Category Archives: pigmentation

Central European farmers, but also Danish "hunter-gatherers" had domestic pigs

It’s often difficult to discern in the archaeological record wild boar remains from those of domestic pigs. Luckily archaeogenetics can solve the problem, sometimes producing striking results.
Ben Krause-Kyora et al., Use of domesticated pigs by Mesolithic hunter-gatherers in northwestern Europe. Nature Communications 2013. Open accessLINK [doi:10.1038/ncomms3348]


Mesolithic populations throughout Europe used diverse resource exploitation strategies that focused heavily on collecting and hunting wild prey. Between 5500 and 4200 cal BC, agriculturalists migrated into northwestern Europe bringing a suite of Neolithic technologies including domesticated animals. Here we investigate to what extent Mesolithic Ertebølle communities in northern Germany had access to domestic pigs, possibly through contact with neighbouring Neolithic agricultural groups. We employ a multidisciplinary approach, applying sequencing of ancient mitochondrial and nuclear DNA (coat colour-coding gene MC1R) as well as traditional and geometric morphometric (molar size and shape) analyses in Sus specimens from 17 Neolithic and Ertebølle sites. Our data from 63 ancient pig specimens show that Ertebølle hunter-gatherers acquired domestic pigs of varying size and coat colour that had both Near Eastern and European mitochondrial DNA ancestry. Our results also reveal that domestic pigs were present in the region ~500 years earlier than previously demonstrated.

The most striking result is surely not the demonstration of pigs being in Central Europe a few centuries than previously confirmed but that Ertebølle hunter-gatherers of Denmark had them as well, quite radically casting doubt on their status as hunter-gatherers and placing them fully in the Neolithic context, even still rather marginal and peripheral. 
Figure 1: Map depicting the location of the archaeological Sus samples from which mtDNA haplotypes were obtained.
Samples were recovered from Neolithic LBK, post-LBK and Mesolithic Ertebølle sites dated between 5500 and 4000 cal BC. Each symbol corresponds to a single sample (triangle, square and circle). Domestic (triangle) and wild (square) pigs discussed in the text are labelled; circles represent Sus specimens of unknown domestication status. The red colour indicates the European haplotypes C and A, and yellow the Near Eastern haplotypes Y1 and Y2.

HERC2 haplotypes worldwide study at Kurdish DNA

I must congratulate again Palisto of Kurdish DNA blog for his excellent work on the description of HERC2 haplotypes and their frequency across world populations. It is not a peer-reviewed academic paper but it could well be, and within the high quality sector.
Palisto, The color of the eyes: at least 17 HERC2 variants in Human gene pool. Kurdish DNA 2013. Freely accessible blog articleLINK
After initially detecting seven haplotypes in the Kurdish genetic pool (which were named ht1-7) and then studying these in the Eurasian gene pool, he decided to study the African haplotypes, largely in the “other” category, as well as comparing them all with the known Neanderthal and Denisovan sequences, at the very least to infer a root. The main result is this tree:
So the ancestral haplotype is ht13, found not just among Neanderthals and Denisovans, but also among scattered populations of H. sapiens both in Africa as in Eurasia-plus. 
From it hang ht8 (Homo sapiens, found in and outside Africa) and ht18 (Neanderthal-exclusive).
This main branch has two major sub-haplogroups, which I will label D and E for convenience (A would be ht13, B ht8, and C Neanderthal-only ht18). Haplogroup D (hts 11, 16 and 17) seems to have remained in Africa (only ht 11 was detected at low frequencies in Lebanon), while haplogroup E (all the rest) massively participated in the migration out of Africa (OoA).
However it must have done already in highly diversified form, as most named haplotypes are found at significant frequencies both outside and inside Africa. There are four exceptions only:
  1. Ht9 is only found in Africa (with a minor Arabian exception), so this haplotype did not took part in the OoA.
  2. Ht15 has not been found in Africa instead, so it is possible that it evolved already in Eurasia.
  3. Ht2 and its descendant ht1 (both of which cause blue eyes, albeit in recessive manner) don’t seem to exist in Africa either (with the exception of the HGDP San sample, which seems notably admixed with Europeans, at levels of almost 20%, not your typical Bushmen really), so again they probably arose already in Eurasia. 
These are the wider regional frequencies:

However at the original article there is a much more detailed list, which is probably more interesting to use when pondering each haplotype. For example the overall data for America is pretty much irrelevant, as it groups native peoples with mixed creole ones.
For example we can see that “blue eyes” ancestral haplotype ht2 looks like originated in West Asia, and it may also be the case of its descendant ht1. 
Ht 15 in turn may well have coalesced in Altai, from where it spread to mostly Native American peoples (represented by Mestizo Colombians). A similar pattern can be seen in ht14, however this must be original from Africa (the Biaka have it, as do Mozabites) and therefore it is found also in some other scattered populations like Cambodians, Sindhi, etc.
Something I wonder about is the low diversity displayed by East Asians in this haplotype. Or inversely, why did West Eurasians evolve so all non-African novel variants? While there is still some left to analyze in the ND box, it is very small in East Asia. I wonder if it has some relation with skin pigmentation pathways indirectly influencing this change somehow.

HERC2 haplotypes, phylogeny and frequencies

Palisto at Kurdish DNA has a most interesting report of his own production on the eye color gene HERC2, its variant haplotypes, their phylogeny and their frequency in West Eurasian and Pakistani populations.
Based on Kurdish haplotypes, he developed the following phylogeny:

All branches produce dark eye color, excepted the two colored in blue, which are associated with light eye color. 
The defining transitions from branch#3 to branch#1 are rs1129038 and rs12913832 (demonstrated to cause blue eyes in 99% of cases) while the transition to branch#2 is found at rs11636232
He also produced haplotype frequency tables for the two light eye color haplotypes (here the one sorted by branch#1 frequencies):

Branch#1 Branch#2
Brahui 2% 2%
Balochi 8% 2%
Balochi 12% 6%
Kalash 12% 16%
Sardinian 16% 4%
Palestinian 18% 3%
Burusho 18% 12%
Basque 19% 21%
Italians 25% 19%
Adygei 26% 6%
Orcadian 28% 41%
Galician 30% 17%
French 32% 30%
Russians 36% 46%
Italians 42% 27%
Swedes 42% 54%
Germans 46% 33%
Danes 52% 32%
Austrian 55% 28%
Swiss 69% 25%
In West Asia and Pakistan (the most plausible ancient origin of the trait), we see how the ancestral #1 variant is generally dominant, with the only exception of the Kalash, reaching the highest frequencies (18%) among the Burusho and Palestinians, among the studied populations. 
This pattern is continued (at overall quite higher frequencies) in Central Europe, Denmark, Italy and Galicia, with peak among the Swiss (69%). Instead the derived haplotype #2 seems dominant among Swedes, Russians and Orcadians. French and Basques are balanced for both types.

Update (Jun 25): map:

Includes also Kurdish data from Palisto’s update.

The two Balochi samples are pooled in one (same weight for each), instead the two Italian samples were retained separated and assumed to be from South and North Italy respectively (not sure but makes sense). 

See also:

Update (Jun 27): Kurdish DNA just published the HERC2 data a much wider sample of populations from all Eurasia and not anymore focusing only on the blue eye haplotypes but all them instead.

It is very interesting that ht3, ancestral to blue eyes’ haplotypes ht1 and, through this one, also ht2 , is widespread through the continent with very few exceptions: Russians, Belorussians, Lithuanians and a Mordvin tribe in Europe, as well as the Kurmi, Nihali, Chenchu and Puliyar in India.

Ht5 and ht6 are also very common in Eurasia, ht7 is rare in most groups but dominant in a few (Kurmi, Melanesians) while ht4 (ancestral to ht3) is rather rare as well (highest in South and Central Asia, as well as Lebanon). Other (undetermined) haplotypes are also concentrated in some populations like the Chenchu and have some importance across Asia.


Posted by on June 9, 2013 in pigmentation, West Eurasia


Eye and skin pigmentation genetics: Cape Verdeans as informative population

Cape Verde from space
Still getting updated with the backlog. Here there is an interesting study on human pigmentation using the heavily admixed Cape Verdean (essentially West African + West Iberian) population as reference.
Sandra Beleza et al., Genetic Architecture of Skin and Eye Color in an African-European Admixed Population. PLoS Genetics 2013. Open accessLINK [doi:10.1371/journal.pgen.1003372]


Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3×10−62, SLC24A5 P = 9.6×10−9) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4×10−27, TYR P = 1.1×10−9, APBA2[OCA2] P = 1.5×10−8, SLC45A2 P = 6×10−9) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (~44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ~70% of the estimated heritability.

Children of Praia
(CC by Otimarte)
Most interestingly maybe the authors conclude that KITLG, a gene which displays large differences in allele frequency between Africa and Eurasia and has been therefore suggested to be a cause of pigmentation differences, does not actually play any obvious role in this matter.
HERC2 (OCA2) is confirmed to be very important in eye color (semi-recessive inheritance for blue color), the only other gene known to affect eye color is SLC24A5, which is mostly involved in skin pigmentation however.  
SLC24A5 and SLC45A2 are confirmed as important pigmentation genes. However two otherwise unsuspecting genes, APBA2 (near OCA2) and GRM5TYR, are found to have also important impact in skin pigmentation.
Still most (~3/5) of the inherited pigmentation traits remain unexplained and are probably caused by some sort of complex interactions. Eye and skin pigmentation have no strong genetic correlation apparently.
Some interesting images from the paper:

Figure 1. Relationship of geography and ancestry to skin and eye color.
Individual ancestry proportions for Cape Verdeans displayed on all four panels were obtained from a supervised analysis in frappe
with K = 2 and HapMap’s CEU and YRI fixed as European and African
parental populations. (a) Bar plots of individual ancestry proportions
for Cape Verdeans across the islands. The width of the plots is
proportional to sample size (Santiago, n = 172; Fogo, n = 129; NW
cluster, n = 192; Boa Vista, n = 27). The proportion of African vs.
European ancestry of the individuals is indicated by the proportion of
blue vs. red color in each plot. (b) Individual African ancestry
distribution in the total cohort of 685 Cape Verdeans (histogram) and in
802 African Americans (kernel density curve) from the Family Blood
Pressure Program (FBPP) [21].
(c) Scatter-plot of skin color vs. Individual African ancestry
proportions. Skin color is measured by the MM index described in
Material and Methods. (d) Scatter-plot of eye color vs. Individual
African ancestry proportions. Eye color is measured by the T-index,
described in Figure 2 and Material and Methods. Points in scatter-plots are color coded according to the island of origin of the individuals.
Figure 3. GWAS results for skin and eye color in the total Cape Verdean cohort.
Results are shown as −log10(P
value) for the genotyped SNPs. Plots are ordered by chromosomal
position. (a,c) Genotype and admixture association scan results for skin
color. (b,d) Genotype and admixture association scan results for eye
color. (a,b) show the P values obtained in the initial scans and (c,d) the P values of the following scans adjusting for the strongest associated SNP (in SLC24A5 for skin color and in HERC2 for eye color). Dashed red lines correspond to the genome-wide significance threshold (P<5×10−8 in the genotype scan; P<7×10−6
in the ancestry scan [see Material and Methods]). The location and
identity of candidate genes are colored to correspond with chromosomal
location; individual SNPs are given in Table 1.
Figure 7. Genetic architecture of skin color variation.
Effect sizes of the loci associated with skin color. Effect values
represent the beta values obtained from a regression model containing
the four associated loci plus ancestry. (b) The pie chart represents the
proportion of phenotypic variation accounted for by the different
components, including non-heritable factors (~20%), the four major loci
(~35%, color-coded as in [a]), and average genomic ancestry (44%). The
heritable contributions were estimated by regression and variance
decomposition as described in Material and Methods, and are also
represented below the pie chart separately as grey (genomic ancestry) or
open (four major loci) areas. However, because of admixture
stratification, the heritable contributions overlap as described in the


Eye color, face shape and perception of trustworthiness

An old popular Galician song said:

Ollos verdes son traidores…
azules son mentireiros,
os negros e acastañados son firmes e verdadeiros.


Green eyes are treacherous…
blue ones are deceitful,
the black and brown ones are loyal and truthful.

Just word of a silly mariner song? Intriguingly science confirms now, in a way, part of this perception (at least for blue and brown eyes).
But notice please that it is the precisely the perception what is being confirmed: people seem to perceive blue eyes in general as somewhat less trustworthy. The study says nothing about people with blue eyes being untrustworthy in fact, just that we tend to distrust them more than people with brown eyes.

Karel Kleisner et al., Trustworthy-Looking Face Meets Brown Eyes. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0053285]


We tested whether eye color influences perception of trustworthiness.
Facial photographs of 40 female and 40 male students were rated for
perceived trustworthiness. Eye color had a significant effect, the
brown-eyed faces being perceived as more trustworthy than the blue-eyed
ones. Geometric morphometrics, however, revealed significant
correlations between eye color and face shape. Thus, face shape likewise
had a significant effect on perceived trustworthiness but only for male
faces, the effect for female faces not being significant. To determine
whether perception of trustworthiness was being influenced primarily by
eye color or by face shape, we recolored the eyes on the same male
facial photos and repeated the test procedure. Eye color now had no
effect on perceived trustworthiness. We concluded that although the
brown-eyed faces were perceived as more trustworthy than the blue-eyed
ones, it was not brown eye color per se that caused the stronger perception of trustworthiness but rather the facial features associated with brown eyes.

So the authors conclude that it is not eye color but associated face shape what drives untrustworthiness because the phenotype associated with blue eyes is more angular, less rounded, at least for males:

Figure 2. Shape changes associated with eye color and perceived trustworthiness.
spline visualizations of the way face shape correlates with eye color
(a–f) and trustworthiness (g–i). Generated face shapes of blue-eyed
woman (a) and brown-eyed woman (c) compared to average female face (b).
Generated face shapes of blue-eyed man (d) and brown-eyed man (f)
compared to average male face (e). Generated face shapes of
untrustworthy-looking man (g) and trustworthy-looking (i) man compared
to average male face (h). The TPS grids of perceived trustworthiness for
women are not shown because shape analysis did not meet statistical
significance. The generated facial images (a–f) were magnified 3x for
better readability.

They claim that they found no correlation with facial shape for women but I find in the image above almost exactly the same pattern for men and women and not only what they detected: notably the blue eyed people (both genders) and the less trusted men all have in my opinion:
  • Smaller eyes
  • More serious (defiant, analytic, unsympathetic) expression
  • Proportionally broader face or at least jaws
In general the faces to the left look significantly colder, less empathic, a perception that blue eyes can only enhance.
The authors ponder if there is a phenotype linkage disequilibrium associating face and eye color, what seems plausible. But then go on speculating about sexual selection and what not. 
In this sense Razib has an interesting critical analysis questioning if selection is behind the blue eye incomplete sweep in West Eurasia or Europe. If I understand him correctly he seems to suggest, never clearly naming it, that blue eye may have been favored because of the associated skin pigmentation trait, a key adaptive value in the dark winters of Europe and very especially the northern half of it.

Update: is this a peculiarity of Central Europe or the Czech Republic?

A reader sent me an email in which it was questioned if this association is peculiar of the Czech Republic, where the study was performed, and can’t be extended for example to Britain. Examples of soft-faced blue-eyed Britons mentioned were Hugh Grant and Alec Baldwin (I’m not sure if Baldwin is such a good counter-example but Grant is for sure one such case). 

I find it a very good criticism and hope that entices debate.

See also: Causes of skin and hair color variance in Europeans remain undetermined.


Posted by on January 10, 2013 in Anthropometry, Europe, pigmentation, psychology, West Eurasia


Causes of skin and hair color variance in Europeans remain undetermined

Portuguese & N. Irish

Our ability to predict pigmentation traits from genetic loci remains limited but this new paper adds some honest research on the matter:

Sophie I. Candille et al., Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0048294]
One of the findings is that women have darker skin shades than men in Europe (but not among peoples with dark skin from several continents, where men are darker). Another unstated but curiously counterintuitive finding is that Portuguese (from Porto) have on average the same skin tone as Polish (from Warsaw) do:

Table 1. Skin, hair, and eye pigmentation by sex and country.

However for hair and eye color, Polish have lighter shades, approaching the Irish (Dublin) extreme values, while Portuguese approach Italians (Rome) in hair color and show darker eyes on average than anybody else among the sampled populations.
Another curiosity of the survey is that Irish women show significantly lighter hair shades than Irish men, a phenomenon not appreciable elsewhere.
The authors found that, in general:

… in this European sample, pigmentation phenotypes are mainly stratified by country, whereas height is mainly stratified by sex.

They also found that:

Skin and eye pigmentation are correlated in Ireland. Hair and eye pigmentation are correlated in Portugal. Skin and hair pigmentation are correlated in Poland and Italy (Table S2).

What I find rather curious and suggestive of complex genetic influences affecting more than just one pigmentation trait at the same time. But which ones? And why do they seem to operate differently in different populations?
The GWAS analysis found these loci as significant:

Table 2. GWAS, replication, and combined association results for all signals with p-value<10−5 in the GWAS.

Apparently neither the SCIN nor the FLNB genes have been related with pigmentation before. Therefore the authors applied a strong test of reliability (replication in the table), correcting for geographical structure, which actually discarded all loci except the already known ones for eye color in relation to OCA2/HERC2, which were: rs1667394, rs8039195, rs1635168, rs16950987, and rs8028689.
However further analysis showed that rs1667394 is in linkage disequilibrium (LD) with rs12913832 (OCA2), which is the actual culprit of blue eyes (a well known SNP that explains some 45% of the eye color variance among Dutch).
In regard to the failure to detect markers of skin and hair color variance, they conclude that:

The fact that we did not detect reproducible associations with skin or hair color suggests that, unlike eye color, skin and hair pigmentation variation in Europe are not determined by major loci.

Furthermore, genes that have been shown to contribute to skin color variance in South Asians (rs1426654 SLC24A5, rs16891982 SLC45A2, and rs1042602 TYR) or in African-European admixed populations (rs1426654 in SLC24A5 again), fail to show any importance in intra-European variance for this trait. However rs1426654 is fixated in Northern Europeans (CEU), so it cannot show any variation.
Other SNPs (rs16891982 and r183671 in SLC45A2, which are in LD) may contribute to skin pigmentation, however the pattern mentioned (in which Italians and Portuguese are contrasted with Polish and Irish) rather reminds me of the variation for hair and eye color instead.
They also mention that rs885479 in MC1R has not provided any clear association in previous studies but that they did find some association with skin color, however they did not practice the replication test for this SNP.
In the end not much new other than some cold water but an straightforward study for the record.

See also:


Blond hair in Melanesia genetically distinct from that of Europeans calls my attention today to this paper:

Naturally blond hair is rare in humans and found almost exclusively in Europe and Oceania. Here, we identify an arginine-to-cysteine change at a highly conserved residue in tyrosinase-related protein 1 (TYRP1) as a major determinant of blond hair in Solomon Islanders. This missense mutation is predicted to affect catalytic activity of TYRP1 and causes blond hair through a recessive mode of inheritance. The mutation is at a frequency of 26% in the Solomon Islands, is absent outside of Oceania, represents a strong common genetic effect on a complex human phenotype, and highlights the importance of examining genetic associations worldwide. 

Actually natural blond hair is also found in West and Central Asia and North Africa, and red hair even in the Horn of Africa now and then. But I guess that’s what the authors mean by “Europe”, duh! It’s also found occasionally among South Asians, specially the young, and among SE Asians regardless of age.
Whatever the case with the authors ethno-geographic misconceptions, the results are still most interesting: the gene causing blond hair among Melanesians (and some relatives like Fijians) is not the same as those involved in blond hair in Europe. Mind you that it is not clear yet which are these European genes of blondism but it is clear that the Melanesian allele is not it either. 
There is also an article at New Scientist.
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Posted by on May 4, 2012 in human genetics, Melanesia, pigmentation