The 10,000 Year Explosion
In lieu of a full review of Greg Cochran and Henry Harpending’s new book, The 10,000 Year Explosion, I’ll keep this short: this book is interesting, well-written, and probably mostly wrong.
The book reads as a series of historical narratives grounded around recent work by the authors in population genetics. In particular, they focus on claims very familiar to readers of this site: that Neandertal introgression was in fact probable, that the IQ of Ashkenazi Jews is a result of strong recent selection, and that thousands of new selected alleles are currently sweeping through human populations (along with novel theories, like that the evolution of lactose tolerance was a major force in population expansions). All of these things are, a priori, vaguely plausible, and are certainly fun to read about, but let’s be honest: in a few years, most, if not all, of these are going to be in the dustbin (if any of them are true, my money is on Neandertal introgression).
In any case, this book is not intended to be “correct”, so to speak–it seems to be more intended as an overarching frame of reference for viewing human history, acting as a counterpoint to that presented by authors like Jared Diamond. But if anthropology has a “Guns, Germs, and Steel problem“, I just hope population genetics doesn’t end up with a “10,000 Year Explosion problem”.
Just to keep it short: I gather that you think that the idea that the Ashkenazi Jews are A. significantly smarter than average and B. this is a consequence of selection – is implausible or unlikely. Why?
I’d bet at 1:10 odds that the Ashkenazi hypothesis (here defined as higher genetic IQ than gentiles due to selection) is true. The IQ advantage, and verbal-over-visuospatial specialization of Ashkenazi intelligence, are just clear empirical facts. The clustering, plus the achievements of the Gaucher’s and torsion dystonia patients, are too vastly unlikely to accept a drift or environmental explanation for the differences.
Also, calling ongoing selective sweeps by thousands of alleles ‘vaguely plausible’ seems like an understatement. There have been recent detectable sweeps by hundreds of alleles with big fitness advantages. Other alleles will have smaller effects that push in the same direction, and will sweep.
You give Neandertal introgression as the most likely claim in the book, but I would class it as one of the less likely ones: we dont know enough about Neandertals to know whether there might have been some major barrier (appearance of adults or offspring, sterile offspring) to successful mating or second-generation reproduction.
I just wish they had chosen a test case other than Ashkenazi IQ. Regardless of whether their theory of this is true or not (and for reasons I will not repeat now I regard it as no better than 50/50) it is tactically a rotten example to choose. Did they sit down and brainstorm to find the most provocative case possible? Compare Darwin’s treatment of human evolution in the Origin: ‘Light will be thrown on the origin of man and his history’. That’s it: one sentence about a page from the end of the book.
“let’s be honest: in a few years, most, if not all, of these are going to be in the dustbin”
The kind of words that can come back to haunt a man.
All of these things are, a priori, vaguely plausible
a priori = “predicted by population genetics theory”
vaguely plausible = “confirmed with empirical observations”
“let’s be honest: in a few years, most, if not all, of these are going to be in the dustbin”: so it’s falsifiable – not, as it were, Genetic Warming.
I gather that you think that the idea that the Ashkenazi Jews are A. significantly smarter than average and B. this is a consequence of selection – is implausible or unlikely. Why?
A. seems reasonable, B. is vaguely plausible. Certainly the evidence is pretty circumstantial-this will probably be answered one way or another in the relatively near future.
The kind of words that can come back to haunt a man.
I know! :)
I have a question about selection. It is obvious to me that, considered by itself, a gene that gives its bearer a one percent advantage will gradually increase in frequency at a certain well defined rate (once it becomes non-rare anyway) until it becomes universal (sweeps).
What is not clear to me is what happens if there are a thousand such genes in the population at once. Is the process additive? Does each advantageous gene increase in frequency independent of the others, as if it was the only advantageous gene in the population? Or does the process get clogged up? If everyone has a random selection of 200 genes each giving them a one percent advantage, then does anyone actually have an advantage over anyone else? How does this work?
You give Neandertal introgression as the most likely claim in the book, but I would class it as one of the less likely ones: we dont know enough about Neandertals to know whether there might have been some major barrier (appearance of adults or offspring, sterile offspring) to successful mating or second-generation reproduction.
greg has discussed this in detail. people fuck sheep. additionally, there’s a large body of data on cross-species interfertility, it is not very likely the offspring would be sterile given the last common ancestor between neandertals and african moderns. introgression needs very few breeding events. it seems me that if this is wrong, is wrong because the s for introduced alleles was not high, so likely went extinct (as most are wont to do after so many generations).
Anonymouse – you seem to be no idiot, since that potential “clogging” was also noticed by none other than Haldane. See the long treatment of the Haldane Limit by David B, in the archives here. Personally I have a hard time deciding what to think of it.
Yes, I know about the sheep-fucking, and it’s a good case, and I agree with the math showing that only a small number of breeding events are required for a variant with a substantial fitness advantage.
But people don’t fuck sheep that often, and if enough big deleterious alleles affected hybrids and their offspring (e.g. looking like a hated enemy and getting exposed as an infant) then some positive alleles that otherwise might have had enough of a fitness advantage to spread wouldn’t.
On second thought,, I prefer to put it a bit more elegantly: people have known to have romantic friendships with oryxes.
Cochran and Harpending’s suggestion of neandertal-human hybridization seems more than plausible in light of early anatomically modern material that shows neandertal features. The same is true of a.m.h.s. and other archaics.
C&H are not merely asserting that Jews are genetically smarter and that this is due to selection. For their model to be correct, this selection occurred hundreds of years ago in European ghettos rather than thousands of years ago in the Middle East, in which case it would also include Mizrahi Jews. So let’s not lower the goalposts yet.
Likewise, C&H are not just proposing that positive natural selection continued since the emergence of a.m.h.s., or even simply that it accelerated. For C&H to be right this acceleration was massive. Just maybe they have overestimated this acceleration by an order of magnitude or two. Perhaps because of surfing and hitchhiking.
I said this before somewhere, but I find that facts that – Neanderthals had red hair
- The Neanderthal red-hair gene is not the same as the modern red-hair gene to be strong evidence against Neanderthal introgression. After all, we know that selection for light skin was very strong in Europe, and African Moderns probably had dark skin. So if any genes introgressed, why didn’t the red-hair gene?
Does the book have a good answer to this problem? I haven’t read it, yet (but I intend to).
people have [been] known to have romantic friendships with oryxes
In Room 473 of the Miami Hilton to be exact. Don’t ask me how I know.
D-Box, neanderthal extinction (>25,000 BP) prolly antedates European coloring (< 15,000 BP).
David,
The book doesn’t address the red-haired gene problem you cite. It does mention that a gene coding for blue eyes probably emerged 6,000 to 10,000 years ago, and that a gene possibly related to language ability (FOXP2) may have introgressed from Neanderthals about 42,000 years ago, which would seem to lend credence to your objection. If pigmentation-affecting genes were being selected for as recently as 10,000 years ago, it seems that Neanderthal-loving Europeans 42,000 years ago would still have been a fairly swarthy* lot, and thus fertile genetic ground for the introgression and spread of any lightening alleles. If Harpending and Cochran don’t reply here, you might want to post the question over at 2Blowhards and see if they answer it on Friday. I’d be interested in what they have to say.
*Get it? “fairly swarthy?…” Eh? Eh? Sorry…
A point: in general, men (and it’s always men, isn’t it?) do not have “romantic friendships with oryxes” unless women are unavailable. I’ve always felt that the reported propensity of human males to screw anything that moves has been rather over-hyped, and I do think that if humans and Neanderthals found each other hideously ugly that could have posed a significant barrier to mating.
I’ve always felt that the reported propensity of human males to screw anything that moves has been rather over-hyped, and I do think that if humans and Neanderthals found each other hideously ugly that could have posed a significant barrier to mating.
who the fuck cares? seriously, these are bullshit objections. most men are not perverts. but some men are perverts. i knew a guy who fucked a chicken in high school (his cousin caught him and narked on him). if you knew the guy you would see why he would do something so bizarre. again, you need only a tiny amount of between group mating for genes to jump if they were selectively favored. most men don’t want to masturbate and would rather have sex with women too.
but let me rollback my irritation: what % of human males would have sex with an animal? i put the figure ~1%. out of curiosity or loneliness. of these, only a minority might have the opportunity. but 0.1% per generation is still a high number assuming two populations Ne on the order of tens of thousands and hundreds of generations.
p.s. no surprise that the chicken-fucking happened on a farm. i think urban americans pervs have fewer opportunities.
D-Box, neanderthal extinction (>25,000 BP) prolly antedates European coloring (< 15,000 BP).
I know about that. I also know that agriculture probably increased selection for light skin. But here’s the thing (as gc used to say): Neanderthals had light skin! So we know that it was an advantage.
p.p.s. in 10 years if there aren’t more suspicious alleles then i will change my assumptions. but right now, i’d still say too early to tell. IOW, 9 other half a dozen alleles as plausible as haplogroup D of microcephalin in 10 years. but i might just write up a javascript with the assumptions more explicit and let readers play around with them….
David Boxenhorn:
The book does not address it. It does assert (and you might be aware, from your objection) that pale skin and variable eye and hair colors are relatively recent. One specific gene influencing skin color, a variant of SLC24A5, could be as young as 5,800 years old. This is recent enough that the modern fitness benefit in modern Europeans could have been related to agriculture in northern climates specifically, and not high lattitudes or mildly cold climates generally. Europeans were brown-skinned for tens of thousands of years.
This seems to support you, if an advantage wasn’t conserved and had to be re-invented. Or, since Neanderthals had more generations than sapiens in the worst of the ice age, it might not have been particularly advantageous in the intermission between the peak of the ice age and the beginning of agriculture in high lattitudes.
They make a circumstantial case that introgression might explain why culture and art bloomed first in Europe before other anatomically modern humans in and out of Africa. Neanderthals had more primitive tools, but they had larger brains, and its conceivable those brains had some different solutions that proved useful to adopt. Really we’ll just have to wait for better DNA testing to know. Y chromosome and mtDNA testing comes up negative for neanderthal DNA, and there have been other specific tests, but we don’t yet have the comprehensive testing of Neanderthal remains or even modern living DNA that would reveal limited introgression and de-linkage.
What I took away from the book is that biologically and behaviorally, limited introgression is the most likely case, not the least likely. It’s possible there were behavioral or genetic incompatibilities, but there’s no particular reason to think so.
I also know that agriculture probably increased selection for light skin. But here’s the thing (as gc used to say): Neanderthals had light skin! So we know that it was an advantage.
well, perhaps it was sexual selection? ;-) or, perhaps h. sap. sap. was WAY MORE proficient at getting vit D from natural sources, such as sea life, so the selective benefits of the lightening alleles might have not been in effect. or perhaps there are other downsides for being depigmented which we don’t know about, but downsides which weren’t downsides for neandertals.
“(and it’s always men, isn’t it?”
Not always. I know of a one-time Congressional candidate whose romantic adventure with a Great Dane went terribly wrong.
you need only a tiny amount of between group mating for genes to jump if they were selectively favored. most men don’t want to masturbate and would rather have sex with women too.
Don’t forget conflict and rape. If even one Neanderthal raiding party managed to subdue a group of human males and rape their women, as hunter-gatherers (and chimps) seem to like to do, that could have been enough.
To me the lactase-based expansion idea is hard to assess without considering fermentation of milk, which is not treated in the book. Dairying is cited as 5x more productive per acre than raising meat. But, while I’m not well-read on this, there is probably some ability to exploit dairying without lactase:
It is generally accepted that fermented milk products such as yogurt can efficiently improve lactose digestion in lactose malabsorbers and therefore that they are well tolerated by most lactose intolerant subjects. [data given, table 3]
http://www.ajcn.org/cgi/reprint/73/2/421S.pdf
Apparently about the same is true of some cheeses.
Obviously it’s still significantly better to have lactase, as the convergent evolution to lactase persistence shows. Fermenting milk takes some labor, fermentation entails some loss of caloric content, and giant vats of cheese preclude nomadism, a way of life which C&H suggest fosters a military culture in the long run as well as providing per se an immediate military advantage.
I do tend to agree the thinking that it should be rather difficult for technology to give its bearers a lasting advantage over enemy peoples, because it can be copied. Even though horse raising, horsemanship, husbandry, and agriculture have their subtleties which surely took a long time to invent de novo, I would think that all this knowledge would be extracted overnight from prisoner culturebearers, under death threats and torture. Valuable breeds and seeds would simply be captured – again overnight; it’s not like they could be outfitted to self-destruct.
I have the hardest time imagining how the Ashkenazi hypothesis could be wrong. Can’t wait to see the direct test of it.
. This is recent enough that the modern fitness benefit in modern Europeans could have been related to agriculture in northern climates specifically, and not high lattitudes or mildly cold climates generally.
frequencies for the “derived” light-skin variant of slc24a5 are on the order of 50% in southern india fwiw* (and 80-90% among pakistani popultions).
* the 50% figure is from sinhalese.
well, perhaps it was sexual selection? ;-) or, perhaps h. sap. sap. was WAY MORE proficient at getting vit D from natural sources, such as sea life, so the selective benefits of the lightening alleles might have not been in effect. or perhaps there are other downsides for being depigmented which we don’t know about, but downsides which weren’t downsides for neandertals.
I agree. Any of these things might be true. Remember, I started out saying merely that I find this to be strong evidence against introgression (“strong” being a relative term – we don’t really have strong evidence for anything). None of the above hypotheses strike me as more plausible than the hypothesis that there simply wasn’t any introgression.
I know about that… But here’s the thing (as gc used to say): Neanderthals had light skin! So we know that it was an advantage
Advantage is contingent. The point is that light skin and red hair were apparently not advantageous for humans living in Europe until a time significantly later than when they were swapping genes with the neanderthals.
But if the evidence showed that pigmentation was selectively important for Europeans at the time they coexisted with Neanderthals, I would agree the lack of pigment-related introgression would argue against other introgression.
You don’t think the reason it took tens of thousands of years for Europeans to lighten up was for want of mutations?
but let me rollback my irritation: what % of human males would have sex with an animal? i put the figure ~1%.
oh, there are a lot of dirty animalfukkers out there. Young males who live on farms out in the middle of nowhere are especially likely to “experiment”. Perhaps a majority!
US bestiality prevalence
Males
1974: 4.9%
1948: 8.3%
Females
1974: 1.9%
1953: 3.6%
i knew a guy who fucked a chicken in high school
Was it a same-sex chicken? Animal sex is one thing, but gay animal sex is just gross.
I’m sick and tired of crappy books that try to sound correct rather than make people think. Cochran’s book will make people think and that’s a damned good thing. Watch his detractors avoid science but be vague, think about that.
On lactase tolerance and fermentation of milk: the book does skip over that, but it seems that people must have been consuming milk in some form in order for lactase tolerance to have been advantageous in the first place. Its hard to see how the first lactose-tolerant individual in a non-milk consuming society would know to try it. And milk fermentation does seem to have ancient roots in some cultures.
From there, you’re right that the benefits of lactase tolerance seem obvious. Even allowing for a broader and more complicated model of dairy adoption, the basic argument that lactose-tolerance was beneficial or it wouldn’t have spread as quickly as it did stands. And if raw milk and more efficient use of fermented milk are significantly advantageous over less efficient use of fermented milk, that still supports, at least weakly, lactase-based expansion.
Its hard to see how the first lactose-tolerant individual in a non-milk consuming society would know to try it.
People try to eat mud in times of extreme hunger. Why not milk?
Jason,
That’s some pretty powerful evidence. I’m updating in favor of more introgression, and thus successful introgression of less advantageous alleles.
“What is not clear to me is what happens if there are a thousand such genes in the population at once. Is the process additive? Does each advantageous gene increase in frequency independent of the others, as if it was the only advantageous gene in the population? Or does the process get clogged up? If everyone has a random selection of 200 genes each giving them a one percent advantage, then does anyone actually have an advantage over anyone else? How does this work?”
See David’s GNXP article: http://www.gnxp.com/blog/2006/04/haldanes-dilemma-should-we-worry.php
Haldane makes assumptions that don’t apply to real world populations.
Sexual selection. The most successful stag will likely have many better alleles compared to his rival. That stag will produce far more offspring than would be predicted by considering the relative fitness value of each allele. In one generation, one stag may propagate hundreds of beneficial alleles.
Nonlinear thresholds where many harmful variants combine in the same animal. The animal dies, is infertile, or fails in mate competition and many inferior alleles are removed.
Chromosome recombination during meiosis alters the fitness coefficient. Suppose “A” and “B” are nearby beneficial variants of a chromosome with wild types “a” and “b”. At first haplotypes “Ab” and “aB” will have a modest selective advantage over haplotype “ab”. Eventually there may be a recombination event creating a new haplotype “AB” which has significant selective advantage over haplotype “ab” and modest selective advantage over haplotypes “Ab” and “aB”. The new haplotype will sweep faster and will replace two wild types at the same time. Hence, nearby beneficial variants on the same autosome could accelerate sweeps.
Many thousands of existing variants persist and new variants arise in large populations. The changing environment gives some variants a selective advantage. In parallel, the frequencies of these rare variants increase. Recombination eventually produces superior haplotypes with even greater selective advantage. Those haplotypes sweep the population. Haldane’s Limit is left in the dust.
Human populations are even more complicated. Population substructure matters. Migration patterns matter. Inheritance of family wealth, power, or prestige matters. Reality is complex with diverse and changing environmental niches, new haplotypes continually arising, balancing selection, partial sweeps, stochastic historical events, etc. Imagine trying to model the spread of Gengis Khan’s Y-chromosome.
I have a question with regards to the IQ of Ashkennazi Jews.
The book presents the case that their increased intelligence is a result of a genetic change that also makes them more susceptible to degenerative diseases such as Tay Sachs and the like. Is this suggestive of an upper limit to IQ in biology? If so, this suggests that the transhumanist fantasies of arbitrarily increasing human IQ to, say, 250 are nothing but, well, fantasies.
Any thoughts?
kurt9, no. the analogy was to “overclocking.” the idea that AJ’s have QTLs of large effect who have not had time for modifier genes to emerge which mask their downsides.
Dear P-ter:
I read most of the “Savage Minds” article you linked to to explain why anthropology has a “Guns, Germs, and Steel” problem.
I would say, judging from that critique of Jared Diamond by a cultural anthropologist, that cultural anthropologists should get down on their knees daily and thank Jared Diamond for writing GGS and rescuing the reputation of their professon. I’m not Diamond’s biggest fan, but his GGS is a huge amount better than the inanities in this attack on GGS.
If “10,000 Year Explosion” is better than most population genetics by the same amount that “Guns, Germs, and Steel” is better than most cultural anthropology, well, they might as well give the Pulitzer for 2009 to Cochran and Harpending right now. (They won’t, but they ought to.)
I kow a guy who fucked a chicken in high school.
Damn, he had nerve! Most chicken fuckers keep it down on the farm.
I read most of the “Savage Minds” article you linked to to explain why anthropology has a “Guns, Germs, and Steel” problem.
oh, sorry to direct you to that, I actually couldn’t get through most of it. I just liked the opening anecdote about having to discuss a book you think is wrong but which defines a field for non-specialists.
You guys are going to get messed up spam for a while after this thread.
Also, most examples, rumors etc. of bestiality are domesticated animals. Isn’t f*cking a Neandertal more analogous to doing a lion or a bear? Neandertals were pretty serious ass-kicking predators, right?
Could there be any modern populations that were Out of Africa and isolated that wouldn’t have any Neandertal alleles even if almost everyone else did. Like Negritos or pygmies perphaps? Flat asses could be Neandertal, and steatopygia the old human normal. That might even leave evidence on bones.
Isn’t f*cking a Neandertal more analogous to doing a lion or a bear?
they had bigger brains than us dude ;-) humans are willing to both *eat* and *fuck* conspecifics.
True, I was more thinking an unwilling Neandertal.
re: Haldane, number of selective sweeps, etc.
I’m not sure this (a large number of strong selective sweeps) is the same situation considered by Haldane; I don’t think Anonymouse’s original questions are trivial.
Hawks et al. propose thousands of strongly selected alleles. If you consider a single selected allele at a selection coefficient of 1%, that 1% is relative to all individuals not carrying that allele (depending on how you model selection). But those individuals are also carrying alleles that, in this model, are highly beneficial. So if this allele had arisen on its own (ie. not in a poppulation with thousands of other selected alleles), I think we have to conclude its selection coefficient would have been orders of magnitude larger?
I’m not sure exactly how to think about this, maybe other people–who actually think this situation is going on–have a better idea?
is there any doubt that neaderthals were light skinned?
is there any doubt that neaderthals were light skinned?
N = 2, one from spain, one from italy, both pale (loss of function on MC1R). unless the individuals were atypical like albinos, their level of loss of function suggests than normal variation would be on the pale side, on the order of northern europeans.
Dear P-ter:
To sum up, the book puts forward one big idea — that anatomically modern humans have varied genetically over time and space — and a whole bunch of possible examples of this concept in action, ranging from the highly certain to the highly speculative.
Are you dubious of the big idea? Or just of the examples? And considering the large numbers of examples suggested, wouldn’t the law of large numbers imply that more than just the Neanderthal idea is true?
In addition to surfing and hitchhiking, could biased gene conversion also possibly contribute to an overestimated signal of positive selection?
journals.org/perlserv/?request=slideshow&type=figure&doi=10.1371/journal.pbio.0020449&id=18144
On another topic, this reconstruction of a neandertal female isn’t too unattractive.
http://biology.plos
Are you dubious of the big idea? Or just of the examples? And considering the large numbers of examples suggested, wouldn’t the law of large numbers imply that more than just the Neanderthal idea is true?
The examples. I think the big idea is more specific than just “humans vary”, but whatever.
The law of large numbers? Sure, the fraction of correct hypotheses should converge in the limit to the overall fraction of true hypotheses in hypothesis space – about zero. :)
p-ter: I guess you’ll have to write a follow-up to explain why the book is “probably mostly wrong”. Obviously many here find the book’s arguments eminently plausible and even appealing. It would be nice to see an informed rebuttal.
Has anybody ever calculated what % of scientific hypotheses pan out?
p-ter is rolling safely with the idea that the grand majority of sci hyp simply don’t pan out. Esp. fun and sexy ones.
Things that are plausible — really, genuinely plausible — are often wrong because the vast limitations in our knowledge genuinely obscure the puzzle. It’s just impossible to see why until all the information is there.
No prob. Keep moving forward.
P-ter: “I’m not sure this (a large number of strong selective sweeps) is the same situation considered by Haldane;”
Right. I didn’t intend to diss Haldane.
In a large, single, connected, panmictic, stable population in an unchanging environment the specie should be highly adapted to that environment. In this case there would be few beneficial mutations of even moderate selective advantage in the population (harmful mutations are quickly removed by selection). The probability that one animal would have several more good variants than a competing animal would be small (sexual selection and thresholding are thus less efficient at propagating the good variants). There would be few opportunities for beneficial haplotypes to recombine to form even better haplotypes. Instead, a good mutation would slowly sweep the population at a rate determined by the selection advantage of that trait. In that case, Haldane’s Limit applies.
P-ter: “If you consider a single selected allele at a selection coefficient of 1%, that 1% is relative to all individuals not carrying that allele (depending on how you model selection). But those individuals are also carrying alleles that, in this model, are highly beneficial. So if this allele had arisen on its own (ie. not in a poppulation with thousands of other selected alleles), I think we have to conclude its selection coefficient would have been orders of magnitude larger?”
P-ter: In my mental model I separate the early stage from the middle and late stages.
In the early stage there are thousands of slightly beneficial variants with selection coefficients of around 0.1% compared to wild type (large population in changing environment generates the variants). These variants are rare so there isn’t much interference between variants. In parallel, all the variants slowly increase in frequency. At this stage, the variants neither slow nor accelerate the sweeping of other variants.
In the middle stage, the frequency of the variants has increased so that the variants are beginning to interact. No one variant is common but with thousands of good variants each animal may have several good variants. At this stage, sexual selection and thresholding begin to be more efficient at replacing the wild types with the good variants, i.e., each “selection death” promotes several good variants. Also, good haplotypes recombine to form even better new haplotypes with increased selection advantage. As the new haplotype replace the wild haplotype, several good variants replace the old wild variants. A few of the new haplotypes will have selection coefficients of 1% or more compared to wild type and will begin sweeping rapidly.
In the last stage, the new haplotypes containing the variants are now common. They interfer with each other, they merge and split creating new haplotypes that are optimal for each specific environmental niche. Some sweep to fixation, some stabilize under balancing selection. Some lose their selective advantage because the environment changes.
With that simple mental model in mind, I then imagine all of the stages occurring simultaneously in populations with complex substructure, spread over a large geographic area with diverse environments.
That Neanderthal reconstruction is certainly someone many human males would plausibly fuck, if she didn’t bite your throat open. She looks Norwegian.
But I thought Cochran and Harpending believed Neanderthals were furry. Shouldn’t that reconstruction really have much more facial and body hair?
It isn’t just positive selection I’m puzzled about. I keep reading that negative mutations are orders of magnitudes more common than positive ones, so alleles with a one percent disadvantage must show up far more often in any population than those with a one percent advantage. Again, it’s obvious how a single disadvantageous allele gets cleared from a population, but what happens when there are thousands? It’s the same problem in reverse, with the added bonus that, since negative mutations are so much more common than positive ones, it applies even to small populations in static environments.
I would think that you would need a very high death rate ? both pre-natal and post-natal to keep up. And perhaps not coincidentally, both humans and animals in the wild do seem to have rather high death rates among the young, even in good environments. Could this be what is going on? And what does it mean for us now, when almost all of our children are surviving? Could it be that our load of negative mutations is growing much more rapidly than people realize? Could that have something to do with the recent apparent increases in conditions like autism?
I am totally speculating here, and I don’t really have my facts down, so I may be talking garbage, but I just don’t have an intuitive feel for how selection operates on large numbers of alleles at once, and it does seem like an important question, something I’d like to understand.
Anonymouse,
JF Crow and some others suggest three new deleterious mutations (generally rather modest in effect) per human individual, with an average life of 100 generations for each of these mutations. Thus, a mean of 300 deleterious mutations per individual. This is more estimate than fact – even in flies I think – it is based on work in flies which I am not conversant with myself.
Unfortunately, beyond that I don’t understand much, and have way more interests than answers. This is an interesting precis of mutation:
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutations.html
Why doesn’t the germline mutation rate approach zero? To me, this is one of the most fascinating fundamentals. Group selection arguments based on the need of the species to evolve are dubious IMO because alleles for high-mutation rate will not remain linked to the rare new beneficial alleles they tend to create. If you have a high mutation rate and I have a low one, the beneficial alleles your descendants produce will introgress into my descendants, whereas the many bad mutations your lineage is always accumulating will not – so I win. Your peeps will be only a few generations ahead of mine in starting to enjoy the new beneficial alleles you produce.
Other people suggest energetic constraints, ie diminishing returns per unit of energy devoted to DNA fidelity and repair – if that’s true, I’d think the germline mutation rate ought to be far lower than the somatic one.
I’m not sure whether every sort of mutation is in principle, given arbitrarily high energy devoted to the task, preventable (during DNA replication) or fixable.
And what does it mean for us now, when almost all of our children are surviving?
It doesn’t seem very good, in the long term, if you assume, reasonably, that a child’s odds of mortality in the past was correlated with that child’s number of deleterious mutations. But this change to near zero child mortality, only a few generations old, may be too recent to have had much impact yet. (The present-day fitness-reducing effects of intelligence, wealth, and education may be a more significant problem.) The calculation is a little opaque to me. Obviously it depends on
1. the mathematical distribution of the number of deleterious alleles per person at the old equilibrium, ie in the year 1880 or 1900 or so (beats me)
2. the strength of correlation between individual fitness and the individual number of deleterious alleles – hard to reckon, as sexual selection will play a role
3. and of course the rate of childhood deaths
I think in principle this will determine what happens.
I suppose the Neanderthals’ range was such that we have no hope of ever finding one preserved in permafrost like a mammoth or woolly rhino?
Mouse – mass harem keeping also comes into play here – it can all be subsumed under the concept of reproductive variance. Presumably Ghengis Khan had a lot less deleterious alleles than most humans; likewise, then, his inconceivably many great grandchildren. In “The red queen” Ridley documents harem keeping all over the agriculture-practicing parts of the world, not just by kings but also nobles, each on a scale according to his rank. It’s rather hard to see how this could have failed to be, broadly speaking, eugenic – or at least “noble-o-tropic,” keeping in mind that not all of a nobleman’s characteristics are necessarily “noble” (consider ruthlessness, greed, the genocidal tendencies of Ghengis Khan, etc – not to say, though, that these traits have never been fitness enhancing for commoners).
Presumably Ghengis Khan had a lot less deleterious alleles than most humans;
we really don’t know the correlation between # of del. alleles & fitness, do we? or even a guess? i mean, on the margins of LOTS of del. i can see it converging on zero. but what the returns-on-fewer-del? where does diminishing returns kick in?
Razib: “we really don’t know the correlation between # of del. alleles & fitness, do we?”
If you could rank the “fitness penalty” of specific mutations you would likely see a power law distribution. A few mutations are fatal, more are moderately harmful, far more are slightly harmful, and the vast majority are essentially neutral. Evolution through natural selection is strongly weighted toward removing the most harmful mutations. I.e., selection preferentially removes the more harmful mutations lying toward the left side of that distribution. More selection pressure results in less harmful mutations also being removed. Flies occupy the peaks of the fitness landscape while humans wander around the foothills. (E.g., human regulatory sequences tend to be less conserved than mouse regulatory sequences.)
we really don’t know the correlation between # of del. alleles & fitness, do we? or even a guess? i mean, on the margins of LOTS of del. i can see it converging on zero. but what the returns-on-fewer-del? where does diminishing returns kick in?
Agreed – we don’t know the function from the burden of bad alleles to fitness. It’s worth observing that it has to be a monotonic function. But I think I see your point. Namely, if the bad alleles synergize to cut fitness, there may be a portion of a pop for which the burden of bad alleles lies below a certain critical value, and for this portion the burden of bad alleles might be a very subordinate component of the variance in fitness. For this portion, one could speculate, an individual’s portfolio of new derived beneficial alleles might be a much more dominating determinant of fitness.
(Especially when environment is relatively less constant, thus causing evolution to be more rapid, and new beneficial alleles more numerous and salient. But even a relatively more constant environment may still not really be all that constant in an absolute sense since there is always the attack from parasites.)
Unfortunately I don’t know the concrete brass tacks of this stuff – I should read the fly work that JF Crow and A Leroi point to.
assume 300 is the mean number of del. mut. ignore the huge effect hits which result in massive fitness penalties (so they aren’t mostly masked as recessive). perhaps there is a much bigger difference between someone with 350 del. vs. 300 than 300 vs. 250. leroi talks about the most beautiful person with almost no mutational load on the tail. they might be hot, but are they really that much fitter in a reproductive output sense? i know there are super-reproducers, but what’s the likelihood that # of del. mutations is a major independent variable which predicts (once you remove the congenital defects?). i guess it also hinges on terms like ‘normal range of variation.’ most humans conceived do not reproduce because they are miscarried. but as for as reproduction is concerned, we also don’t have the enormous realized reproductive variances (normally) which are common to many species.
Someone mentioned Mizrahi. Would the Sephardics be lumped in with them or did they undergo similar selection as Ashkenazi?
I wish C & H would give some attention to Sephardic Jews. Specifically, Sephardic Jews tended to be merchants and business people around the middle-east, and were money-lenders as well, so I don’t know how unique the role of Ashkenazi jews was. Furthermore, throughout north Africa and the Middle East, Jews were also economically successful, and I think maintain an “IQ advantage” relative to the populations they lived among. They also achieved far more relative to their population. However, as a Sephardic Jew, and someone who has spent enough time around both groups, in Israel and in New York, the biggest difference I’ve noticed is that the sort of aspergy-autisticish jewiness (I’m allowed to say this as a self-mocking jew) that is somewhat common amongst ashkenazi jews is relatively rare amongst sephardim, even very intelligent ones. IF you look at highly successful sephardic jews over history, you’ll notice an abundance of writers, politicians, philosophers, scholars etc. But nothing like the overwhelming presence of jews in the hard sciences.
Maybe someone could shed some light on this. It seems that the Sephardic Jews became a wealthy merchant class in europe hundreds of years ago, mostly in holland, and I haven’t heard so much of them other than Spinoza and Disraeli. It seems they kind of just blended into european society or something.
Razib,
most humans conceived do not reproduce because they are miscarried.
True – but “most” of the abortions are “probably” aneuploid according to C&H… the aneuploids don’t count in inquiries into mildly bad alleles; the rest may count.
but as for as reproduction is concerned, we also don’t have the enormous realized reproductive variances (normally) which are common to many species.
Fascinating… I did not know that. I still need to hit some textbooks.
So, I looked back at Crow’s cites – I was mistaken that everything about mildly deleterious mutations in man is carried over from work in flies. Crow cites Keightley who worked on this directly in man:
Eyre-Walker, A. and Keightley, P. D. (1999).
High genomic deleterious mutation rates in hominids.
Nature 397: 344-347
I haven’t read it yet. Keightley has been blogged on by RPM, and has other papers that look interesting re mildly deleterious alleles and related ideas like the Kondrashov theory of sex. A whole slew of Keightley’s PDFs are free here:
http://homepages.ed.ac.uk/eang33/publications/pkpubs.html
“is there any doubt that neaderthals were light skinned?”
In a human body, the Neanderthal MC1R allele would lead to red hair and light skin. But it’s unclear whether the same would occur in a Neanderthal body. The metabolic pathways for expression of MC1R may have been quite different.
This question may be academic anyway, since Neanderthals probably had little exposed skin, i.e., they were as furry as bears. They almost certainly did not have tailored clothing, unlike early modern Europeans. At best, they might have made ponchos from animal hides, which would have still exposed much of their body surface to sub-zero temperatures. In addition,the human body louse (which lives in clothing) seems to have arisen only 50,000 years ago.
In a human body, the Neanderthal MC1R allele would lead to red hair and light skin. But it’s unclear whether the same would occur in a Neanderthal body. The metabolic pathways for expression of MC1R may have been quite different.
this is a ridiculous assertion. anyone who reads this blog notes analogies (if admittedly imperfect) between pigmentation pathways between fish & horses & humans. it is not logically impossible that neandertals would be very different, but the probability of genetic background having a major effect should be scaled in proportion to genetic distance. neandertals were relatively close to the other mammalian analogs (e.g., MC1R work was originally done on mice).
I love the naked honesty here on gnxp. I think it is fascinating the interest in the genetic basis for intelligence. I have not yet got a copy of 10,000 Years but I would be very interested in a possible genetic basis for diligence. The characteristic I notice most in my friends who hold Ph.D’s in chemistry, math, engineering etc is their diligence.
The assertion is reasonable. The distribution of MC1R receptors varies among primate species. Even if the MC1R allele is identical in two species, it may have different effects because the receptors may be distributed differently (see Mundy & Kelly, 2003, Am J Phys Anth, 121, 67-80).
I would also submit that MC1R receptors should be distributed differently between Neanderthals and modern humans. If Neanderthals were furry, cutaneous MC1R receptors would have been subject to different selection pressures.
The assertion is reasonable. The distribution of MC1R receptors varies among primate species.
no it’s not reasonable. there’s debate whether neandertals and moderns are even separate species. the genetic difference between neandertals and moderns are far smaller than between humans and any other primate, on the order of magnitudes.
Peter,
This question may be academic anyway, since Neanderthals probably had little exposed skin, i.e., they were as furry as bears.
How do you know this? Modern human populations living in extreme cold, usually have a layer of fat under their skin, and are relatively hairless – like Inuit people. They are similar to seals, in other words.
Neanderthals could have worn reindeer skins – which have a unique hollow hair follicle – and are warmer and lighter than most other natural fabrics. In other words, dressed like the Saami people.
old article from NY TIMES on fur.
Razib,
blogspot.com/2007/11/neanderthal-redheads.html
I don’t follow your reasoning. Biological difference is not a function of genetic relatedness. You can get major differences between sibling species and minor differences between distantly related species. The relevant factor is difference in adaptive landscape and in attendant selection pressures.
pconroy,
There is no evidence that Neanderthals had tools, such as darning needles or the like, to make tailored clothing. At best, they could have made ponchos, which would have still left much of their body surface exposed. This is in contrast to early modern humans, whose sites show much evidence of tailored clothing.
A second line of evidence is that the human body louse (which has adapted to living in human clothing) seems to go back only 50,000 years in time. I discuss both of these points in the following blog post:
http://evoandproud.
I don’t follow your reasoning. Biological difference is not a function of genetic relatedness. You can get major differences between sibling species and minor differences between distantly related species. The relevant factor is difference in adaptive landscape and in attendant selection pressures.
gene X gene interactions are more of an issue with divergences in genetic background. relatedness tends to track differences in total genome content, the genetic background. your original contention was that we can’t make inferences about neandertal pigmentation phenotypes based on their genetic architecture on the loci we know result in variation in modern humans because of differences in the way genotypes and phenotypes map.* then you pointed out interspecific differences. logically neandertal genetic architecture of pigmentation could be very different from modern humans. i really doubt that. i’d give it 4:1 odds that there aren’t major differences. you obviously wouldn’t, but then your theoretical presuppositions for why depigmentation occurs is different from most people. you have a theory, and if genomic data don’t fit the theory (e.g., the late sweeps of slc24a5 or oca2), you tend to bring up the wild card of gene X gene interactions and population substructure.
* as it is, when it comes to depigmentation the alleles might differ, but the same genes seem to be implicated across human populations.
pconroy said “How do you know this?” in response to Peter’s assertion that Neanderthals were covered with fur.
A clue is that the finger bones of an infant chimp are quite rugose because the baby uses his hand to cling to mom’s fur. Human infant finger bones are not rugose at all because they have not been exposed to a lot of muscle pull.
Neanderthals are like chimps in this respect, suggesting fur to many of us.
Henry
henry,
do you believe they refurized? the likely emergence of the MC1R consensus sequence which results in dark skin the world over on the order of 1 million years ago implies that the ancestors of neandertals were defurized to some of your colleagues….
(if so, then perhaps paabo et al & company will see it evidenced in their genome)
A clue is that the finger bones of an infant chimp are quite rugose because the baby uses his hand to cling to mom’s fur. Human infant finger bones are not rugose at all because they have not been exposed to a lot of muscle pull.
Neanderthals are like chimps in this respect, suggesting fur to many of us.
Wow, you mean that they looked something like this? That could explain why Neanderthals had an extra need for light skin.
That could explain why Neanderthals had an extra need for light skin.
well, remember that most primates unexposed skin is light. if you follow the NY times link it offers up a date when MC1R in humans changed so as to confer dark skin. it seems reasonable that if the neandertals were furry they’d lose function around MC1R….
A few AJPA 09 abstracts (via) that may be of interest to 10k Year Explosion readers:
Sign, Sign, Everywhere a Sign:
High density haplotype maps of
the dog, human, and cow
genomes reveal extensive human
reorganization of domesticated
genomes.
C.D. Bustamante et al.
We have developed high-density
SNP and Haplotype maps of the
bovine, human, and domestic dog
genomes. These maps came about
through three separate efforts: (1)
The CanMap Project which
genotyped 1,000 dogs and wolves
spanning 85 AKC registered breeds
using the Affy 2.0 canine array
(~127K SNPs), (2) The Bovine
HapMap project which genotyped
25K SNPs on ~500 animals from
two dozens breeds belonging to the
two main subspecies of cattle (Bos
taurus and Bos indicus), and (3) the
GSK-POPRES project which
documented SNP and haplotype
variation across ~7,000 humans of
diverse ethnic and geographic
origin using Affy 500K human
arrays.Comparing patterns across
species we find several striking
features: First, the domesticated
species show genetic clustering of
individuals within breeds before
clustering between breeds. This
clustering results in levels of
relatedness on the order of (at least)
first cousins for the most
“unrelated” animals from a
breed. Secondly, while humans
show a very high correlation at the
megabase scale in estimated
population recombination rates
across subpopulations, cows and
domestic dogs show a striking lack
of correlation across breeds. Lastly,
both dogs and cattle show pervasive
signatures of recent selection using
SNP and haplotype-based statistics.
We also find that all breeds
examined demonstrate high degrees
of cryptic relatedness, even when
close relatives are avoided at the
time of sampling. This implies that
great care must be taken in
interpreting nominal and genome-
wide corrected p-values in whole
genome association mapping within
domesticated species.
***************
Selection, drift, and geography in
recent human evolution.
J. K. Pritchard et al.
Various observations argue for a
role of adaptation in recent human
evolution, including selection
signals at candidate genes and
genome-wide selection scans.
Nonetheless, using genome-wide
SNP data from the HapMap,
Perlegen, and Human Genome
Diversity Panel studies, we find
evidence that strong sustained
selection has been rare in recent
human evolution (the last ~70,000
years). There are few fixed or
nearly fixed differences between
human populations, and most
fixation events have occurred in the
populations that show the most drift
at neutral loci. Moreover, the
geographic distribution of
putatively selected alleles almost
invariably conforms to population
clusters identified using randomly
chosen genetic markers; this
indicates that selected alleles have
rarely spread across historical
barriers to neutral gene flow. In
summary, we propose that the
geographic distribution of favored
alleles is largely determined by
population history and migration,
and that the geographic distribution
of many SNPs with
extreme Fst is best described by a
model of relatively weak selection
with genetic drift. When humans
adapt to new environments it may
often be via modest allele
frequency changes in multiple
genes simultaneously.
***************
Genetic adaptations to spatially-
varying selective pressures and
the susceptibility to common
diseases.
J. K. Pritchard et al.
Selective pressures due to
environmental variation influence
a range of phenotypes in humans,
including body mass and skin
pigmentation. We previously
showed that allele frequencies in
genes involved in energy
metabolism, which are likely to be
central to heat and cold tolerance,
are strongly correlated with
latitude and climate variables. To
test the hypothesis that climate and
other aspects of the environment
shaped variation in the human
genome, we analyzed a genome-
wide data set of more than 650,000
SNPs genotyped in the 52
worldwide populations in the
Human Genome Diversity Project
panel with regard to the correlation
between allele frequencies and a
broad set of environmental
variables including climate, diet,
subsistence and ecology.
Consistent with the notion that
these aspects of the environment
reflect selective pressures that
acted during human evolution, we
find a significant excess of strong
correlations among SNPs in genic
regions and among non-
synonymous SNPs compared to
non-genic regions. We also find
that many susceptibility SNPs for
common diseases are strongly
correlated with environmental
variables; in particular, some
disease phenotypes related to
immune response appear to have
an excess of risk SNPs associated
with signals of spatially-varying
selection. We are now using this
population genetics approach to
detecting genetic variants that
influence inter-individual variation
in stress response.
***************
Historical patterns of traumatic
injury and violence in Europe.
Everybody but your grandma et al.
Traumatic injury data from the
skeletons of 10,975 Europeans
studied by Global History of Health
Project members provide a unique
opportunity to study the
socioeconomic correlates of
skeletal injuries in a historically
well-documented human
population. The much higher
(x2=104.6, p < 0.0001) injury rates
of males (19.4%) relative to those
of females (10.6%) is consistent
with modern clinical data. Injury
rates vary significantly through
time. During Classical Antiquity
and the Early Middle Ages injury
rates were relatively low with 9-
11% of the individuals exhibiting
them. During the High Middle
Ages, injury rates rise to nearly
15% and then decline again during
the Late Middle Ages, especially
among women. Logistic regression
controlling for age at death and sex
effects shows that both this High
Middle Ages increase (z=8.0,
p < 0.0001) and the later decline
(z=8.0, p < 0.0001) in injuries are
highly statistically significant.
Analysis of injury locations shows
that the Late Middle Ages saw a
marked increase in head trauma;
this is an area of the body
frequently targeted during
interpersonal violence. Of interest
in this regard is the exceedingly low
nasal fracture rate (0.13%) among
Medieval Europeans. This contrasts
starkly with the high rates of nasal
fractures (> 25%) seen in the
skeletons modern people of
European and African American
ancestry who lived during the early
20th century. Such differences point
strongly to the key role that cultural
factors play in structuring patterns
of interpersonal violence in human
populations.