Landmark ancient-genome study shows surprise acceleration of human evolution

Posted by unsuspecting 12 hours ago

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Related: Ancient DNA reveals pervasive directional selection across West Eurasia [pdf] - https://news.ycombinator.com/item?id=47791282 (64 comments)

https://x.com/doctorveera/status/2044679999450664967 (https://xcancel.com/doctorveera/status/2044679999450664967)

Comments

Comment by Mikhail_K 9 minutes ago

From the article:

We finally observed signals of selection for combinations of alleles that today are associated with three correlated behavioural traits: scores on intelligence tests (increasing 0.74±0.12), household income (increasing 1.12±0.12) and years of schooling (increasing 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 tends towards zero.

That's the part that the speech police is afraid of.

Comment by like_any_other 10 hours ago

Is there any species, other than humans, that is found all across the globe (i.e. geographically separated), and has not differentiated into subspecies? Wolves, elephants, tigers, bears, and foxes have all been categorized into multiple subspecies each, distinct but able to interbreed.

Comment by abc123abc123 8 minutes ago

So have humans. There are white, red, black, brown, yellow people, and they live in their own happy places on the planet, except for the fact that we now move them around by plane, boat and goat.

Comment by samsartor 5 hours ago

My understanding is that humans have very limited genetic diversity compared to most other animals, because of the population bottlenecks we've been through. And further, that diversity is mostly between individuals, not between groups. The distinction is easy to see in cats vs dogs: they both have similar overall genetic diversity but two Chihuahuas have virtually all the same genes (the small angry ones) while two tabby cats are more distinct. The two cats have different combinations of big/small nice/mean smart/dumb, but the genes average out to the same "typical" kind of cat in both cases.

Because humans get around so much, and because we think interesting-looking people are hot, the diversity is spread pretty broadly across the whole population. The average european person and the average east asian person are a little bit different genetically, but way less different than any two real europeans or two east-asians are to one another.

In short, the distributions of individuals overlap so much that the trendlines are pretty close to useless. And historically speaking, the people who tried to make a hard distinction out of those trendlines had awful motives.

Comment by greazy 9 hours ago

The definition of what constitutes a species is a human construct.

Two bird populations living in the same locale but divided by a mountain range therefore not naturally breeding with each other would classify as a different species, even if they could breed with each other.

So your question is hard to answer.

Comment by nelox 9 hours ago

I’ve often dreamt of breeding with that mythical bird far, far away.

Comment by greazy 8 hours ago

If you do cross the barrier, you could successfully mate with that mythical bird!

Comment by 8 hours ago

Comment by John7878781 6 hours ago

> Two bird populations living in the same locale but divided by a mountain range therefore not naturally breeding with each other would classify as a different species, even if they could breed with each other.

Really? I thought the requirements for species classification were: (1) must be able to reproduce and (2) offspring must be fertile.

Is it less objective than that?

Comment by rcxdude 1 hour ago

There are a lot of subtleties. Ring species are a particularly fun one: you can have a population that live around some natural obstacle (like a large body of water) where individuals can breed successfully with individuals near to them but not with ones further way (like directly across the barrier), in a continuum of variation.

Comment by Archelaos 5 hours ago

Polar bears can have furtile offspring with grizzly/brown bears. See: https://en.wikipedia.org/wiki/Grizzly%E2%80%93polar_bear_hyb...

Comment by whycombinetor 5 hours ago

Interfertility is not an equivalence relation, does not form equivalence classes https://en.wikipedia.org/wiki/Ring_species

Comment by showerst 9 hours ago

How about Taraxacum officinale, the common dandelion?

It’s not quite all across the globe but pretty close, and is so adapted that it is not considered invasive any more in most places.

Comment by chrisweekly 8 hours ago

Or, it's equally invasive everywhere.

Comment by cwmoore 30 minutes ago

Lol everywhere there are manicured lawns?

Comment by redsocksfan45 1 hour ago

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Comment by IncreasePosts 8 hours ago

Do humans not fit the standards for being broken into multiple subspecies? I assumed that they would but "the science community" is too scared of the implications when idiots learn about it.

I look at a sumatran tiger and a Siberian tiger and I see a lot less variance than I see when I look at a pygmy, a Norwegian, an sentinel islander, and a han Chinese person

Comment by krapp 8 hours ago

>Do humans not fit the standards for being broken into multiple subspecies?

No. Multiple human subspecies did once exist (examples being Neanderthals, Denisovans, Homo Erectus, and Homo Floresiensis) but only our species, Homo Sapiens, remains (with traces of Neanderthal DNA so there was some interbreeding.) However race is a cultural and social construct. Different human races are not different human subspecies. A Pygmy, a Norwegian, a Sentinel Islander, and a Han Chinese person are all the same species. The superficial variations in average height, skin color, etc. do not vary enough to constitute species differentiation - humans share 99.9% of their DNA, and the vast majority of genetic variation exists within populations (in other words, within "races") and not between them.

Comment by red75prime 5 hours ago

> the vast majority of genetic variation exists within populations

This particular argument (I am not talking about anything else) always looked to me as "inkblot defense" (Cephalopods muddy water to defend themselves).

Genome is discrete. A single nucleotide polymorphism can have far-reaching consequences. So it's a bit like arguing that this collection of pentagons is not statistically different from this collection of hexagons because radius variation within collections is greater than between collections.

One day I've got into trouble by pointing to another genetic adaptation (EPAS1 SNPs) rather than the poster child of genetic differences: an SNP in the 6th codon of the β-globin gene. But that's another story.

Comment by vjjsejj 1 hour ago

Well humans and chimpanzees share almost 99% of their DNA despite being quite distant relative so that number is somewhat deceptive. Not disagreeing with the overall point of course

Comment by 5 hours ago

Comment by MrBuddyCasino 5 hours ago

But the DNA of the sumatran tiger and a Siberian tiger is also over 99% identical?

Comment by beloch 5 hours ago

The DNA of humans and chimps is 98.8% identical.

The percent difference between genomes of species is one of those tricky measures that doesn't really give good intuition. I find it much more useful to think in terms of the time since two species shared a common ancestor.

e.g. For humans and chimps, that's several million years. For Sumatran and Siberian tigers, it's around a hundred thousand years.

Comment by vjjsejj 1 hour ago

> it's around a hundred thousand years.

So not that far away since modern humans began splitting up into separate subgroups outside of Africa? Of course there have been quite a bit of intermixing since then (more so in Eurasia than the more isolated parts of the world before the modern times, though)

Comment by IncreasePosts 4 hours ago

What's the most recent common ancestor between an North Sentinel islander and a Norwegian? Mitochondrial Eve is 150kya

Comment by vjjsejj 1 hour ago

Probably less than 40k? Since it took a while for modern humans to leave Africa.

Comment by MrBuddyCasino 8 minutes ago

I don’t think the out-of-africa hypothesis is defensible in light of recent archeological findings, and, incidentally, DNA complexity analysis.

Comment by api 9 hours ago

Not many. Part of why we are like this is extreme mobility. Even before modern times we were always good at getting around and seem to have a desire to roam. Or at least enough of us do to mix up those gene pools.

Comment by like_any_other 9 hours ago

If that were true before modern times, distinctions in appearance never could have developed.

Edit as reply because "pOsTiNg tOo FaSt":

> Before modern times there was enough mixing to keep speciation from occurring but not enough to fully homogenize.

I see. Is there some quantitative genetic similarity measure, by which it was determined that it was worth categorizing foxes and wolves and bears into distinct subspecies/breeds/whatever taxonomical categories, but not humans? I assume that's what your "speciation did not occur [enough to merit taxonomical distinction]" is based on.

I.e. by what measure are a Pygmy and a Norwegian more similar than a Sumatran and a Siberian tiger [1]?

[1] https://news.ycombinator.com/item?id=47812581

Comment by api 8 hours ago

It’s not binary. Before modern times there was enough mixing to keep speciation from occurring but not enough to fully homogenize.

If our modern world continues for thousands of years eventually our differences will start to dissolve.

Comment by yabutlivnWoods 9 hours ago

> ...distinct but able to interbreed

I mean people won't like the idea but that's not my point; what you describe variety in superficial traits while maintaining common traits

Applied to humans; skin color, eyes, dwarfism, hypertrichosis... can still interbreed

When it comes to categorization and taxonomy in leaky abstractions like languages the boundaries get a bit hand wavy and usually land on whatever fits the prevailing social desirability bias of the day

Comment by like_any_other 9 hours ago

> you describe variety in superficial traits

The same selection pressures that produced the variety of "superficial" traits also act on "non-superficial" traits - nature does not recognize this distinction.

Comment by yabutlivnWoods 8 hours ago

You cherry picked one idea from my post. I was not addressing nature but human social tropes.

What is a subspecies and species is random gibberish of the living humans

Comment by meroes 10 hours ago

Dogs?

Comment by paulryanrogers 10 hours ago

Aren't dogs technically one species?

Comment by hooo 9 hours ago

This distinction seems more arbitrary over time. Growing up I was taught different species couldn’t interbreed. But what about Neanderthal and Sapiens?

Comment by chrisweekly 8 hours ago

Funny tangent: this comic has strong feelings about such distinctions, using "dog" as the canonical example:

https://youtu.be/dNLLXZgN4Mc?si=SUhHZ2uzMZ7jgejI

Comment by like_any_other 10 hours ago

I don't think you could have chosen a worse example. Dogs are themselves a subspecies, and are split into many different breeds, of wildly different character and physiology: https://en.wikipedia.org/wiki/Dog#Taxonomy

Comment by idiotsecant 9 hours ago

Breeds and species are different things. Parent post is making a (very good) point that dogs can pretty much all breed with one another.

Comment by SloppyDrive 8 hours ago

We dont categorize humans that way; not because humans are different but because of cultural norms.

The generous idea is that "subspecies" does not provide an anthropologist a useful lens to look at humanity, therefore we do not classify.

The alternative is that "subspecies" is too close to "race" for scientists, publishers, and funding bodies to touch, so its deliberately ignored.

Comment by verisimi 5 hours ago

I agree - cultural educating trumps scientific definitions.

Comment by vjjsejj 1 hour ago

It’s not like those scientific definitions are particularly consistent or stable, though. In a large part it’s still a matter of convention when it comes to non human species as well

Comment by renewiltord 9 hours ago

They have to be. The snail darter is genetically identical to another animal and is a separate species. Most likely different humans are as well.

Comment by erichocean 9 hours ago

Humans have, obviously. Just interbreeding with ancient species was enough to do it, even without separate evolution.

Comment by NelsonMinar 8 hours ago

Every time I read about ancient DNA work, it's about Reich's research. Can anyone expert in the field shed light on that? He certainly seems to have a successful research group. And he's a good communicator, I got a lot out of his 2018 book. Who else should I be reading or reading about?

Comment by rolph 8 hours ago

chromosomal fusion as the explanation for the "loss" of a chromosome pair, in humans.

https://www.johnhawks.net/p/when-did-human-chromosome-2-fuse

also , independent confirmation of observations, are gold for research, however needless repetition of effort is not.

thus when someone is prolific,or uncannily mad about a topic it tends to be dominated by that persons submissions, and often any other contributors are on that lead researchers team.

Comment by A_D_E_P_T 11 hours ago

Not that surprising when you consider, as the paper does, the explosion of very meaningful traits such as the ability to digest lactose and various anti-malaria adaptations e.g. Sickle Cell and the Duffy-null mutation.

It's just controversial for obvious reasons. The notion that human groups may have meaningfully evolved in different ways over the past 10,000 years, and may still be evolving, is an unpopular one on both ends of the political spectrum.

Comment by AlotOfReading 10 hours ago

The reason no one wants to talk is that these discussions are always co-opted by racists wanting to affirm their beliefs, regardless of the underlying science. Reich in particular is borderline deliberate about attracting those sorts with his lab's research, because of how badly he chooses to handle the topic and terminology of race.

Comment by MontyCarloHall 9 hours ago

>Reich in particular is borderline deliberate about attracting those sorts with his lab's research, because of how badly he chooses to handle the topic and terminology of race.

Sorry, do you have any examples? His views that I've read [0, 1] are scientifically rigorous and terminologically precise, deftly navigating the politics that some consider extremely controversial. To wit, one of my favorite passages from [1], which deals specifically with terminology:

   But “ancestry” is not a euphemism, nor is it synonymous with “race.” Instead, the term is born of an urgent need to come up with a precise language to discuss genetic differences among people at a time when scientific developments have finally provided the tools to detect them. It is now undeniable that there are nontrivial average genetic differences across populations in multiple traits, and the race vocabulary is too ill-defined and too loaded with historical baggage to be helpful. If we continue to use it we will not be able to escape the current debate, which is mired in an argument between two indefensible positions. On the one side there are beliefs about the nature of the differences that are grounded in bigotry and have little basis in reality. On the other side there is the idea that any biological differences among populations are so modest that as a matter of social policy they can be ignored and papered over. It is time to move on from this paralyzing false dichotomy and to figure out what the genome is actually telling us.
This particular passage is on p. 253 of [1], but everything in Chapter 11 ("The Genomics of Race and Identity," pp. 247-273) is well worth the read.

[0] https://www.nytimes.com/2018/03/23/opinion/sunday/genetics-r...

[1] https://sackett.net/reich_who_we_are_and_how_we_got_here.pdf

Comment by AlotOfReading 9 hours ago

It's unfortunate that the URL happens to be buzzfeed, but there was an open letter to Reich by other academics about his terminology in the book you're quoting [0]. The short of it is that social categorizations we believe in like race intersect with genetics in a very complicated way. Reich is a world-class expert in genetics. He simply commits the same error as many other other experts in discounting the complexity of subjects he's adjacent to, but not directly an expert in.

I get that this is a high standard to hold him to (and I sure as heck don't meet it myself), but he should do better given his visibility in public discourse.

[0] https://www.buzzfeednews.com/article/bfopinion/race-genetics...

Comment by MontyCarloHall 8 hours ago

The crux of that letter is the "need to recognize that meaningful patterns of genetic and biological variation exist in our species that are not racial." This is true. However, this does not mean that there aren't also meaningful patterns of genetic and biological variation that do stratify according to ancestry (not race!). The letter tries to handwave this away, claiming that "[f]or several decades billions of dollars have been spent trying to find such differences. The result has been a preponderance of negative findings despite intrepid efforts to collect DNA data on millions of individuals in the hope of finding even the tiniest signals of difference." This is simply not true, as studies like the subject of this discussion demonstrate.

The letter also states that "[t]he public should not cede the power to define race to scientists who themselves are not trained to understand the social contexts that shape the formation of this fraught category." Also true! This is exactly why Reich explicitly avoids discussing "races" but rather populations and ancestries, which are rigorously defined strictly in terms of genetics. With respect to population structures and ancestry, Reich is indeed an expert.

I'll add that very few of the signatories of that letter have any experience, let alone expertise in genetics. Here are the first few:

  Jonathan Kahn, James E. Kelley Professor of Law, Mitchell Hamline School of Law

  Alondra Nelson, Professor of Sociology and Gender Studies, Columbia University; President, Social Science Research Council

  Joseph L. Graves Jr., Associate Dean for Research & Professor of Biological Sciences, Fellow of the American Association for the Advancement of Science, Section G: Biological Sciences, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University, UNC Greensboro

  Sarah Abel, Postdoc, Department of Anthropology, University of Iceland

  Ruha Benjamin, Associate Professor, Department of African American Studies, Princeton University

  Sarah Blacker, Postdoctoral Research Fellow, Max Planck Institute for the History of Science, Berlin

  Catherine Bliss, Associate Professor, Social and Behavioral Sciences, UC San Francisco
Out of the 67 signatories, I counted approximately 5 who might have sufficient genetics expertise to offer a meaningful scientific counterpoint to Reich's work (this is being charitable, as I included titles like "Professor of Biological Sciences," which is no guarantee.) The rest were in fields like anthropology, sociology, law, and history.

Comment by AlotOfReading 8 hours ago

     This is simply not true.
Yes, because it's not an argument the letter is making. Everyone can name a meaningful genetic patterns of genetic variation that follow ancestry like lactase persistence. The argument is in the second paragraph:

    But his skillfulness with ancient and contemporary DNA should not be confused with a mastery of the cultural, political, and biological meanings of human groups.
It's not an argument that Reich gets the science wrong, so other geneticists being on the list is neither here nor there. When he says things like:

    But as a geneticist I also know that it is simply no longer possible to ignore average genetic differences among “races.”
in NYT opinion pieces, it's that he's not understanding how terminology interacts with public discourse. The next paragraph goes on to use the unclear term "west african", not exactly a great example of careful language either.

The list is mainly people in fields that deal with these things, as you'd expect.

Comment by MontyCarloHall 8 hours ago

>Yes, because it's not an argument the letter is making.

It literally is though. The full quote from the Buzzfeed piece is:

  Reich’s claim that we need to prepare for genetic evidence of racial differences in behavior or health ignores the trajectory of modern genetics. For several decades billions of dollars have been spent trying to find such differences. The result has been a preponderance of negative findings despite intrepid efforts to collect DNA data on millions of individuals in the hope of finding even the tiniest signals of difference.
>The argument is in the second paragraph:

  But his skillfulness with ancient and contemporary DNA should not be confused with a mastery of the cultural, political, and biological meanings of human groups.
Reich never purports to make cultural or political arguments, just biological ones.

>When he says things like: But as a geneticist I also know that it is simply no longer possible to ignore average genetic differences among “races.”

Note that he put "races" in quotes. The point he was making here is that sometimes genetic ancestries can intersect quite well with traditional notions of "race" [0]. But often times they do not, especially in the case of admixed populations [1].

[0] https://www.nature.com/articles/s41598-023-32325-w/figures/1

[1] https://link.springer.com/article/10.1186/s12859-019-2680-1/...

Comment by AlotOfReading 7 hours ago

    Note that he put "races" in quotes.
I know, but we both see how a random member of the public could easily read it. My argument, after all, is that the way he communicates is sloppier than it should be for the subject matter and prone to public misunderstandings.

Comment by GorbachevyChase 8 hours ago

Fortunately, there are many wise laymen such as yourself in the internet to correct him.

Comment by dmitrygr 8 hours ago

> race intersect with genetics in a very complicated way

Please explain the complications. Use scientific terms only.

Comment by dmitrygr 6 hours ago

> but he should do better given his visibility in public discourse.

Why? He presented real verified science. Anyone who is offended or does not like it ... well, too bad... the world does not care. Facts are facts. He does not owe you or anyone else comfort. He presents cold hard truth, and sometimes truth hurts. Tough.

Comment by jltsiren 8 hours ago

I haven't read much from Reich, so I don't know his position. But I've understood that the current best practice in human genetics is to explicitly justify the population descriptors chosen for each study, rather than using any fixed set of descriptors given from the outside.

There are two main types of genetic descriptors: those based on genetic similarity and those based on ancestry groups. Genetic similarity is quantitative, and individual samples often have multiple labels attached to them. Ancestry groups are discrete categories based on quantitative measures. If it's appropriate to use descriptors based on genetic ancestry groups in a study, it's usually also appropriate to drop samples that don't fit neatly in any single group.

Sometimes it's more appropriate to use descriptors based on environmental factors, such as ethnicity or geography. Environmental descriptors tend to be correlated with genetic descriptors, but they are not the same.

Comment by nostromo 10 hours ago

Science is about truth not social outcomes.

People keep wondering why trust in scientific findings is in free fall. A big part of it is because many scientists have become comfortable lying when they feel it’s for a noble cause.

Comment by orsorna 9 hours ago

I really don't care if the people around me have physiological differences from me. It would be wonderful to explore that and such differences. But as OP pointed out the discussion gets co-opted by people who would kill others over physiological differences. How is such a viewpoint conducive to a peaceful society where millions of people with physiological differences exist?

For good reason, the wider community isn't able to have a productive conversation about it. I wouldn't even call that a noble reason, but a necessary one, unless you would be okay with inviting people that want you dead into discussion on scientific consensus.

Comment by coderenegade 8 hours ago

The problem is that if you don't stick to truth and make an attempt at objectivity, others will step in to fill the void. This is how you sow division and undermine trust in science.

Comment by orsorna 7 hours ago

I'm having a very hard time understanding a society where research is openly conducted on innate physiological differences between people, and bad actors don't use this official research to practice open discrimination. The lesser of the two evils is to draw a line and tell people to just accept these differences.

Comment by like_any_other 9 hours ago

> people who would kill others over physiological differences

Most of them just want to enforce borders. And then the dogma that we are all the same is co-opted by people who would see their ethnic group wiped out, as they are told that they don't even exist except as a meaningless social construct, and their desire for ethnic self-preservation is therefore illegitimate - there is nothing to preserve!

The same rhetoric targeting Palestinians: https://blogs.timesofisrael.com/perpetuating-the-myth-of-a-p...

Comment by orsorna 8 hours ago

>And then the dogma that we are all the same is co-opted by people who would see their ethnic group wiped out

Are you referring to certain people? People sympathetic to Palestinians? I mean yeah obviously it's wrong to preach equity for me but not for thee, but I'm not really going to get into a pissing match about Israel/Palestine, sorry, because that's deflection from my point.

So there are two choices here:

1) Allow scientific discussion on physiological differences or avoid it. Particulary, physiological differences that don't necessarily effect health outcomes but also performance metrics.

2) Do not allow such discussion, and declare an axiom: normalize physiological differences across homo sapiens.

You're right to call the latter dogma, although not in the pejorative sense.

You brought this infamous conflict up to propose that because option two can be used by bad actors, then we should not normalize option two, and freely discuss physiological differences between people.

If you are of a group that has physiological differences scientifically proven to be inferior, you are immediately in an outgroup. You will experience discrimination. Because few (and I'm being generous, perhaps no one truly) can talk about physiological differences without building and holding prejudice. Pragmatically that is just not the case. It's why endless ethnic conflicts exist.

I simply cannot formulate an argument for why this should ever be allowed. It sounds like a horror show if you're on the receiving end. A horror show minorities of many types live through every day.

To lay "ground rules" so that we do not scrutinize our fellow brothers and sisters on unalienable traits is an ethical imperative to prevent us tearing each other apart. This then leaves only one line, the line where people are more than happy to discriminate based on these unalienable traits, and I think it's perfectly acceptable to ostracize them since they encourage ripping each other's throats out, willingly or as a useful peon.

Comment by teamonkey 1 hour ago

Scientists are not lying. Reich is notable in his field and no-one is disputing his genetic research.

What scientists are wary of is how any discussion in the field gets jumped on and twisted into ammunition to reinforce racist beliefs, whether the science actually supports this or not.

Comment by Nesco 8 minutes ago

“What scientists are wary of is how any discussion in the field gets jumped on and twisted into ammunition to reinforce racist beliefs”

Yet nothing ruined the reputation of the scientific establishment more in recent time than their tendency to change their behaviours and adapt their beliefs for political motives

Comment by phainopepla2 10 hours ago

Is it unpopular on the right? Genuine question. I have only seen people associated with the left deny or downplay this.

Comment by jetrink 10 hours ago

The religious right, specifically. They would say that all people are descended quite recently from Noah and his family.

Comment by FunHearing3443 9 hours ago

Not all of us. Many are evolutionary or old earth creationists that generally don’t have an issue with many aspects of evolution.

Comment by 10 hours ago

Comment by burnto 10 hours ago

Evolution itself has some skeptics among the religious right.

Comment by vomayank 11 hours ago

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Comment by kevinten10 8 hours ago

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Comment by idiotsecant 9 hours ago

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Comment by vivzkestrel 7 hours ago

funny how racists on twitter havent learnt that skin color is a function of natural selection, how do we get this message to them in a non offensive yet informational enough way to change their perceptions of colored people

Comment by Rekindle8090 5 hours ago

Are the twitter racists in the room with you now?

Comment by mohamedkoubaa 11 hours ago

"To supercharge the search, Reich, Ali Akbari, a computational geneticist at Harvard Medical School, and their colleagues amassed the largest-ever collection of genomic data from ancient humans — from a total of 15,836 individuals from western Eurasia — including more than 10,000 newly sequenced genomes."

Without commenting on the content of this sentence or article, I will say that it is refreshing to see sentences like this in the wild after being regularly and constantly subjected to LLM slop.

Comment by sho_hn 11 hours ago

And yet you managed to center AI in the discussion.

Comment by nefarious_ends 10 hours ago

Seriously what’s the point of this comment