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.
Category Archives: pigmentation
- Ht9 is only found in Africa (with a minor Arabian exception), so this haplotype did not took part in the OoA.
- Ht15 has not been found in Africa instead, so it is possible that it evolved already in Eurasia.
- 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.
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).
Causes of skin and hair color variance in Europeans remain undetermined (includes data for eye color)
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.
|Cape Verde from space|
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)
|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) .
(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.
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.
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.
- Smaller eyes
- More serious (defiant, analytic, unsympathetic) expression
- Proportionally broader face or at least jaws
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.
|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:
|Table 1. Skin, hair, and eye pigmentation by sex and country.|
… in this European sample, pigmentation phenotypes are mainly stratified by country, whereas height is mainly stratified by sex.
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).
|Table 2. GWAS, replication, and combined association results for all signals with p-value<10−5 in the GWAS.|
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.
- Predicting pigmentation phenotypes with genetic information (at Yan Klimentidis blog)
- Some population structured SNPs and also one epigenetic factor
- Category “Pigmentation”
- The height of Europeans and the myth of the North-South cline
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.
One complication is that traits such as hair color are controlled by multiple genes. To determine the cumulative impact of multiple genes on one trait, the authors assumed they could simply add together the impact of individual genes. The female Neandertal known as Vi33.26, for example, had seven genes for brown eyes, one for “not-brown” eyes, three for blue eyes, and four for “not-blue eyes.” By the researchers’ reckoning, that means a six-gene balance in favor of brown and a negative balance for blue, so Vi33.26’s eyes were probably brown. According to this method, all three Neandertals had a dark complexion and brown eyes, and although one was red-haired, two sported brown locks.
You know: the stuff that should have been commented if I was perfect or a paid professional – but was not:
|These marks are the first evidence of humans in Ohio|
|One of the dolmens found in Alcónetar|
Numerous genome-wide scans conducted by genotyping previously-ascertained single nucleotide polymorphisms (SNPs) have provided candidate signatures of positive selection in various regions of the human genome, including in genes involved in pigmentation traits. However, it is unclear how well the signatures discovered by such haplotype-based test statistics can be reproduced in tests based on full resequence data. Four genes, OCA2, TYRP1, DCT and KITLG, implicated in human skin color variation, have shown evidence for positive selection in Europeans and East Asians in previous SNP-scan data. In the current study, we resequenced 4.7-6.7 kb of DNA from each of these genes in Africans, Europeans, East Asians and South Asians.
Applying all commonly-used allele frequency distribution neutrality test statistics to the newly generated sequence data provided conflicting results in respect of evidence for positive selection. Previous haplotype-based findings could not be clearly confirmed. The application of Markov Chain Monte Carlo Approximate Bayesian Computation to these sequence data using a simple forward simulator revealed broad posterior distributions of the selective parameters for all four genes providing no support for positive selection. However, when we applied this approach to published sequence data on SLC45A2, another human pigmentation candidate gene, we could readily confirm evidence for positive selection as previously detected with sequence-based and some haplotype-based tests.
Overall, our data indicate that even genes that are strong biological candidates for positive selection and show reproducible signatures of positive selection in SNP scans do not always show the same replicability of selection signals in other tests, which should be considered in future studies on detecting positive selection in genetic data.