Convergent evolution in skin color – part n

Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians:

…these results point to the importance of several genes in shaping the pigmentation phenotype and a complex evolutionary history involving strong selection. Polymorphisms in two genes, ASIP and OCA2, may play a shared role in shaping light and dark pigmentation across the globe while SLC24A5, MATP, and TYR have a predominant role in the evolution of light skin in Europeans but not in East Asians. These findings support a case for the recent convergent evolution of a lighter pigmentation phenotype in Europeans and East Asians.

Related: A post on SLC24A5 and one on OCA2. Earlier commentary on the lead author’s work (a correction from her). Convergent evolution on skin color.
Skin color is a very salient trait, we notice it pretty easily. So I believe it is a very good thing in terms of public understanding of the postgenomic era that this character is now being elucidated on a fine grained scale. Within 5-10 years I predict this will be a rather uninteresting trait because we’ll have a good grip on 95% of the variation between and within populations.
Via Dienekes.
Addendum: After I initially drafted this post I found this paper which isolates the DCT locus as implicated in light skin in East Asias, but not Europeans. The science here is pretty fast, loci build up as I write!

Human Genetics round-up

The new issue of Human Genetics has three articles that may interest GNXP readers. A study on the genetics of height looked at two groups of normal Japanese males (i.e., no cases of Marfan Syndrome), one tall (+2 SD; N =219) and one average (+/- 1 SD; N = 209). A SNP in the FBN1 gene was significantly overrepresented in the tall group, and the number of copies was significantly positively correlated with height within each group too. The mutation doesn’t result in an amino acid change.

A study on the genetics of skin color variation looked at loci from Europeans, Africans, and Chinese (HapMap and Perlegen data) and performed tests of Fst (a measure of within-group vs. between-group variation) and decay of haplotype homozygosity (a measure of positive selection similar to the integrated Haplotype Score statistic used in the Voight et al 2006 study). They largely confirmed previous findings, but they also discovered a new locus involved in skin color differences between Chinese and non-Chinese populations, DCT (p. 617, all square brackets mine):

The core SNP was chosen as the SNP within the DCT gene with the most extreme riEHH value [i.e., their measure of positive selection]. This SNP, rs2031526, has a riEHH value within the top 1.7% of the riEHH distribution and has Fst values within the top 0.6 and 0.3% of the Afr–Chn and Eur–Chn HapMap Fst distributions respectively (AC Fst = 0.718; EC Fst = 0.607). Figure 2 demonstrates that the derived A allele in the Chinese is found on a high frequency haplotype with long-range homozygosity, while the Europeans and Africans show substantial breakdown of homozygosity over the same physical distance on the high frequency, ancestral G allele haplotype. Similar results were obtained when other core SNPs with extreme riEHH values from the DCT gene were used (data not shown). Thus, the DCT gene harbors a signature of local positive selection in Chinese using both Fst and LRH-based tests [LRH = Long-Range Haplotype], and is therefore a potential candidate to account for the differences in skin pigmentation between the Chinese and other human populations.

So here we have yet another example of different populations converging on more or less the same phenotype (lightish skin) via somewhat different evolutionary genetic paths. UPDATE: Dienekes links to another new study of convergent evolution of skin color in Europeans and East Asians.

Lastly, a study on the make-up of neutral portions of the African-American genome examined how much Europeans and Africans have contributed. The gist, including numbers, is contained in the abstract. In brief, they found sex-biased gene flow: European male – African female pairings are primarily responsible for admixture, a pattern which the authors note is also common in Native American – European admixed populations in the Americas. And apropos of a recent query at Razib’s ScienceBlog, here’s what they found on the Native American contribution to African-Americans:

A small contribution from Native American and Asian populations to the founding of African Americans has previously been reported (Parra et al. 2001; Smith et al. 2004; Reiner et al. 2005). In those analyses, the genetic contribution from Native Americans and Asians in individuals is at most 2.6% and generally falls between 1 and 2%. Reiner et al. (2005) showed that there was a greater likelihood that the African American population descended from two populations (as opposed to one, three, or four) which was consistent with our own STRUCTURE analysis, where two populations fit the data best. These analyses showed that it was not necessary to include Native Americans and Asians in the founder populations. Our Y chromosome analysis also supported that there was little contribution from Native Americans since the predominant Y haplogroups found in Native Americans P(xR) were not observed in this sample of African Americans.

Gay sheep, forbidden science?

Science told: hands off gay sheep:

Scientists are conducting experiments to change the sexuality of “gay” sheep in a programme that critics fear could pave the way for breeding out homosexuality in humans.

You can read the whole article yourself. Randall Parker has been saying for years that genetic engineering will accentuate human differences as parents will choose to invest in alternative enhancements with their finite dollars. The vectors may remain the same, but the magnitudes could increase, as religious parents breed super-religious offspring, secular parents start spawning born atheists, and what not. There is a pretty obvious and straightforward way for homosexuals to calm down their fears that straight parents will genetically engineer out their orientation (ergo, community): breed gay babies. If scientists can understand homosexuality well enough to “cure” it, then they could certainly turn fetuses gay.

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2006 Darwin Awards

So, they are here. Moral of story: Obey the laws of physics kids! With no further ado – the winners:

Hammer of Doom: A Brazil man tried to disassemble a missile by car, and by sledgehammer…

Copper Kite String: Precautions must be taken to avoid sudden electrocution…

High on Life: Four feet found protruding from a helium advertising balloon…

Score for Goliath: A mythical giant felled by a humble slingshot: a modern speargun versus an underwater leviathan…

Faithful flotation: a pastor who could literally walk on water…

Stubbed out: If a doctor advises that the one thing you must avoid is an open flame, most people ould not strike a match…

Star Wars: Luke vs. Darth Vader, with light sabres made from fluorescent tubes and gasoline…

And if you didn’t win this year, you have all of 2007 to make a go for it! Happy new year!

Appendix: Darwin Awards 2006 Demographics:

England – 3 winners
Florida – 3 winners
Gabon – 1 winner
Belize – 1 winner
Brazil – 1 winner

Average winner age: 29 years

Winner gender:
8 men
1 woman

I'm brown dammit!

I was in a public place the other day and some small Arab-looking guy was talking really loudly in what sounded like Arabic on the phone. I was reading a book and eventually the guy was like, “Hey, do you speak Arabic?” I was like, “No.” And he replied, “Do you speak Mexican?” And I replied, “Uh, no.” So he goes on, “Where you from?” I reply, “My family is from Bangladesh.” His response? “Is that India?” I say, “Kind of.” “I was born in India. Abu Sabbas. You know Abu Sabbas?” I replied, “No.” He continued, “It’s north of Napali. You know Napali?” I didn’t, but I smiled and nodded. “My father was working in India. I’m from Israel.” Finally he left me alone.

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Speech and motor feedback

I am really enjoying Buzsaki’s book. The chapter I’m in now is about perturbations of the intrinsic network activity of the nervous system. He examines some of the earliest developing examples of intrinsic neural activity: self-generated activities that help organize the retina to visual cortex mapping and the twitches and kicks of the developing fetus. He is building the point that a nervous system that cannot generate motor output cannot really perceive the world in a meaningful way.

“Only through movement can distances be measured and incorporated into our sensory scheme. For an immobile observer, direction, distance, and location of sensory information are incomprehensible and meaningless concepts.”

At another level of analysis he notes that a baby’s babbles are self-organized output that is then perturbed by parents via their reaction to babbles that chance upon parts of their own words. Perturbation can reshape the weights of the network and organize them in terms of experience.

It made me wonder about the FOXP2 story. There has been some debate about where exactly the deficit lies in the KE family, the family that has a heritable language disorder. Some have suggested that the main effect of FOXP2 loss is to reduce fine motor control of the face and jaw (and tongue?) that would allow for speech production. I wonder if this motor loss might propagate backwards to a more general loss of language functions. Buzsaki covers some studies in which developing rats are immobilized in one way or the other. The inability to produce motor outputs disallows the creation of coherent sensory maps, presumably because the spontaneous motor programs activate sets of muscles that cause corresponding sets of sensory receptors to be co-activated. At a coarse level, if you move your arm, it might run into something and now the parts of your arm that are near each other get to make coherent sensory input. Cells that fire together, wire together and a somatotopic sensory map is born.

So I think you can see the analogy I am imagining. Since the fine motor control output in KE family members is dysfunctional, the fine sensory perceptions that motor control should map to are also disturbed. I suppose this is one way that a developmental defect that leads to a specific motor problem could affect perception of language as well. Thinking this way would probably still require some sort of magic trick where the sensory patterning fails fairly deep in the hierarchy of language perception processing.

I wanted to make sure I was right about the motor dispute, so I pulled out the latest review. No discussion of intrinsic oscillations and language development, but in case y’all want an update here are some key areas researchers are focusing on:

1) Finding other natural mutations in the FOXP2 gene that lead to a phenotype similar to the original KE family.

2) Using Chromatin-Immunoprecipitation Chip (ChIP-Chip, I dread when they come up with a version of this specifically for our primate cousins) to discover molecular targets downstream of FOXP2. FOXP2 is a transcription factor, which means it binds to DNA. ChIP-Chip allows you to lock the FOXP2 onto whatever DNA it is associated with at the moment, pull those specific pieces of DNA out of solution, and see which pieces of DNA you pulled out by seeing if they stick to other chunks of DNA of which you know the identity.

3) Pursuing the observation that FOXP2 is actively regulated (they make more or less of the protein) during different types of vocal behavior in birds.

4) Pursuing the recent discovery that mice make ultrasonic vocalizations. If we can draw clear analogies between these vocalizations and birdsong or language then we can bring to bear the full arsenal of transgenic manipulations available in the mouse model.

Maybe this review was biased towards certain a certain approach, but I’m not seeing much here in terms of further characterizing the developmental phenotype associated with FOXP2 mutations. Is it not ethical or something? Did the KE family stop breeding? I think it might be worth taking a look at their very early EEGs. Finding a network-level signature for the disorder could provide an intermediate level phenotype and obviate the need to justify analogies between birdsong, mouse vocalizations, and human speech.

Bailey vs. Ann Althouse

Ron Bailey and Ann Althouse get into it over the Frank-Meyer-is-racist-issue. Virginia Postrel defends Ron. No one who reads this blog will be surprised with my general sympathy for Ron in this matter, in part because I agree with his analysis on the merits (even removing the new data he brings to the table), and in part because there is a non-trivial overlap in our political worldviews. That being said, I don’t want to make Ann into the devil, my main exposure to her is via Bloggingheads.TV, and she seems like a nice enough person. I empathize with her discomfort in the various political camps which have coalesced on the American scene. Since Ann is a law professor at the University of Wisconsin I don’t doubt that she has some g-mojo. Nevertheless, my own impression of Ann is that she is somewhat thin in her exposure to various flavors of the American ideological spectrum (e.g., her general pose is the heterodox “right-winger” among ultra-Liberals). At one point in this Bloggingheads.TV dialogue with Jim Pinkerton Ann confronts the fact that Jim was an Iraq War Skeptic from a Right-realist perspective (I would point you to a segment, but I don’t recall with confidence which one!). That such beasts exist seem to be clearly something of a surprise to her from what I could tell by her facial expression (ironic, considering her own heterodox posturing). Ann’s own experience had conditioned her to simply connect anti-War sentiment with Leftism, and here she found herself faced with a reality-based conservative. This was not a critique of the Iraq War in language she understood, that is, the lexicon of social justice and utopian idealism, it was a hard-headed and cynical take on the Darwinian competition between nations and the right and wrong choices which emerge out of the utilitarian calculus.

What I’m trying to say is that Ann Althouse has a finite set of mental schemas. As an A-list blogger and Iraq War hawk who is generally socially liberal without the Maoist Puritanism (e.g., she isn’t an ideological feminist) she is preloaded for a particular sort of discourse based on a particular range of common assumptions and disjunctions. A mild paleo-conservative like Jim Pinkerton is a species which Ann doesn’t have any defenses or offenses against, and so their “discussion” was somewhat like watching two ships pass in the night. I am bringing this all up because I think Ann was faced with the same issues at the Liberty Conference. I’ve been to CATO events. There are a wide range of characters, and I mean characters, who show up, from fat cat oil speculators to mainstream journalists to the libertarian math professor from a fundamentalist college. You get all sorts of oddballs as you shift several deviations away from the norm in the American political spectrum, and various questions normally not entertained are now fair game. Again, I suspect Ann was operating in a domain where her mental schemas were ill-fitted, and she obviously couldn’t get her bearings. Not only was she not steeped in the abstruse intellectual history of the American political Right before 1964, when conservatives, whether traditionalists like Russell Kirk or libertarians such as Frank Meyer, were in the wilderness and excluded from access to the establishment, but I also suspect that the sea of peculiar background assumptions common to “professional libertarians” was simply lost on her. Discussions about the right to discriminate may seem very bizarre, immoral even, when extracted outside of the context of a matrix of assumptions about liberty, justice and freedom, in other words, what makes the Good Society. Ann might have seen naked dispassion and a cruel lack of historical sensibility, but I suspect that her unfamiliarity with the libertarian subculture, its working assumptions, rendered the debates even more other-worldly than they should have been.

Which leaves me to the final point which I want to reiterate, and that is the role of intellectuals in transgressing manners and mores of society. Humans are social creatures and we are bound by particular conventions, whether it be cultural or biologically informed (or, more usually a synthesis). Men walking around with their penises hanging out of their pants in public would be problematic even though a penis is just a collection of atoms. Nevertheless, in the context of modern performance art it is perhaps more understandable. Whatever you think of art, for most humans the goals of inducing awe, exhibiting virtuosity, or shocking and disgusting, are easily attained. Many artists are good at what they do. But I hold that intellectuals, those who peddel ideas, should be no different in the proper context. We should go where conventional society does not go, explore, entertain, and discuss ideas which are not conventionally discussed. GNXP has done quite a bit of that over the years, and I myself am known personally to many of my friends as the sort that causes a collective dropping of the jaws becaues of a flip assertion or question. This does not mean that intellectual discourse is proper for normal social intercourse, but, I think it has a role to play in modern post-Enlightenment societies. Though Descartes was a Roman Catholic, he entertained the possibility of the non-existence of God (only to later to “prove” His existence). This was blasphemy to many contemporaries, but I believe that Descartes is the archetype of the modern intellectual, taking logic where normal reason dictates that you stop.

As I noted before I believe emotion plays a role in human affairs, and am willing to grant that it is the ends of life. That being said, just as normal social interaction is bounded by a modicum of custom, manners and etiquette, so intellectual discourse must be characterized by emotional detachment for it to truly be effective. Emotions are a powerful tool. When you see another human cry you feel for them, you empathize, and they are humanized. All of a sudden the dance with ideas seems less important and we are brought back to normal convential sociality. Anger, happiness, all these are the ends of life, but they are also tools and weapons of interpersonal manipulation. Ron recounts that Ann broke down and cried at one point. This to me is the real “money shot,” I’ve made people cry or break down myself because of the questions I asked and where I went. It happens. But if you fancy yourself someone of some intellectual daring, you must go where the conventional do not dare, where they cannot. Someone has to.

Of course a meeting of libertarians is bounded by their own rules and bounds of discourse. But when you go into the house of a neighbor with whom you are not familiar you need to be careful to respect their ways and habits even if you are shocked and appalled (barring abominations like child sacrifice!). Many libertarians don’t live in reality, they aren’t grounded, and their fantasies of the minimal state are more of a “Secondary World” than Middle Earth ever was, but, they have a role to play in the ecology of ideas. The fact that they exist, and that they are who they are, is no crime against humanity.

I’ve posted on this topic more than once in part because it offers us lessons for this blog “community.” It is certainly bounded by rules and conventions, but it is pretty diverse in its own way. The main lesson is that if things posted by the authors of this weblog (not in the comment boxes!) make you want to c
ry you might withdraw and find some place more congenial. Questions of how the world should be are important, Liberty Conferences are part of the universe, but here I would rather focus on how the world is.

(now you hot ones can go back to your science fiction)

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The reality of epistasis

Earlier this week I sketched out the general theoretical basis for not denying unexpected deviations from expectation, so to speak, when it comes to quantitatve traits. The main issue is that varying genetic backgrounds leave unaccounted for gene-gene interactions, and so our predictions when two populations are crossed maybe confounded (within a population ceteris paribus is far more likely to hold). In any case, I thought I’d give you two obvious examples from humans.
First, in 2005 Helgadottir et. al. found that African Americans are at greater risk for myocardial infarction vis-a-vis their parental populatons, Africans and Europeans, because of a combination of alleles of one population against the genetic background of the other (genetic and historial studies tend to converge upon a median admixture proportion of 20-25% European and 75-80% African in black Americans, with variance of course between subpopulations and families). Since genomic data suggest that the Out of Africa event and expansion into Eurasia induced multiple selective sweeps in populations which left the ur-heimat I would not be surprised if more studies like this emerge which suggest decreases in fitness because of problematic genetic combinations. As I’ve said before, racial admixture increases variation and genetic diversity, and I see no reason why this would not result in an increase in the proportion of those who are far more and less fit than is in the norm in major racial groups (corrected for some possible masking of deleterious recessives and so hybrid vigor). The Neandertal-modern introgression story was in part an illustration of how novel genetic combinations may have unexpected positive benefits. Though on average I think racial admixture is probably a wash for most populations I do believe that the likelihood for the arrival of a genuine Übermensch will increase as powerful assortative mating across a few valued characters proceeds apace.
A second example of epistasis is the Pakistani family that can’t feel pain. Note:

The SCN9A gene is active both in nerves that mediate pain and in those of the sympathetic nervous system, which controls vital bodily functions like heart rate. But for reasons that are not yet understood, the affected members of the Pakistani families had no symptoms of a disordered sympathetic nervous system, such as irregular heart rate, and seemed entirely normal apart from the occasional self-inflicted damage caused by their inability to feel pain.

Though we don’t know the precise genetic reason for this family’s insulation from the normal debilitations which follow from their condition, theoretically I think it is very likely to be a modifier gene which lurks in the clan’s genetic background and is not generally present in others who exhibit this mutation. If individual X carries mutation Y which should result in a decrement in fitness Z, but does not, I think an a priori plausible hypothesis is that there are other loci which mask the deleterious affects. Many single locus Mendelian diseases with moderate or low penetrance may simply be polygenic in nature and exhibit variation which is cryptic because those without the ailment aren’t tested for the mutation.

"Western ideals" of beauty look to the South

Following a recent suggestion, I was just checking out the Lacey Chabert spread at Maxim’s website, where I noticed a hottie ranking of theirs called 2006 Hot 100. Granted, individuals may quibble with aspects of the ranking, but it is presumably the product of many minds with diverse tastes in female appearance, so it’s objective enough to get a rough idea of what young American guys find attractive. There is a bias toward current “it” girls, but I doubt the racial variation would be changed much if we looked at “it” girls from five years ago. And because Maxim panders to the lowest common denominator of male interests, it would have to be suicidal to feature a significantly lower proportion of women of a certain appearance if red-blooded males truly desired to oogle women of that appearance (e.g., if it featured few blondes when the average potential reader was blonde-crazy). We can thus test whether the ranking actively glorifies or passively reflects a desire for Nordic features, whose hegemony is a common canard in discussions about standards of beauty and ethnic variation in appearance.

Top 10 by hair color and race below the fold:

10 Christina Milian. Brunette. Cuban.
9 Keira Knightley. Brunette. Scottish, Irish, English.
8 Kate Bosworth. Brunette. English?
7 Cameron Diaz. Blonde. Cuban, English, German, Cherokee.
6 Scarlett Johansson. Blonde. Ashkenazi Jewish, Danish.
5 Stacy Keibler. Blonde. German?
4 Angelina Jolie. Brunette. French, Iroquois, Czech.
3 Lindsay Lohan. Auburn. Italian, Irish.
2 Jessica Alba. Brunette. Mexican, Danish, French.
1 Eva Longoria. Brunette. Mexican.

If Nordic looks reigned supreme, we should expect to see more blondes than 3 of 10, which appears at or below expectation for a majority Northern European country, judging by the graphic at the Wikipedia entry on hair color. On an absolute level, there’s no shortage of blondes, so if the media devils really wanted push the “blondes are more beautiful” idea, they could’ve easily packed the top 10 with them. The racial backgrounds underrepresent the average Northern European phenotype: since Keira Knightley and Lindsay Lohan have the “Black Scottish / Irish” look, that leaves just Stacy Keibler, Kate Bosworth, and Scarlett Johansson who look Nordic.

Turning to the entire 100 (go to the bottom for more detail on the following numbers), those of African and East Asian descent are not well represented. In fact, only 2 of 100 are East Asian, and they rank very low. That’s at expectation, since Americans of Korean, Chinese, and Japanese descent make up 2.1% of the population. Vanessa Minnillo ranks highly at 15, but she’s mixed Filipina / Pacific Islander and Irish-Italian, not East Asian. Overall, 3 of 100 are African-American. This is quite below their percentage of 13.7% in the general population, and none score very highly. Finally, 9 of 100 have partial African or East Asian ancestry, and they are fairly evenly distributed in the ranking from 90 to 22.

Latin Americans, though, do pretty well. I make no claim about what their neutral markers would tell us about the individuals’ racial backgrounds, and I therefore included a couple “half”-Latin Americans for the same reason I included “full” Latin Americans. The point is simply to show how a mixed-race, decidedly non-Nordic group does. There are 14 of 100 who are Latin American (including Daniella Alonso, who I also put in the “part-East Asian” group), which appears at expectation since Hispanics make up 14.1% of the US population as of 2004. However, the Hispanic population surged in the US in the wake of the 1986 amnesty, and since the women in the ranking are mostly in their 20s or older, the Hispanic percentage among their age group is surely lower than 14.1%. So, Hispanics are likely somewhat overrepresented. Furthermore, the lowest-ranking Hispanic clocks in at 71, and 4 of the top 10 are Hispanic, including 1 and 2. The strong performance of Latin Americans in international beauty pageants is nothing new, so one wonders why the Nordic hegemony idea has persisted into the second half of the 20th C. (In this respect, it is like the idea that the WASPs are keeping the Sicilians and Semites under their golf cleat — perhaps true awhile ago, but clearly false for decades.)

The numbers:

East Asians

98 Yunjin Kim
93 Grace Park


82 Vanessa Simmons
77 Ciara
43 Gabrielle Union

Interracials of African or E.Asian background

90 Chilli (1/2 Af-Am, 1/2 East Indian)
88 Tila Tequila (3/4 Vietnamese, 1/4 French)
84 Amerie (1/2 Af-Am, 1/2 Korean)
79 Halle Berry (1/2 Af-Am, 1/2 English)
53 Moon Bloodgood (Korean, Irish, Dutch)
45 Beyonce (1/2 Af-Am, 1/2 Louisiana Creole)
41 Daniella Alonso (1/2 Puerto Rican, 1/2 Japanese-Peruvian)
40 Alicia Keys (1/2 Irish-Italian, 1/2 Jamaican)
22 Mariah Carey (1/2 Afro-Venezuelan, 1/2 Irish)


71 Roselyn Sanchez
68 Cinthia Moura
60 Shakira
59 Jordana Brewster
55 Vanessa Marcil
41 Daniella Alonso
39 Nadine Velazquez
27 Eva Mendes
19 Jamie-Lynn Sigler
16 Christina Aguilera
10 Christina Milian
7 Cameron Diaz
2 Jessica Alba
1 Eva Longoria

From the archives: see here & links therein.
Update: changed the info on Chilli, Beyonce, and Vanessa Minnillo.

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