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John Hawks illustrates what can be gained at the intersection of old data and analysis and new knowledge, Quote: Boyd on New World pigmentation clines:
I’m using some statistics out of William Boyd’s 1956 printing of Genetics and the Races of Man[1]. It gives a good accounting of blood group data known more than fifty years ago, which I’m using to illustrate my intro lectures. Meanwhile, there are some interesting passages, from the standpoint of today’s knowledge of the human genome and its variation.
On skin pigmentation — this is the earliest statement I’ve run across of the argument that the New World pigmentation cline is shallower than the Old World cline because of the relative recency of occupation….
Looking at what was said about pigmentation generations ago is of interest because it’s a trait which in many ways we have pegged. See Molecular genetics of human pigmentation diversity. Why humans vary in pigmentation in a deep ultimate sense is still an issue of some contention, but how they do so, and when the differences came about, are questions which are now modestly well understood. We know most of the genetic variants which produce between population variation. We also know that East and West Eurasians seem to have been subject to independent depigmentation events. We also know that some of the depigmentation was relatively recent, probably after the Last Glacial Maximum, and possibly as late as the advent of agriculture.
On the New World cline, which is clearly shallower than that of the Old World. The chart below from Signatures of positive selection in genes associated with human skin pigmentation as revealed from analyses of single nucleotide polymorphisms is useful:
What you’re seeing here are patterns of relationships by population when it comes to the select subset of genes which we know are implicated in between population variation in pigmentation. The peoples of Melanesia are arguably the darkest skinned peoples outside of Africa (and perhaps India), and interestingly they are closer to Africans than any other non-African population. But in total genome content they’re more distant from Africans than other non-African populations, excluding the peoples of the New World.
This disjunction between phylogenetic relationships when looking at broad swaths of the genome, as opposed to constraining the analysis to the half a dozen or so genes which specifically encode between population differences on a specific trait, is indicative of selection. In this case, probably functional constraint on the genetic architecture. From the reading I’ve done on skin pigmentation genetics there is an ancestral “consensus sequence” on these genes which result in dark complexions. In contrast, as has been extensively documented over the last few years there are different ways to be light skinned. In fact, the Neandertals which have been sequenced at those loci of interest also turn out to have a different genetic variant than modern humans.
How to explain this? I think here we can go back to our first course in genetics in undergrad: it is easier to lose function than gain function. The best current estimate is that on the order of one million years ago our species lost its fur, and developed dark skin. And it doesn’t look like we’ve reinvented the wheel since that time. All of the peoples termed “black” across the world, from India, to Australasia, to Africa, are dark because of that ancestral genetic innovation. In contrast, deleterious mutations which “break” the function of the genes which gave some of us an ebony complexion occur relatively frequently, and seem to have resulted in lighter skinned groups in more northerly climes. It turns out that some of the pigmentation genes which are implicated in between population variance in complexion were actually originally discovered because of their role in albinism.
So how does this relate to the New World? I think the difficulty in gaining function once it has been lost explains why the people of Peru or the Amazon are not as dark skinned as those of Africa, Melanesia, or South Asia . They haven’t had enough time to regain function which they lost as H. sapiens traversed northern Eurasia. So there you have it. A nice little illustration of how the genetics taught to 18 year olds can be leveraged by the insights of modern genomics and biological anthropology! In the end, nature is one.
Image Credit: Dennis O’Neil
I admit I don’t know that much about the genetic architecture behind skin color, but I wouldn’t think that the pathway to produce skin pigment is “broken” in most fair-skinned individuals, it’s just down-regulated, isn’t it? Why would it be so “difficult” to up-regulate the pathway again? Also, are Tropical America and Tropical Africa also equivalent as far as selective factors (e.g. incident sunlight?). A shallower cline could result from weaker selection as well.
, but I wouldn’t think that the pathway to produce skin pigment is “broken” in most fair-skinned individuals, it’s just down-regulated, isn’t it?
that’s another, more precise way to put it. fair enough.
? Why would it be so “difficult” to up-regulate the pathway again?
because once functional constraint is removed other mutations start to build up on a locus. i assume that the SNPs which we use as markers aren’t the only issues, and turning the gene “back on” would require a sequence of back mutations.
Also, are Tropical America and Tropical Africa also equivalent as far as selective factors (e.g. incident sunlight?).
i’ve heard arguments about how the amazon is shaded by forest. so is the congo jungle and much of melanesia. additionally, peruvians are dark for amerindians, but still not as dark as africans. they’re at higher elevations in relatively dry climes.
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I couldn’t imagine the red-haired Irish regaining their hue, but scandos seem to tan quite well.
Has there been any studies on how these kind of localised adaptions have affected world history? As an example – is the relative success of Iberian colonisation of America (compared for instance to the earlier but unsuccessful Norse expedition) due to the ability of Iberians to withstand a wider range of climates…
Interesting.
Why would it be so “difficult” to up-regulate the pathway again?
because by the second day of incubation, any cells that have undergone reversion mutation give rise to revertant colonies, like rats leaving a sinking ship; then the ship… sinks. – ethyl, methane, sulfinate as an alkylating agent and potent mutagen; created a virus so lethal the subject was dead before it even left the table.
… a repressor protein, that would block the operating cells… wouldn’t obstruct replication; but it does give rise to an error in replication, so that the newly formed DNA strand carries with it a mutation – and you’ve got a virus again… but this, all of this is academic…
It is difficult to find a way back to the same way of doing things but mammals (whales) took to the water and although their tails go up and down rather than side to side that lets them swim pretty good. I can”t see the problem for S. American natives evolving new pigmentation – if there was a selection pressure for it. For that matter why do the Bushmen and the other pre Bantu expansion people the Oromo ( ancestral to everyone else) not need black skins San woman
I can”t see the problem for S. American natives evolving new pigmentation – if there was a selection pressure for it.
the issue is time. isn’t that clear? or did you not read johns’ quoted passage? fwiw, amazonian tribals also still have a moderately “siberian” body plan as well (far stockier than tropical peoples normally are).
For that matter why do the Bushmen and the other pre Bantu expansion people the Oromo ( ancestral to everyone else)
they’re not ancestral to everyone else. please don’t repeat that dumb meme again. it’s embarrassing.
Sorry I thought this was about pigmentation
Sorry I thought this was about pigmentation
southern africans have higher proportions of OCA2 loss of function mutations last i checked, like just eurasians.
also, i have only modest confidence in this, but probably lean to the position that the mbuti are basal, not the bushmen. though it seems unclear now. i should probably just post that people should use the word *basal*, that’s what you really mean….
I’m still skeptical that this constitutes genetic constraint rather than just weaker selection pressure or different population demographics. In most organisms, I would argue that melanism is at least as common a mutation as albinism. Again, I don’t know how pigment pathways are regulated, but screwing up a regulatory sequence with a mutation seems like it could just as easily upregulate pigmentation as it could downregulate it. Also, why not actually measure the genetic variance in pigment coloration in South American populations? If there’s genetic constraint, then there should be little genetic variation. I sincerely doubt that is the case. While sunlight in certain patches may be equivalent between the two environments, you would need to take a weighted average dependent on the density of the populations across a fairly broad range, to account for gene flow. Furthermore, sunlight alone may not be the only parameter. Certainly, lighter skinned individuals can survive just fine in tropical regions with the help of a society there to support it. The New World tropics seemed to have more economically prosperous civilizations than Tropical Africa over the last few thousand years (I could be wrong on this, you know would know better than me; I’m just thinking of Mayans), and at the very least, it doesn’t have a biota that coevolved with its population of humans for millions of years, and could potentially have experienced ecological release.
The last thing to think about is how is pigment measured? It could be that genetic variation in pigment is constant on the logarithmic scale, but not the scale they used here. For example, I could argue that Elephants evolve faster than shrews because an elephant can change 500 lbs in 10 generations of selection, while a shrew evolves only a gram or two in the same period. Of course this is true on the additive scale, as genetic variation for body size on the additive scale increases with increasing mean. However, if you convert to the log scale, than both shrews and elephants are equally evolvable in body size, as measured as percent change in size. A similar argument could be made for skin pigment, and fair-skinned populations are slower to evolve because of the nature of genetic variation for the trait, and especially, how we measure skin pigment intensity.
“because once functional constraint is removed other mutations start to build up on a locus. i assume that the SNPs which we use as markers aren’t the only issues, and turning the gene “back on” would require a sequence of back mutations.”
I think there’s a big difference between turning a gene “back on”, which may be difficult, and turning a gene that was never actually off “back up”, which may be a much simpler proposition because you never lost functionality. Do we know enough about how these pathways work to say that anything has been actually turned off?
josef, if you’re interested in the topic you’ll familiarize yourself with the literature. i think it’ll clarify/modulate a lot of what you’re saying. since you stated “I admit I don’t know that much about the genetic architecture behind skin color,” you’re just thinking off the top of your head. a lot of your questions would be interesting to follow up and engage with, as i think you might be correct in some areas…but i’m not really in the mood to recapitulate five years of genomics papers 🙂 the first paper is a place to start with in the literature.
I think there’s a big difference between turning a gene “back on”, which may be difficult, and turning a gene that was never actually off “back up”, which may be a much simpler proposition because you never lost functionality. Do we know enough about how these pathways work to say that anything has been actually turned off?
herc2-oca2 is to my knowledge the best one that’s been elucidated for people with blue eyes. google it. honestly all i remember is that herc2 seems to be regulating the expression of oca2, though the details were still to be worked out last i checked. it’s a relatively new mutant (~10,000 years) from what we know, so i assume that “going back” wouldn’t be so hard. in the native american case i assume that depigmentation has an older time depth.
and at the very least, it doesn’t have a biota that coevolved with its population of humans for millions of years, and could potentially have experienced ecological release.
this is a very good point btw. need to think on it. the main objection i have is that australians and papuans encountered the same lack of coevolved organisms. though they had ~30,000 years on amerindians in terms of habitation.
Jablonski and Chaplin (2010) says “Depigmented and tannable skin evolved numerous times in hominin evolution via independent genetic pathways under positive selection”.
Europeans certainly have a load of ‘functionally impaired variants’ that keep them white. Yet when exposed to intense sunlight many Europeans (incuding some blue eyed blond ones) can still tan to a light brown. That has evolved since they got white skin. By my way of thinking it suggests European skin is not adaptive to UV at the European latitudes.
Jackson(06)”HapMap Consortium data6 found that SLC24A5 was within a chromosomal region that has a striking reduction of heterozygosity of SNPs in the European population.[…]Such a long conserved homozygous haplotype indicates that there has been strong selection on a gene or genes”
Jackson(06)”HapMap Consortium data6 found that SLC24A5 was within a chromosomal region that has a striking reduction of heterozygosity of SNPs in the European population.[…]Such a long conserved homozygous haplotype indicates that there has been strong selection on a gene or genes”
just so readers know, this long haplotype is at 90-100% in the middle east and ~90% in pakistan, and around ~50% in south india (a study showed it above 50% in sinhalese, a bit below 50% in sri lanka tamils). i’m homozygous for the “european” variant btw. on the other snps i’ve looked at i’m just like africans. i’m about the complexion of the typical indigenous meso or andean american i’d say.
re: tanning, etc. aside from whites as pales as redheads, albinos, and nilotic east africans, i assume everyone tans. i can tan quite dark from medium to dark brown, though not quite to the complexion of east africans.
tx to the new lit citation! i hadn’t seen they’d come out with a new paper this year.
ok, makes more sense. i was in europe then and wasn’t checking my rss….
Jablonski and Chaplin (2010) says “Depigmented and tannable skin evolved numerous times in hominin evolution via independent genetic pathways under positive selection”.
it was an OK paper. but just note that tannable is different from the type of skin very dark skinned peoples have. so it seems to be addressing a different question.
Following Josef Uyeda, I would caution against attributing the milder cline in skin pigmentation in America to the relative recency of human habitation there. We don’t have any hard evidence to ascertain when and how America was peopled vis-a-vis other regions, hence using “recency” as an explanation for skin pigmentation is too risky. From the map of skin pigmentation it appears that only Europe and Africa harbor the extremes of skin color. And I agree that “screwing up a regulatory sequence with a mutation seems like it could just as easily upregulate pigmentation as it could downregulate it.” We also know that in Africa foragers (Pygmies and San) are lighter than agriculturalists, and since the San are the clear genetic outliers in Africa, their antiquity is not associated with darker skin color. See also http://blogs.discovermagazine.com/gnxp/2010/09/not-all-genes-are-equal-in-the-eyes-of-man/ So, I would rather talk about the cline of progressive extremization of skin pigmentation away from a source characterized by a more moderate skin color (12-23 range on the map above, covering America, Asia and North Africa) and the accretion of the extreme values on the margins of the human geographic range (Europe, Africa, Australia).
We also know that in Africa foragers (Pygmies and San) are lighter than agriculturalists, and since the San are the clear genetic outliers in Africa, their antiquity is not associated with darker skin color.
what is that supposed to mean? are the san are insects trapped in amber who preserve all the ancestral traits or something? they’re no more antique than any other population. though i think of course it is plausible that the ancestral human population was not quite as dark as nilotic groups or even west african bantu. there’s a difference between the 6 genes which explain most intercontinental pigment variation, and the larger number of small effect genes which produce the smaller gradations.
Cool post! What puzzles me is the assumption that ancestral humans were light and only became ‘dark’ after losing bodily hair. Why were they expected to be light before? Chimps, bonobos and gorillas (especially the latter) as as dark as the darkest humans (see gorilla face cover of the Nature issue with the malaria origin paper). Shouldn’t we assume that even when our ancestors were furry they could also be dark? I agree that the San could be secondarily light.
apparently they’re not dark when shaved. that’s what jablonski says.
“We don’t have any hard evidence to ascertain when and how America was peopled vis-a-vis other regions”
We have plenty of hard evidence. Carbon-dated skeletons.
What puzzles me is the assumption that ancestral humans were light and only became ‘dark’ after losing bodily hair.
I wonder if the mechanism for fur+light skin vs hairless dark skin in those apes is along the lines of whatever being responsible for promoting hair growth inhibiting melanisation of the skin in that area (or some other kind of linked tissue differentiation mechanism). There mightn’t’ve been any “lag” between fur+light skin -> hairless dark skin, if that were the case.
Razib: “what is that supposed to mean? are the san are insects trapped in amber who preserve all the ancestral traits or something?”
American Indians are not dark because they constitute a population recently derived from East Asia. The San – who are not dark either and in fact are often likened to “Mongoloids” in their skin color – because they are not insects trapped in amber. And then “they’re no more antique than any other population.” This is the jungle of an argument. Skin color is a complex trait driven by a combination of effects of natural and sexual selection, and not a litmus test for population antiquity.
Gcochran: “We have plenty of hard evidence. Carbon-dated skeletons.”
I guess you keep those skeletons in your closet. There’s not a single skeleton ever found in the New World that says on it “I was a pioneer in a new land.” The earliest New World skulls are not Mongoloid in appearance. The earliest Siberian skulls apparently post-date the emergence of “generalized Mongoloid morphology” in the New World. See Peter Brown (1999). “The First Modern East Asians?” The Upper Cave skull – non-Mongoloid – is closer to Paleoindian skulls such as Lagoa Santa than to any other skulls in Asia. See Hubbe et al. 2010. Testing Evolutionary and Dispersion Scenarios for the Settlement of the New World. It’s a complex picture and as time goes by will have more skulls to judge from.
American Indians are not dark because they constitute a population recently derived from East Asia. The San – who are not dark either and in fact are often likened to “Mongoloids” in their skin color – because they are not insects trapped in amber. And then “they’re no more antique than any other population.” This is the jungle of an argument. Skin color is a complex trait driven by a combination of effects of natural and sexual selection, and not a litmus test for population antiquity.
very few people accept your position on the settlement of the new world. you’re fine to have your opinions, but please don’t confusingly interject yourself into an unrelated issue which is premised on the orthodox consensus. i had no idea what you were talking about because i don’t grant your premise.
re: bushmen complexion, it’s lighter than other subsaharan africans, but all the photos i’ve seen indicate they’re a thoroughly brown-skinned group. if mongoloid = cambodian or javanese, perhaps. but if mongoloid = han or japanese, no.
“very few people accept your position on the settlement of the new world.”
Typical for any new theory.
“please don’t confusingly interject yourself into an unrelated issue which is premised on the orthodox consensus.”
Sorry, Nurse Ratched, but Gcochran provoked me.
“if mongoloid = cambodian or javanese, perhaps. but if mongoloid = han or japanese, no.”
Right on the botton. It’s grade 18-20 on your map, way below the 30+ for some of the Bantu-speakers/West Africans. As Harpending and Eiler, Human Diversity and History(2000) wrote, “[Kalahari Bushmen] resemble, to European eyes, at least, east Asians. They have yellowish rather than black skin, epicanthic folds, shovel-shaped incisors, and many newborns have “Mongoloid spots” at the base of the spine. The Asian appearance is not just a perception of Europeans. In the !Kung language, there are three kinds of mammals: !a is an edible animal like a warthog or a giraffe, !oma is an inedible animal like a jackal, hyena, black African, or European, and zhu is a person. Vietnamese in Botswana were immediately identified as zhu by Bushmen. In other words, their perception of their similarity to Asians is the same as ours (i.e. Europeans’).” (p. 311). The Kalahari Bushmen case study in Harpending and Eiler was supposed to illustrate the possibility that Bushmen preserved in their phenotype some ancient kinship with East Eurasians, which was lost entirely in neutral genetic markers because of gene flow, drift, etc.
I don’t know what Harpending’s take on the issue is in 2010, but it’s still an interesting perspective, don’t you think?
The Kalahari Bushmen case study in Harpending and Eiler was supposed to illustrate the possibility that Bushmen preserved in their phenotype some ancient kinship with East Eurasians, which was lost entirely in neutral genetic markers because of gene flow, drift, etc.
that sort of thing might be testable. the genes would probably be able to tell us if something is an ancestral character or a independent convergence.
“that sort of thing might be testable. the genes would probably be able to tell us if something is an ancestral character or a independent convergence.”
I’m not aware of any follow-ups to Harpending and Eiler 2000. But, coincidentally or not, the oldest skull from South Africa, namely Hofmeyr at 36,000 PB shows the “strongest affinities with Upper Paleolithic Eurasians rather than recent, geographically proximate people.” (Grine et al. 2007). Modern San morphology is of Holocene age (Stynder et al. 2007. Early to mid-Holocene South African Later Stone Age human crania exhibit a distinctly Khoesan morphological pattern) and we can’t deduce skin color from a skull. So there’s no point-to-point comparison. But if the modern San are descendants of an ancient population represented by the Hofmeyer skull and this population was morphologically Eurasian and the modern San’s skin color falls within the variation found in (admittedly, southern) Eurasia (and middle America, if I may), then there’s a good chance the Hofmeyr population was also only very moderately dark, just like modern San are. This would make the San in your map representatives of the early African skin pigmentation type, which was later displaced by black populations with 24+ pigmentation range. This provides indirect support to Harpending and Eiler 2000.
Vexed by Red-Headed Conundrums
” Robinson et al. describe their use of mouse transgenics to demonstrate that the MC1R signaling pathway influences cancer risk via mechanisms in addition to pigmentation.”
Red hair is a dead loss as far as natural selection is concerned. ‘ Well it must confer an ability to synthesize more ‘vitamin’ D . Nope – Pigmentation and Vitamin D Metabolism in Caucasians: Low Vitamin D Serum Levels in Fair Skin Types in the UK Speaks for itself really, see also
Vitamin D Production after UVB Exposure Depends on Baseline Vitamin D and Total Cholesterol but Not on Skin Pigmentation “The increase in 25(OH)D level after UVB exposure was negatively correlated with baseline 25(OH)D level (P<0.001) and positively correlated with baseline total cholesterol level (P=0.005), but no significant correlations were found with constitutive or facultative skin pigmentation. In addition, we paired a dark-skinned group with a fair-skinned group according to baseline 25(OH)D levels and found no differences in 25(OH)D increase after identical UVB exposure"
I am pretty sure 'vitamin' D supplementation is particularly harmful to people with more pigmented skin
I don't think the switch to agricuture is the cause of Euro skin lightening myself but here is one about the influence of diet Meat consumption reduces the risk of nutritional rickets and osteomalacia.
“The mechanism by which meat reduces rachitic and osteomalacic risk is uncertain and appears independent of revised estimates of meat vitamin D content. ”
Re tanning did you know a tanning drug working by melanocyte-stimulating hormones produces sexual arousal . Melanotan II
” A clinical study published in 2000 of 20 men with psychogenic and organic erectile dysfunction conducted at the Section of Urology of The University of Arizona College of Medicine concluded, “that Melanotan II is a potent initiator of penile erection in men with erectile dysfunction.” [15] […] A January 2009 report in Wired Science described the site’s forum as having more than 50,000 posts primarily covering “Usage and Experimentation” by members with many covering detailed regimens on how to attain skin darkening and/or sexual function [with Melanotan II] improvements.[22] In May 2010 the Norwegian tabloid Verdens Gang published a story based upon a report by the Norwegian Pharmacy Association stating that 10,000 syringes are sold annually to Norwegian users of melanotan-1 and melanotan II” Melanotan.org
Rather than giving a lecture the discoverer of DNA structure should have conerered the market with a product – ‘ Dr. Watsons Bang On Pills – satisfaction guaranteed.’
Something I forgot to say is that I remember reading on some zoo website that chimps noticeably tan when they are allowed out again after the winter.
Razib, would you write a post on hair type evolution some time?
i would if i knew something. all i know is the emergence of EDAR in east asians.
Is is possible we non-africans inherited straight hair from Neanderthals? I would assume tighty curled hair is the ancestral condition.
i’ve seen speculation on that. if so, this would be a SNP/locus where selection was operative. there are non-african groups with “wooly” hair. melanesians for example.
Hairless solar panel? Does degree of baldness influence vitamin D status? No.
Some good news ‘vitamin’ D is good for (killing) pesky mammals Toxicity of cholecalciferol to rats in a multi-species bait
“readily eaten when presented as the sole food source or with other food, and was effective at killing rats in both situations […]Fortunately, the toxicity to birds is low”
enough links. we get the picture.
you are right, melanesians. But outside Africa, hair type is quite variable, while in Africa I am unaware of straight hair, so I would presume the selective pressure would occur there (not sure if the same would apply to Melanesians or Andaman, there it could be a matter of drift fixing a particular hair type (http://indiacurrentaffairs.org/wp-content/uploads/2010/06/jarawa.jpg).
Beards are obviously sexually dimorphic.
It is my opinion that heavy skin pigmentation is an anti-cancer mechanism, and that it originated long before the appearance of humans. It provided any Bilaterian lacking non-cellular outer covering (fur, scales, shells) with protection from cancer caused by environmental radiation, including UV. (Even polar bears have black noses, which they reportedly attempt to cover when stalking prey.)
If black is the default color of exposed skin because it protects against cancer
why did many humans lose that pigmentation? Once again, the answer is to
provide cancer protection — by permitting better absorption of Vitamin D.
Support for the later view is found in Garland et al’s 2006 paper “The Role of Vitamin D in Cancer Prevention” —
http://www.ncbi.nlm.nih.gov/pubmed/16380576
— where they examined lethal cancer rates for African Americans living in Northern US cities and found that rates for colon, breast, prostate and ovarian cancers were all significantly higher than for whites. They also exhibited significantly lower rates of Vitamin D absorption.
I didn’t know Blade Runner had such an effect on people as to quote from it, lol.
The SNP most associated with lighter skin pigmentation in Europeans is fixed in that population yet Europeans still vary in skin pigmentation.
It will be interesting to see in my country Australia whether there is a trend for people from Queensland, the high UV State with high skin cancer rates, becoming noticeably darker hued. Maybe what will actually happen is that Europeans who are darker and have greater abilities to darken under UV exposure will gradually move to that State, and become the dominant population without the actual fair skinned older European residents changing at all but just being gradually replaced.
I cannot see how vitamin availability is an issue. People ate meat, fish and vegetables centuries and millenia ago, and did not need exposure to UV light in order to make vitamins or the precursors of vitamins. I think the vitamin issue is rather hoary and not applicable to why Europeans or East Asians lightened their skin. The answer probably is rather simple. The mutations for light skin took off in a small group of Caucasoid people because dark skin was not needed as those people had cultural mechanisms to go around the need for darker skin like clothing, housing, foods eaten, and lost the ability to make dark skin. Those people just happened to also be expansive and militaristic and gradually imposed themselves and their languages on to the darker inhabitants of Europe. It probably happened less than 10,000 years ago, and coincided with the ability to digest lactose in raw milk which Mesolithic peoples of Europe totally lacked. Retention of lactase in adults is just about universal in NW Europe, but gradually decreases as you head south and southeast from NW Europe.