the individual directly. I.e. they confer fitness.

Wrong. Fitness is not "beyond" increasing the odds of survival, fitness is ONLY that. Fitness is not about quality of life.

- in that ecosystem they are inhabiting, be more healthy than those who don't.

Survival of the fittest says nothing about how healthy they are, only whether they survive and reproduce or not.

So it should really be "If it survives it must have been fit"

Comment by pixl97 9 hours ago

Survival of the fit enough

Comment by Symmetry 1 day ago

Not a tautology but a definition.

https://en.wikipedia.org/wiki/Fitness_(biology)

Comment by bcjdjsndon 1 day ago

But other than it surviving, there's no way to define fitness.

Comment by Symmetry 1 day ago

It's more reproducing than surviving. If the population of some species increases and the number of copies of some allele remains constant we could consider than gene less fit than the other alleles, in the population genetics sense. So it's frequency rather than survival that geneticists look at. But that proves that there are indeed other ways that they could have defined fitness if they wanted to.

Comment by bcjdjsndon 10 hours ago

> It's more reproducing than surviving

Well that's a given mate, nobody's talking about populations that dont reproduce are they? And even then you're still making the same tautological mistake.... If they survived they must have been fit

Comment by Tagbert 2 hours ago

That tautological is not a mistake. Surviving to reproduce is the definition of fitness from an evolutionary standpoint.

Comment by jryb 2 hours ago

You’re conflating the colloquial meaning of “fitness” with the technical definition. It’s unfortunately overloaded.

Comment by johngossman 1 day ago

That is correct. Biology uses the term fit slightly different than the general public

Comment by fluidcruft 1 day ago

The flip side is everything is being degraded by random mutation.

It's like holding a large ball in place on a hill that sees frequent tremors. If the ball is still halfway up the hill it's being held in place, if it's being held in place it's still halfway up the hill. It might be considered a tautology if you're only working with symbols and ignore all the mechanistics.

Comment by astrobe_ 1 day ago

> The flip side is everything is being degraded by random mutation

"degraded"? Aren't random mutations precisely one of the core mechanism of adaptation?

Comment by MarkusQ 1 day ago

But most of them are still deleterious.

Remember, all improvements are changes, but most changes aren't improvements. The trick that makes evolution works is this: out of lots of random changes, most of which are harmful, the harmful ones tend to be weeded out and the useful ones tend to spread.

Comment by nine_k 1 day ago

Whatever does not survive stops registering in later times; most of the time, what helps survival is retained, and what helps survival is what increases fitness.

Comment by taeric 1 day ago

As stated, this feels wrong. Specifically, it does not account for traits being appropriate for environment. I like to say it as what was needed for one stage could be the problem for the next stage.

That is, traits that stop registering may no longer be something that helps survival. But that does not mean they were not necessary for survival at an earlier point.

Comment by SubmarineClub 1 day ago

How exactly does that contradict the concept of fitness?

Several examples from the paper are exactly that. E.g dark skin was better for survival in Africa, but as populations moved north light skin was strongly selected for. Given the levels of sunlight in Europe, lighter skin increased fitness.

Comment by taeric 1 day ago

It is against the idea that the beneficial traits will survive to the present. It could be that there was some trait/gene that was absolutely needed for survival in the past, that flat out became irrelevant and dropped off before the present.

That is, it is not an argument against any of the traits that are present. Is why I said the problem is with how it was stated. But you do not have everything with you to provide evidence for all of the things necessary for you to have gotten here. At best, you have evidence that nothing you have with you prevented you from getting here.

That make sense? I grant that pulling it back up, I see the comment I was responding to was hedged. My concern is largely against the idea that things that "were selected for" in the past can be determined by evidence. I'm not convinced it can't be. But I find this presentation of it to be somewhat weak.

Comment by MarkusQ 1 day ago

More to the point, TFA is specifically addressing the issue (which is part of what makes it a big deal).

They aren't saying "we see these things now, so they must be good" but rather things like "we see these selected for from 9kya to 3kya, but from then to the present they were selected against"; they are specifically looking at how apparent selective pressures changed over time.

> the idea that things that "were selected for" in the past can be determined by evidence

When the evidence is a copious selection of ancient genomes, distributed over both space and time, they certainly can be.

Comment by taeric 1 day ago

Apologies, I only meant my gripe with the comment I was responding to. Is why I put "as stated." I meant that to be that I was not arguing what I think they were messaging towards.

The callout on "evidence" I have there is that I meant that to only be present evidence. And again, I am not convinced it can't be done. It takes a lot of work. Which, the article is doing. But just saying that traits that helped you survive are typically retained, so by definition increase fitness, does not.

Comment by bonsai_spool 1 day ago

Here's the paper - we ideally shouldn't be linking to PDFs of these things but it's paywalled https://www.nature.com/articles/s41586-026-10358-1

Comment by shadowtree 1 day ago

Blank Slate hypothesis is now officially refuted, correct?

Different evolutionary paths between races/regions, with impact on mental health and cognitive performance.

Comment by svnt 1 day ago

No one in adjacent fields has been seriously engaging tabula rasa speculation from the 17th century for quite some time prior to this paper.

What you think the implications are of that for your present day lived experience, that might be a different conversation.

Comment by lukev 1 day ago

To be clear: most people who are keen on making such an argument, or who are identifying racial genetic differences as the primary takeaway of studies like this, are doing so to justify racism, either implicitly or explicitly.

But that's a strawman. Racism is wrong, even if there are minor genetic variances across populations (which... seems obvious?) Variance within a population strongly dominates the weak cross-population effects, and personal history (nutrition, education, etc) strongly dominates that.

And that's setting aside the moral implications of judging someone or changing your behavior towards them even if you have somehow measured them to be "less intelligent," as if that was a single axis of worth.

Because, apparently, this needs to be said.

Comment by timmg 1 day ago

> most people who are keen on making such an argument, or who are identifying racial genetic differences as the primary takeaway of studies like this, are doing so to justify racism, either implicitly or explicitly.

That may certainly be true.

(Not OP, but) I always shutter when we want to deny scientific results because it might be "helpful" for someone making a racist argument.

My personal belief is that truth is the goal of science. Even in cases where the truth is uncomfortable.

Comment by kstenerud 1 day ago

It's very nice to believe in a pure system that exists outside of politics, but that's simply not how the world works, and it never will be.

There is no scientific breakthrough that has occurred sans politics. Politics choose the winners and the losers, and the realm is science is no exception.

All science is political, because the scientific institutions are made up of people, who are political. Your research project lives and dies by politics, as does your dissertation, who gets published, who receives awards, etc.

So when it comes to research of limited utility that has a nasty cadre waiting in the wings to pounce upon it, the wise person would think twice.

Comment by timmg 1 day ago

As I said to another person on this thread: if scientists let their political views override their pursuit of truth, the public will (rightly) lose faith in science.

So when you tell them to "trust the science" -- be it vaccinations, climate change or something else -- they have no reason to trust that science.

Comment by kstenerud 16 hours ago

People don't have faith in inanimate things like science. They have faith in their leaders, who then lead the way in what to believe.

If those leaders believe in the integrity of the scientific institutions, their flock will follow. If they're anti-vax, their flock will follow. If they believe in some medical quackery, their flock will follow. If they believe in eugenics, their flock will follow. It's happened before.

What was fringe yesterday can become mainstream today, with the right leaders.

Comment by Nicook 1 day ago

I enjoy that you are framing this as somethings that "may" happen in the future.

Comment by suzzer99 1 day ago

There are a few scientific topics that are too easily manipulated by bad actors who ignore all the nuance. You have to tread very, very carefully on those and ask yourself what good vs. what harm can come from it. We know from history that giving opportunist leaders a chance to classify humans into distinct sub-groups based on intelligence and other key traits ends in catastrophe.

Comment by timmg 1 day ago

I understand what you are saying and I don't disagree with the idea that bad actors will use science in bad ways.

But I think going down this path of denying (or hiding) science that can be used for bad ideas ends up causing (rightly, imho) a distrust of science -- which is far worse.

A distrust of science (not saying it was caused by this particular issue) is how we ended up with so much anti-vax sentiment in the US. And that is the reason we are seeing outbreaks of diseases that used to be minimal.

I think if you want people to "trust the science", you have to trust the people.

Comment by convolvatron 1 day ago

it seems like you are simultaneously arguing for a science that holds itself outside public opinion, and one that is beholden to it.

no, wait, I get it.

all scientists should expect mistrust because of perceptions of bias of any of them, regardless of how well founded. that seems at the very least unproductive.

Comment by timmg 1 day ago

> it seems like you are simultaneously arguing for a science that holds itself outside public opinion, and one that is beholden to it.

Apologies if I did a bad job explaining my opinion. But I was attempting to argue the exact opposite of that.

My view is that science should be the search for truth. And that if the truth is inconvenient for some political (or other) reason, so bet it. The truth is the goal. Full stop.

My feeling is that if scientists stop pursuing truth in cases where it doesn't fit their politics, they will (rightly, IMHO) lose the trust of the public. (Of course, in particular, those in the public who have different politics.)

Comment by convolvatron 1 day ago

so, because science as whole is not pursuing the idea that people with different genetics as a population are inferior in some ways to others with sufficient vigor, that we should expect a justifiable general distrust of science including completely unrelated results like global warming. I don't see how this is prescriptive in any way, except maybe to ... I guess find scientists that are will to accepting funding for ideas that are popular with some people? do you think that would help if they found those ideas to be meritless? or even if they didn't?

Comment by JuniperMesos 20 hours ago

Unironically yes. Because it means that scientists are willing to lie or suppress results that offend their moral and poltical sensitbilities, and this should affect your credence in literally any scientific result reported by the institutional scientific research system.

Comment by suzzer99 19 hours ago

It doesn't necessarily mean they lie or suppress results, it can just mean they don't pursue areas of study where the outcome is either a) nothing happens or b) bad actors use your results to "other" a whole group of people. What good can come from yet another study on race and IQ? Be specific.

Just saying, "We should do science for science's sake" is not enough. We've done that. Go read The Bell Curve and knock yourself out. What people like you seem to want is continued, motivated hammering of the issue.

Comment by convolvatron 6 hours ago

you're asking science to give you some excuse for treating some people worse than others. maybe that's just not a very well formed question for a scientist to answer. if we just strip away the race nonsense and ask a more .. meaningful question like 'what is the genetic basis for intelligence', then no one is shirking that question because of what the answer might be. its just a really hard and also pretty fuzzy question.

but you still won't be satisfied with the answer, because even if one set of genes gets you 5% more 'intelligence' score, that still doesn't justify a apartheid state. do you think we should have different rules for people with different IQ scores?

you're saying that because science as a whole isnt particularly interested in assuming _your_ biases, that the whole enterprise is meaningless and corrupt, and thus we can't trust anything those white coats say.

Comment by JuniperMesos 23 hours ago

The actual reason this matters is because of the implications it has for race-based affirmative action programs in cognitively-demanding fields; i.e. "why are there visibly no black people and lots of Asians in this advanced math class, and what should we do to fix the problem?"

There is no political agreement on whether having or not having affirmative action programs is racist (or against which racial groups).

Comment by card_zero 1 day ago

This interest in IQ has a negative effect on the concept of intelligence, never mind human unity. It attaches exaggerated importance to test scores, jobs, and school. It tends toward snobbery.

Comment by gnerd00 5 hours ago

reading about Howard Gardner’s Theory of Multiple Intelligences stuck with me.. seven is a common list

Comment by lopsotronic 1 day ago

I think the discussion in recent years has refocused, embracing ethnonatalist implications and challenging the core assertion that "racism is wrong".

My main resistance to that is much the same as yours: the differences are so small, that re-architecting society around them is not going to be enough juice for the squeeze.

But one could also argue that the juice is not even the point: by re-architecting society in this way, you "pre-brutalize" your population so that their threshold for violence against "others" is lowered. Thus your population is closer to being wholly militarized, and theoretically is more effective in war, and is less captured by "weak" or "unmanly" moral ideals, such as empathy.

While this might seem a virtue to someone of an expansionist mindset, in application this principle never, ever works well - again, thanks to those tiny differences. If a citizen is pre-brutalized to have a lowered resistance to killing those with curly hair, how long is it before they kill their next door neighbor with wavy hair, over something like lawn furniture?

Pre-brutalizing your populace to killing any sapiens is enough to brutalize them towards harming anyone else. This is the core of the "imperial boomerang", or the colonial boomerang theory, as to why the great wars of the 20th century took on such a nasty character. The ease with which we dehumanized subject populations was - all too easily - redirected against the neighbors, most memorably with Germany trying to re-create the American West to their East.

Comment by georgeburdell 1 day ago

And yet you are also likely to argue “weather is not climate”. Differences in population characteristics of all kinds have massive societal implications and we should lean into addressing them.

Comment by lukev 1 day ago

Well if you are talking about environmental stuff (like leaded gasoline), sure.

If you’re talking about trying to improve the genetics of populations at scale… yikes.

Comment by convolvatron 1 day ago

people trying to force everyone else to accept their poorly defended notions of race superiority have a much larger social impact than any quantifiable differences in the genetics of populations.

Comment by Tor3 1 day ago

Just where did you get that from? Certainly not from the paper.

Comment by kloop 1 day ago

I think they're talking about this bit:

> We finally observed signals of selection for combinations of alleles that today are associated with three correlated behavioural traits: scores on intelligence tests (increasing γ = 0.74 ± 0.12), household income (increasing γ = 1.12 ± 0.12) and years of schooling (increasing γ = 0.63 ± 0.13). These signals are all highly polygenic, and we have to drop 449–1,056 loci for the signals to become non-significant (Extended Data Fig. 10). The signals are largely driven by selection before approximately 2,000 years )*, after which γ tends towards zero

Presumably pressure in different regions lead to different combinations of those alleles, which I think they are shorthanding a bit, but the fact that those alleles exist makes blank slate theory a kind of rough assumption

Comment by asdff 1 day ago

It is important to consider that these alleles are merely correlated to behavior and are not proved to be causal of any behavior. For example, maybe you sample bankers in NYC. You can probably assume you'd get a lot of perhaps semitic genetic background in this dataset. Now, would you conclude that Jewish people have some inherent gene that makes them want to be bankers like a moth to a lamp? Maybe you would. But more likely situation is that people tend to follow the profession of people in their lives who work that profession and can inform them about it, and for centuries there were real legal restrictions in a lot of places preventing anyone but jews from being allowed to charge interest. So, pretty good odds today as a jew you know someone who works in finance and can help at least to some degree point you towards that field.

So really when you say select for household income among western populations, it might be hard to actually find any real signal that is actually causal that isn't due to simple demographic and historical reasons, due to the lack of power you have in sampling rare demographics within a given category such as high income.

Comment by svnt 1 day ago

I haven’t had time to really dig in to the paper but these data (from only one region) are limited in their ability to compare regions, right?

If anything they seem to support homogenization of intellectual capacity/mental health in Eurasia since 2kya.

The methodology, if it holds up, seems to hold a lot of promise for answering questions like this in the future.

Comment by kloop 1 day ago

No, this paper doesn't seem to talk about regional differences. The implication seems to be that it wouldn't be surprising to find differences between groups that separated more than 2kya, as there was active changes going on before that time. Not that it predicts any specific differences

> If anything they seem to support homogenization of intellectual capacity/mental health in Eurasia since 2kya.

I would be interested in how you came to that conclusion, unless I'm misleading your post and you specifically mean West Eurasia

Comment by svnt 1 day ago

I meant West Eurasia, I agree it doesn’t seem to support any broader conclusion.

Comment by ano-ther 1 day ago

Yes, they only had data for West Eurasia.

> Just because an allele, SNP, or trait swept into or out of West Eurasia during this time doesn’t mean this happened only in West Eurasia. Researchers can use the new computational methods to look for directional selection in other populations worldwide that have enough ancient DNA sequences and construct a clearer picture of what’s unique to different groups and what generalizes across populations.

> Reich expects that future studies will show that shared selective pressures acted on some of the same core traits across diverse human groups, even as those groups split off and migrated to different parts of the world over tens of thousands of years.

https://hms.harvard.edu/news/massive-ancient-dna-study-revea...

Comment by Nesco 1 day ago

There is a graph arguing “intelligence” has been positively selected in west Eurasian population in this paper according to a polygenic score (page 8 fig. 4)

Now I would be quite curious to know how they constructed this polygenic score

Comment by AlgorithmicTime 1 day ago

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Comment by tokai 1 day ago

Racists are hilarious. They will twist and bend anything remotely applicable to fit and underpin their prejudices.

Comment by trallnag 1 day ago

Big and true

Comment by damnitbuilds 1 day ago

I always knew I was smarter than my parents.