The timing of pigmentation lightening in Europeans
Sandra Belezal et al. 2012
The inverse correlation between skin pigmentation and latitude observed in human populations is thought to have been shaped by selective pressures favoring lighter skin in order to facilitate vitamin D synthesis in regions far from the equator. Several candidate genes for skin pigmentation have been shown to exhibit patterns of polymorphism that overlap the geospatial variation in skin color. However, little work has focused on estimating the timeframe over which skin pigmentation has changed and on the intensity of selection acting on different pigmentation genes. To provide a temporal framework for the evolution of lighter pigmentation, we used forward Monte Carlo simulations coupled with a rejection sampling algorithm to estimate the time of onset of selective sweeps and selection coefficients at four genes associated with this trait in Europeans: KITLG, TYRP1, SLC24A5, and SLC45A2. Using compound haplotype systems consisting of rapidly evolving microsatellites linked to one SNP in each gene, we estimate that the onset of the sweep shared by Europeans and East Asians at KITLG occurred about 30,000 years ago, after the out-of-Africa migration, while the selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 started much later, within the last 11,000-19,000 years, well after the first migrations of modern humans into Europe. We suggest that these patterns were influenced by recent increases in size of human populations, which favored the accumulation of advantageous variants at different loci.
Victor A. Canfield*,1, Arthur Berg†‡, Steven Peckins§,**, Steven M. Wentzel§,**, Khai Chung Ang§,**, Stephen Oppenheimer†† and Keith C. Cheng*,†,**,1
(excerpts)
Abstract
Divergent natural selection caused by differences in solar exposure has resulted in distinctive variations in skin color between human populations. The derived light skin color allele of the SLC24A5 gene, A111T, predominates in populations of Western Eurasian ancestry. To gain insight into when and where this mutation arose, we defined common haplotypes in the genomic region around SLC24A5 across diverse human populations and deduced phylogenetic relationships between them. Virtually all chromosomes carrying the A111T allele share a single 78-kb haplotype that we call C11, indicating that all instances of this mutation in human populations share a common origin. The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation. The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa. The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.
Human skin pigmentation varies widely between populations, generally decreasing with distance from the equator. According to a hypothesis proposed by Loomis (1967) and elaborated by Jablonski and Chaplin (2000), decreased exposure to solar ultraviolet at high latitudes produces a strong selective advantage for decreased skin pigmentation because it permits increased dermal vitamin D synthesis. Consistent with this hypothesis, in people of European descent, the pigmentation locus SLC24A5 shows strong evidence of selection (Lamason et al. 2005; Sabeti et al. 2007; Grossman et al. 2010) A specific coding polymorphism in this gene (rs1426654) is a major contributor to the pigmentation difference between Africans and Europeans (Lamason et al. 2005; Stokowski et al. 2007). Frequencies display strong population differentiation, with the derived light skin pigmentation allele (A111T) fixed or nearly so in all European populations and the ancestral allele predominant in sub-Saharan Africa and East Asia (Lamason et al. 2005; Norton et al. 2007). The genomic region of diminished sequence variation in Europeans spans ~150 kb (Lamason et al. 2005). To learn about the time and location of origin of the A111T mutation, we studied haplotypes in the region around SLC24A5 across world populations.
Results and Discussion
Global distribution of the A111T mutation in SLC24A5 The geographical distribution of the A111T allele of SLC24A5 (Norton et al. 2007), updated with the use of additional population samples (Figure 1), shows that A111T is nearly fixed in all of Europe and most of the Middle East, extending east to some populations in present-day Pakistan and north India. A111T shows a latitudinal decline toward the Equator, with high frequencies in Northern Africa (>0.80), intermediate (0.4−0.6) in Ethiopia and Somalia, and lower (<0.35) in sub-Saharan Africa. This pattern is broadly consistent with strong positive selection for decreased skin pigmentation throughout Europe. There is a cline of decreasing frequency of A111T in indigenous populations east of approximately longitude 75° in Central Asia, with near-absence in East Asia, Oceania, and the Americas. The extent to which the spread of A111T to the east has been inhibited by the absence of substantial eastward population migrations postdating its origin or by the presence of other loci responsible for decreased skin pigmentation in East Asia is presently unclear.
Can we date the A111T mutation? The preceding analysis is consistent with a wide range of possible dates for the origin of A111T, including the period before the initial colonization of Europe by anatomically modern humans >40 thousand years ago (kya) (Mellars 2006). An estimate for the date of origin of A111T based on microsatellites (Beleza et al. 2012) places the origin at 19 kya (95% confidence interval 6−38 kya), for a dominant model, or 11 kya (95% confidence interval 1−56 kya), for a more plausible additive model. To create an independent estimate, we applied a molecular clock approach to 1000 Genomes data by using the combined C and D subregions. Because proportions of different classes of nucleotide substitutions in the C11 + D4 variants and in the human-chimpanzee alignment are not significantly different (χ2 = 4.42, df = 5, P = 0.49; Table S15), we combined these classes for analysis. For the combined population samples, before making corrections for undercounts in the source data, we obtained an estimate of 7.8 kya for the most recent common ancestor of the C11 + D4 haplotype combination (Table 3). Corresponding 95% confidence limits are 4.8−12.2 kya, whereas uncorrected estimates derived from individual European samples or the combined New World samples (also of European origin) ranged from 5.2 to 10.4 kya (Table 3). These values are clearly underestimates as a result of low sequence depth (1000 Genomes Project Consortium 2012). Adjustment for undercounting is substantial, increasing the estimated age for the combined samples to 12.4 (95% confidence interval 7.6−19.2) kya. If mutation rates in recent humans are lower than predicted from the human-chimpanzee divergence (Scally and Durbin 2012), true ages will be even older. Our adjusted dates overlap those previously reported (Beleza et al. 2012) and are also consistent with the lower limit for the origin of A111T set by the finding that the Alpine “iceman” dated to 5.3 kya was homozygous for this variant (Keller et al. 2012). This date range implies an origin clearly preceding the Neolithic transition in Europe. These dates are later than the initial colonization of Europe but are consistent with an A111T origin before or after post-glacial population expansions.
Obtaining a better date for the origin of the A111T mutation is challenged by a number of issues. Our approach provides a date for the common ancestor of the sampled C11-D4−containing chromosomes. This common ancestor may be significantly younger than the origin of A111T if positive selection was initially weak or nonexistent, or if there was a subsequent bottleneck. In addition, our date estimation relies on samples of predominantly European origin. Inclusion of Middle Eastern or South Asian examples would be expected to yield a more representative result. Incomplete detection of rare variants is a limitation that can be improved with higher-coverage sequencing. More direct limits on the age of A111T could result from genotyping of ancient human DNA.
Where did C11 originate? The precursors to C11, haplotypes C3 and C10, are common in East Asia and the New World (Figure S5), but the distribution of C11 indicates that these locations are not likely sites for the origin of C11 or its immediate precursor. Similarly, B6 not associated with C11 is distributed widely in East Asia and the New World (data not shown). The paucity of C3 and C10 among existing African haplotypes suggests that both events leading to the origin of C11 took place outside this continent. Our dating for this haplotype is consistent with a non-African origin. The most likely location for the origin of C11 is, therefore, within the region in which it is fixed or nearly so. As both models for the origin of C11 imply that C3 and C10 were present in ancestors of Europeans, the observed and inferred distributions of these autosomal haplotypes are consistent with the single-out-of-Africa hypothesis derived using uniparental markers (Oppenheimer 2003; Macaulay et al. 2005).
The presence in Africa of A111T only in association with C11 indicates that the observed examples, like those of C3 and C10, resulted from introduction into the continent subsequent to origin. The low diversity of B-region haplotypes associated with C11 in MKK, equivalent to that seen in European samples (Figure 5 and File S2) supports this view because those individuals live among a majority population with high B-region diversity. Although too few African C11 sequences have been determined to draw strong conclusions, those available from the 1000 Genomes Project show no evidence of greater age in the form of greater SNP diversity than the European examples. It should be noted that the relatively high abundance of A111T in several equatorial East African samples indicates the absence of sustained strong negative selection against this allele at low latitudes.
Although a non-African origin for C11 is clear, near fixation of this haplotype over a wide geographical region prevents strong inferences regarding a precise location of origin. Existing data are consistent with a model in which the C11 precursor did not extend outside the geographical region in which C11 is now nearly fixed, a conclusion subject to limited haplotype sampling in some neighboring regions, such as India. With sufficiently strong positive selection for C11, it is possible that this haplotype could have originated anywhere within its current range and spread via local migration. However, selection acting in concert with major population migrations would have facilitated a much more rapid dispersal. Archeological, mitochondrial, and Y-chromosomal data suggest involvement of multiple dispersals in shaping the current populations of Europe and the Middle East (Soares et al. 2010). Because A111T is far from fixation in most Indian samples (Table S1), the high diversity of B-region haplotypes associated with C11 in the GIH sample may be the result of prolonged recombination rather than early arrival of A111T. In fact, the decrease in frequency of A111T to the east of Pakistan suggests that C11 originated farther to the west and after the initial genetic split between western and eastern Eurasians. On this basis, we hold the view that an origin of C11 in the Middle East, broadly defined, is most likely.
Traditionally, uniparental markers have been used for the construction of phylogenetic trees due to the absence of recombination. Here, autosomal haplotypes and the characterization of recombination events have helped us to define the genotypic phylogeny of a genomic region known to have been subject to strong natural selection. Such an approach to studying the phylogeny of autosomal regions may also be useful for the study of other loci under selection in humans and in other organisms.
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The timing of pigmentation lightening in Europeans
Sandra Belezal et al. 2012
The inverse correlation between skin pigmentation and latitude observed in human populations is thought to have been shaped by selective pressures favoring lighter skin in order to facilitate vitamin D synthesis in regions far from the equator. Several candidate genes for skin pigmentation have been shown to exhibit patterns of polymorphism that overlap the geospatial variation in skin color. However, little work has focused on estimating the timeframe over which skin pigmentation has changed and on the intensity of selection acting on different pigmentation genes.
The Vitamin D nonsense was debunked years ago, but the Albinos are still working it like it was real.
Why - they have nowhere else to go. The alternative is to admit the truth, that they ARE Albinos.
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The point is that the protective role against UV rays was not needed by those who migrated to areas where UV rays were less invasive. Such groups eventually lost their pigmentation according to the principle of desuetude. In other words: use it of lose it.
The loss of pigmentation followed the principle of a kind of relativism given the general rule of less UV rays then less protective pigmentation--grosso modo. Examples: NE Asians and SE Asians. Northern Europeans and Southern Europeans.
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quote:Originally posted by lamin: The point is that the protective role against UV rays was not needed by those who migrated to areas where UV rays were less invasive. Such groups eventually lost their pigmentation according to the principle of desuetude. In other words: use it of lose it.
The loss of pigmentation followed the principle of a kind of relativism given the general rule of less UV rays then less protective pigmentation--grosso modo. Examples: NE Asians and SE Asians. Northern Europeans and Southern Europeans.
Come-on lamin, are you thinking that anyone still believes that you are a Black African?
Silly fool, they're not that stupid.
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LOL. Cartesian answer: I do, at least. As is well known Mike, you are a riot--and an amusing one.
But seriously, what does a commonsense theory as to how pigmentation indices track the intensity of impacting UV rays have to do with the origins of the theorist?
I guess-LOL--it goes back to your amusing thesis that Africans are simple-minded. LOL squared--I am not--so fill in the blanks from your fevered and upside-down mind. There's still time for the men-in-white-coats Mike.
This Guardian article has some interesting comments on your favourite racial term. Maybe you can drop a line to Lupita.
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Mike, If--to use use your racial appellate--"Albinos" suffer from a biological disability how do you explain the fact that other humans are so obsessed with imitating their aesthetic standards--of which "colour" is most important--to the point of absurdity?
quote:Originally posted by lamin: Mike, If--to use use your racial appellate--"Albinos" suffer from a biological disability how do you explain the fact that other humans are so obsessed with imitating their aesthetic standards--of which "colour" is most important--to the point of absurdity?
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But most others are in the same boat Mike. LOL. Asians--all over: India, China, and other countries. It is rampant in the Americas too Mike--from Baffin Bay down to Tierra del Fuego.
So as a--LOL, "Black European"-- explain why your kin Europeans have been so empowered.
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posted
Mike, Check your reading comprehension skills. The piece from Ghana is not about Ghana per se. Akon(born in the U.S. to Senegalese parents) and Wizkind are both African Americans and traveled to Ghana to record for U.S. consumption.
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^Culturally African is Culturally African regardless of where they are.
See there Albino boy, I got you braggin on your people.
The fact is that it is normal for the "Almost" Albino, mulatto races like Mongols to want to be closer to their recent creators.
What is surprising is how many of them reject your people and side with Blacks - their originators.
And what are you going to do with the Turk and Arab mulattoes? Seems your relationship with the Albino Khazars has caused a real problem with them.
The why of it is quite simple, POWER! The weak-minded like to identify with the powerful, and right now your people have the best weapons.
This condition has lasted for about 200-300 years. That is not really very long you know, but already the contraction has started.
Want to sh1t your pants? Compare the world of today, with the world as it was in 1900 in regards to Albino power and possessions.
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. I knew about Akon but not Wizkid. Well, both have imbibed American and Western aesthetic standards which proves my point--that Mike's "albinos" have the colour thing all wrapped up.
The question is why are such people--defective "albinos" in Mike's eyes--so influential world-wide especially with people who are non-albinos. Why do the non-albinos allow this?
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quote:Originally posted by lamin: The question is why are such people--defective "albinos" in Mike's eyes--so influential world-wide especially with people who are non-albinos. Why do the non-albinos allow this?
I wish Cass was here so he could respond to your que. You want desperately to have someone say "Because White people are better". Well you're just going to have to say it yourself. Go ahead, it will make you feel better, and it will convince the last Negro that you are an Albino. Some of them simply won't believe anything unless an Albino tells them so.
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quote:Originally posted by Mike111: I wish Cass was here so he could respond to your que. You want desperately to have someone say "Because White people are better". Well you're just going to have to say it yourself. Go ahead, it will make you feel better, and it will convince the last Negro that you are an Albino. Some of them simply won't believe anything unless an Albino tells them so. [/QB]
This is Mike's message to himself. He shits on Africans and tries to convince American blacks they were European. Subliminally "Because White people are better".
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quote:Originally posted by Mike111: The fact is that it is normal for the "Almost" Albino, mulatto races like Mongols to want to be closer to their recent creators.
What is surprising is how many of them reject your people and side with Blacks - their originators.
And what are you going to do with the Turk and Arab mulattoes? Seems your relationship with the Albino Khazars has caused a real problem with them.
The why of it is quite simple, POWER! The weak-minded like to identify with the powerful, and right now your people have the best weapons.
This condition has lasted for about 200-300 years. That is not really very long you know, but already the contraction has started.
Want to sh1t your pants? Compare the world of today, with the world as it was in 1900 in regards to Albino power and possessions.
Japanese airline sorry over 'racist' commercial
Tokyo (AFP) - Japanese carrier All Nippon Airways (ANA) said Monday it was modifying a TV commercial after apologising to customers who complained it used racist stereotyping, but insisted they had meant no offence.
ANA started airing the new 30-second television advertisement on Saturday, aimed at promoting its beefed up schedule of international flights from Tokyo's Haneda airport in March.
In the commercial, two Japanese men in ANA uniform discuss in English how they might boost the image of the airline as an international carrier.
One of them says: "Let's change the image of Japanese people." "Sure," replies the other, who is now wearing a blonde wig and an improbably long rubber nose.
White westerners are often believed in Japan to have big noses, blue eyes and blonde hair, characteristics generally thought desirable among Japanese.
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^Some may be moved to ask "how is it that you know these things". Sufficed to say that I do, and leave it at that.
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