Natural selection in Britain during the last 2,000 years

The latest ancient DNA studies from the British Isles (Schiffels et al and Martiniano et al. and Cassidy et al.) support continuity over the last 2,000 years. Sure, there were continued migrations like the arrival of the Anglo-Saxons, but these were very similar groups in the grand scheme of things.

But, while ancestrally the modern Briton is probably a descendant of the Britons of 2,000 years ago with some admixture from similar continental European groups, he is not the same, as (apparently) substantial genetic adaptation has continued to operate in Britain over the same period. A new preprint by Field, Boyle, Telis et al. makes the case for adaptation in a variety of traits in the ancestors of Britons over this period. Mind you, the genetic underpinnings of many important human traits known to have high heritability are currently unknown, but there is little doubt that selection would have affected traits beyond those detected in this study. I am quite curious to see whether the striking efflorescence of cultural achievement in Britain over the last half millennium could have (at least in part) a genetic underpinning.

Depigmentation is a trait whose genetic architecture is as well as understood as any. The results of this study might surprise writers of decades and centuries past who supposed that the spectrum of pigmentation of modern Europeans was the result  of admixture-in varying measure- between Xanthochrooi and Melanchrooi races of primordial antiquity. All indications seem to be that depigmentation of hair, skin, and eyes did not co-occur in such a hypothetical race, but rather in different parts of the Caucasoid range, only reaching a high combined frequency in northern Europe to form the distinctive physical type that is distinctive of the natives of that region. It would be quite interesting to see how these traits evolved in Fennoscandia and the Baltic, regions that sport an even higher depigmentation than the British Isles. Traditionally, these areas were viewed as refuges of the Xanthochrooi but it may very well turn out to be that for whatever reason selection has acted in that area as well, as it did in the Eastern European plain where rather dark Bronze Age steppe groups gave way to rather light pigmented living eastern Slavs.

bioRxiv doi: http://dx.doi.org/10.1101/052084

Detection of human adaptation during the past 2,000 years

Yair Field, Evan A Boyle, Natalie Telis, Ziyue Gao, Kyle J Gaulton, David Golan, Loic Yengo, Ghislain Rocheleau, Philippe Froguel, Mark I McCarthy, Jonathan K Pritchard

Detection of recent natural selection is a challenging problem in population genetics, as standard methods generally integrate over long timescales. Here we introduce the Singleton Density Score (SDS), a powerful measure to infer very recent changes in allele frequencies from contemporary genome sequences. When applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past 2,000 years. We see strong signals of selection at lactase and HLA, and in favor of blond hair and blue eyes. Turning to signals of polygenic adaptation we find, remarkably, that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we report suggestive new evidence for polygenic shifts affecting many other complex traits. Our results suggest that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.

Link

Bronze Age warrior from Poland

Google translation of original article:

Skull warrior was in such good condition that the museum was tempted by an experiment - a reconstruction of his face. Tasks undertaken by the research team of Dr. Dorothy Lorkiewicz-Muszyńska of the Department of Forensic Medicine, University of Medical Sciences. Every day with their ability to use the police, for example, when you need to identify a murder victim. The first step was to make a 3D scan of the skull.

- At the base using a special computer program was applied to the muscle tissue - explains the director Bartecki. - Method shows more than 90 percent. compliance with the real appearance of a man - says.

Proved invaluable assistance skeleton results Rogalin. Also genetic. Thanks to them, we know that the warrior had a dark complexion, dark hair and eyes.

This combination of traits is rather uncommon in modern Poles. It seems that eastern Europeans looked quite different four thousand years ago than they do today.

A molecular basis for classic blond hair (Guenther et al. 2014)

Nature Genetics (2014) doi:10.1038/ng.2991

A molecular basis for classic blond hair color in Europeans

Catherine A Guenther et al.

Hair color differences are among the most obvious examples of phenotypic variation in humans. Although genome-wide association studies (GWAS) have implicated multiple loci in human pigment variation, the causative base-pair changes are still largely unknown1. Here we dissect a regulatory region of the KITLG gene (encoding KIT ligand) that is significantly associated with common blond hair color in northern Europeans2. Functional tests demonstrate that the region contains a regulatory enhancer that drives expression in developing hair follicles. This enhancer contains a common SNP (rs12821256) that alters a binding site for the lymphoid enhancer-binding factor 1 (LEF1) transcription factor, reducing LEF1 responsiveness and enhancer activity in cultured human keratinocytes. Mice carrying ancestral or derived variants of the human KITLG enhancer exhibit significant differences in hair pigmentation, confirming that altered regulation of an essential growth factor contributes to the classic blond hair phenotype found in northern Europeans.

Link

Dark pigmentation of Eneolithic and Bronze Age kurgan groups from eastern Europe

This is a very exciting new study that seems to parallel some results from early west Europeans. The authors invoke selection as a possible cause for the massive change in frequency between the Bronze Age and present-day Ukrainians.

An invocation of selection as an explanation requires evidence population continuity, otherwise changes in allele frequency may involve migration of a new frequency-differentiated new population; for example, the massive change in pigmentation in North America over the last 500 years is not due to selection but to migration of Europeans. The authors cannot reject population continuity on the basis of mtDNA haplogroup frequencies, although autosomal data may be more informative for that purpose.

In any case, the fact that the limited sample from western Europe and the much more extensive sample from eastern Europe both show a darker pigmentation than modern Europeans does suggest that interesting changes happened in Europe over the last few thousand years and samples from more recent time periods may better determine the pace of this change.

From the paper:

In sum, a combination of selective pressures associated with living in northern latitudes, the adoption of an agriculturalist diet, and assortative mating may sufficiently explain the observed change from a darker phenotype during the Eneolithic/Early Bronze age to a generally lighter one in modern Eastern Europeans, although other selective factors cannot be discounted. The selection coefficients inferred directly from serially sampled data at these pigmentation loci range from 2 to 10% and are among the strongest signals of recent selection in humans.

UPDATE: 

The classical Greeks did of course notice that the inhabitants of the north Pontic hinterland, collectively known as Scythians, were extraordinarily light-pigmented. This would imply that major pigmentation change occurred in the steppe over a time span of Bronze Age-Classical Antiquity rather than Bronze Age-present; this would imply even higher selection coefficients (if selection over a population exhibiting continuity is at play).

The Scythians were also thought to be recent arrivals from the east so it is not clear if they were descended from the Bronze Age population of eastern Europe; the crazy selection coefficients that would need to be assumed if there was indeed population continuity might imply that Herodotus got it right again, and the Scythians did in fact arrive from elsewhere. That would of course also imply that people from Central Asia and Siberia (where the Scythians may have come from) were originally lighter than Europeans which does find support from an older study on southern Siberian remains. Ironically, if that is the case, it would mean that the famous light-pigmented mummies of different parts of Inner Asia may not be long-lost European descendants -- as it has sometimes been presumed on the basis of modern-day clines of pigmentation. As usual, ancient DNA continues to surprise.

PNAS doi: 10.1073/pnas.1316513111

Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y

Sandra Wilde et al.

Eye, hair, and skin pigmentation are highly variable in humans, particularly in western Eurasian populations. This diversity may be explained by population history, the relaxation of selection pressures, or positive selection. To investigate whether positive natural selection is responsible for depigmentation within Europe, we estimated the strength of selection acting on three genes known to have significant effects on human pigmentation. In a direct approach, these estimates were made using ancient DNA from prehistoric Europeans and computer simulations. This allowed us to determine selection coefficients for a precisely bounded period in the deep past. Our results indicate that strong selection has been operating on pigmentation-related genes within western Eurasia for the past 5,000 y.

Link

Multiplex determination of eye and hair color

From the paper:

Sample S24 represents a controversial case from the Benedictine Abbey in  Tyniec near Krakow. During the work undertaken in the crypt of the St. Peter and Paul  church belonging to the Abbey, 17 skeletons of alleged abbots were found. The burial was  dated to the period of the 12th to 14th centuries. Unexpectedly, the anthropological  examination revealed that two skeletons may be of female origin, which indeed was  confirmed by DNA analysis (data not shown), while only male monks were expected. One of the two DNA samples was sufficiently preserved to enable analysis of other nuclear markers  (data not shown) and was used here for HIrisPlex analysis. The mysterious woman was  predicted to have dark blond/brown hair (accuracy of 78.5%) and brown eyes (accuracy of 90.4%), (Table 2 and Figure 2B). 

... 

Two medieval  skeletons were found under the floor between the chancel and the nave of the church. Based  on historical markers the grave was dated to originate from the 14th century. Further  anthropological examinations indicated that the S25 male died at the approximate age of 60,  whereas the S26 male was approximately 75 years old at the time of death. It is alleged that  the skeletons belong to members of the Teczynski family, representing noble Polish magnates  of medieval times. The tooth collected from the deeper burial (S25) was found to be seriously  affected by decay, which was reflected by a very low DNA concentration (3 pg/µl) and  incomplete autosomal and Y chromosome STR profiles (NGM and Yfiler). Complete  mtDNA HVI and HVII profiles were generated in both teeth (data not shown). From these  data it was possible to conclude that both skeletons are of male origin and are unrelated in  both maternal and paternal lines. From the partial HIrisPlex profile ascertained from S25 we  successfully inferred blue eye colour (P = 0.899, accuracy of 95.6%), but hair colour could  not be inferred because of missing genotypes at three DNA variants (N29insA, rs1805005,  rs2228479). The sample S26 revealed a prediction of blond hair colour (P = 0.784) together  with a light hair colour shade (P = 0.918) concluding that the individual had light blond hair  (accuracy of 69.5%). Eye colour prediction of S26 revealed blue eyes (P = 0.919, accuracy of  97.4%) (Table 2).

Wikipedia article on Tęczyński family.

Investigative Genetics 2013, 4:3 doi:10.1186/2041-2223-4-3

Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains

Jolanta Draus-Barini

Abstract (provisional)

Background

DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing persons, disaster victims or family relationships. They may also provide useful information towards unravelling controversies that surround famous historical individuals. Retrieving information about a deceased person's externally visible characteristics can be informative in both types of DNA analyses. Recently, we demonstrated that human eye and hair colour can be reliably predicted from DNA using the HIrisPlex system. Here we test the feasibility of the novel HIrisPlex system at establishing eye and hair colour of deceased individuals from skeletal remains of various post-mortem time ranges and storage conditions.

Methods

Twenty-one teeth between 1 and approximately 800 years of age and 5 contemporary bones were subjected to DNA extraction using standard organic protocol followed by analysis using the HIrisPlex system.

Results

Twenty-three out of 26 bone DNA extracts yielded the full 24 SNP HIrisPlex profile, therefore successfully allowing model-based eye and hair colour prediction. HIrisPlex analysis of a tooth from the Polish general W[latin small letter l with stroke]adys[latin small letter l with stroke]aw Sikorski (1881 to 1943) revealed blue eye colour and blond hair colour, which was positively verified from reliable documentation. The partial profiles collected in the remaining three cases (two contemporary samples and a 14th century sample) were sufficient for eye colour prediction.

Conclusions

Overall, we demonstrate that the HIrisPlex system is suitable, sufficiently sensitive and robust to successfully predict eye and hair colour from ancient and contemporary skeletal remains. Our findings, therefore, highlight the HIrisPlex system as a promising tool in future routine forensic casework involving skeletal remains, including ancient DNA studies, for the prediction of eye and hair colour of deceased individuals.

Link

GWAS study of pigmentation in four European countries

From the paper:

Males (M) have consistently lighter pigmentation (lower scored) than females (F) in all four countries. Among countries, the largest pigmentation difference is with Ireland, where, in our sample, individuals have lighter pigmentation or lower M index on average than in Poland, Italy, or Portugal. Hair pigmentation histogram (C) and boxplot by country (D) in 341 individuals showing the distribution of hair pigmentation and the differences among countries. In our sample, individuals from Northern European countries (Ireland, Poland) have on average lighter hair pigmentation than individuals from Southern European countries (Italy, Portugal). The distributions in males are similar to those in females in all countries except Ireland, where, in our sample, males have darker hair color than females (not shown). Eye pigmentation histogram (E) and boxplot by country (F) in 468 individuals showing the bimodal distribution of eye pigmentation and the differences among countries. Comparison with self-reported phenotypes shows that the two modes of the distribution correspond to blue and brown eye color, while individuals reporting green and hazel eye color have intermediate C’ values. As with hair pigmentation, in our sample, individuals from Northern European countries have on average lighter eye pigmentation than individuals from Southern European countries. 

...   

Interestingly, our analysis of variation in skin color in Europe demonstrates a consistent difference in skin color between the sexes. By the DermaSpectrometer M index measure, males are more lightly pigmented than females in each of the four European countries we studied. The same trend in M index was reported previously in a sample of European Americans [38]. Our results in populations of European ancestry contradict earlier anthropological studies that have concluded females are more lightly pigmented than males in most populations (reviewed in [2]). One potential reason for the conflicting results is the different instruments used. In early studies, which used the Evans Electric Limited (EEL) and Photovolt broad-spectrum spectrophotometers, skin pigmentation estimates may be confounded by the hemoglobin level to a greater extent than for the DermaSpectrometer used in the present study [46].

Some data (lower = lighter):

One thing of interest is that while Irish males/females are both lighter-eyed than other Europeans, including Poles from northern Europe, Irish females appear to be lighter-haired than Irish males (96.3 vs. 106.7), but no such substantial sex difference exists in the Poles in this trait (107.5 vs. 109.5). Sexual dimorphism seems to lean in the direction of lighter male skins and lighter female hair across the four countries.

Peter Frost has offered the theory that "gentlemen prefer blondes" because during the Ice Age boreal hunters lived a harsh lifestyle that killed many of them, but the remainder could not adopt a polygynous lifestyle, because provisioning for a wife was expensive. As a result, women had to compete for the remaining men, and men could be picky, preferring those with a "rare color advantage." It is not immediately clear to me how this might explain the Ireland vs. Poland differentiation, assuming it reflects a broader NW/NE trend, since NE Europeans are more likely to be descended from hunter-gatherers of the tundra-steppe.

PLoS ONE 7(10): e48294. doi:10.1371/journal.pone.0048294

Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations

Sophie I. Candille et al.

Pigmentation of the skin, hair, and eyes varies both within and between human populations. Identifying the genes and alleles underlying this variation has been the goal of many candidate gene and several genome-wide association studies (GWAS). Most GWAS for pigmentary traits to date have been based on subjective phenotypes using categorical scales. But skin, hair, and eye pigmentation vary continuously. Here, we seek to characterize quantitative variation in these traits objectively and accurately and to determine their genetic basis. Objective and quantitative measures of skin, hair, and eye color were made using reflectance or digital spectroscopy in Europeans from Ireland, Poland, Italy, and Portugal. A GWAS was conducted for the three quantitative pigmentation phenotypes in 176 women across 313,763 SNP loci, and replication of the most significant associations was attempted in a sample of 294 European men and women from the same countries. We find that the pigmentation phenotypes are highly stratified along axes of European genetic differentiation. The country of sampling explains approximately 35% of the variation in skin pigmentation, 31% of the variation in hair pigmentation, and 40% of the variation in eye pigmentation. All three quantitative phenotypes are correlated with each other. In our two-stage association study, we reproduce the association of rs1667394 at the OCA2/HERC2 locus with eye color but we do not identify new genetic determinants of skin and hair pigmentation supporting the lack of major genes affecting skin and hair color variation within Europe and suggesting that not only careful phenotyping but also larger cohorts are required to understand the genetic architecture of these complex quantitative traits. Interestingly, we also see that in each of these four populations, men are more lightly pigmented in the unexposed skin of the inner arm than women, a fact that is underappreciated and may vary across the world.

Link

Iceman stories begin arriving!

The National Geographic has info, a teaser for an October 26 Nova special:

The genetic results add both information and intrigue. From his genes, we now know that the Iceman had brown hair and brown eyes and that he was probably lactose intolerant and thus could not digest milk—somewhat ironic, given theories that he was a shepherd. Not surprisingly, he is more related to people living in southern Europe today than to those in North Africa or the Middle East, with close connections to geographically isolated modern populations in Sardinia, Sicily, and the Iberian Peninsula. The DNA analysis also revealed several genetic variants that placed the Iceman at high risk for hardening of the arteries. ("If he hadn't been shot," Zink remarked, "he probably would have died of a heart attack or stroke in ten years.") Perhaps most surprising, researchers found the genetic footprint of bacteria known as Borrelia burgdorferi in his DNA—making the Iceman the earliest known human infected by the bug that causes Lyme disease.

It seems that my prediction that the Iceman will turn out to be Mediterranean in terms of his autosomal genetic components was right!

I don't get, however, how lactose intolerance is incompatible with being a shepherd, since milk is widely used in southern Europe both as a raw product and for its cheese. I lack the lactose tolerance gene myself, but that doesn't keep me from having a glass of milk nearly every day. Lactose tolerance makes it possible for people to drink lots of milk; lactose intolerance does not make it impossible for them to drink any, or to enjoy its secondary products (such as cheese and butter).

British men's hair color preferences

Scand J Psychol. 2011 Aug 29. doi: 10.1111/j.1467-9450.2011.00911.x. [Epub ahead of print]

British men's hair color preferences: An assessment of courtship solicitation and stimulus ratings.

Swami V, Barrett S.

Abstract

British men's hair color preferences: An assessment of courtship solicitation and stimulus ratings. Scandinavian Journal of Psychology. Two studies examined the influence of women's hair color on approach behavior by British men and on ratings of physical attractiveness and personality. In Study 1, a female confederate whose hair color was dyed blonde, brunette, or red was instructed to sit in several nightclubs. It was found that she was approached significantly more frequently by men in the blonde condition. In Study 2, images of the same confederate were rated by 126 men. Results showed that the brunette stimulus was rated as more physically attractive, intelligent, approachable, competent, and arrogant, whereas the blonde stimulus was rated as more needy. These results are discussed in relation to the literature on hair color and attractiveness, but also in terms of women's own perceptions of their hair color.

Link

Population differentiation in gene classes (Wu & Zhang 2011)

BMC Evolutionary Biology 2011, 11:16doi:10.1186/1471-2148-11-16

Different level of population differentiation among human genes

Dong-Dong Wu, Ya-Ping Zhang

Abstract (provisional)

Background
During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations.

Results
Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection.

Conclusion
Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

Link

Model-based prediction of hair color

Human Genetics doi:10.1007/s00439-010-0939-8

Model-based prediction of human hair color using DNA variants

Wojciech Branicki et al.

Abstract

Predicting complex human phenotypes from genotypes is the central concept of widely advocated personalized medicine, but so far has rarely led to high accuracies limiting practical applications. One notable exception, although less relevant for medical but important for forensic purposes, is human eye color, for which it has been recently demonstrated that highly accurate prediction is feasible from a small number of DNA variants. Here, we demonstrate that human hair color is predictable from DNA variants with similarly high accuracies. We analyzed in Polish Europeans with single-observer hair color grading 45 single nucleotide polymorphisms (SNPs) from 12 genes previously associated with human hair color variation. We found that a model based on a subset of 13 single or compound genetic markers from 11 genes predicted red hair color with over 0.9, black hair color with almost 0.9, as well as blond, and brown hair color with over 0.8 prevalence-adjusted accuracy expressed by the area under the receiver characteristic operating curves (AUC). The identified genetic predictors also differentiate reasonably well between similar hair colors, such as between red and blond-red, as well as between blond and dark-blond, highlighting the value of the identified DNA variants for accurate hair color prediction.

Link

mtDNA of Napoleon Bonaparte

From the paper:

In a subsequent search of a public database, EMPOP http://www.empop.org webcite, containing data on 4,475 individuals, the 16184C→T mutation was found to be present in three individuals of West Eurasian origin, giving a frequency of 0.0007%. In a personal database comprising about 37,000 control region records (Dr M. Pala, personal communication), the HSV1 sequence with the single mutation 16184C→T was also present in three samples (one from Crete and two from Italy), giving a mutation frequency for 16184C→T of 0.00008%. All three samples belonged to the mtDNA haplogroup H.

On the left, the locks of Napoleon's hair. I am told that full mtDNA sequencing and Y-STR results are in the pipeline.

Investigative Genetics 2010, 1:7 doi:10.1186/2041-2223-1-7

A rare variant of the mtDNA HVS1 sequence in the hairs of Napoléon's family

Gérard Lucotte

This paper describes the finding of a rare variant in the sequence of the hypervariable segment (HVS1) of mitochondrial (mtDNA) extracted from two preserved hairs, authenticated as belonging to the French Emperor Napoléon I (Napoléon Bonaparte). This rare variant is a mutation that changes the base C to T at position 16,184 (16184C→T), and it constitutes the only mutation found in this HVS1 sequence. This mutation is rare, because it was not found in a reference database (P less than 0.05). In a personal database (M. Pala) comprising 37,000 different sequences, the 16184C→T mutation was found in only three samples, thus in this database the mutation frequency was 0.00008%. This mutation 16184C→T was also the only variant found subsequently in the HVS1 sequences of mtDNAs extracted from Napoléon's mother (Letizia) and from his youngest sister (Caroline), confirming that this mutation is maternally inherited. This 16184C→T variant could be used for genetic verification to authenticate any doubtful material and determine whether it should indeed be attributed to Napoléon.

Link

Predicting Phenotype from Genotype: Normal Pigmentation (Valenzuela et al. 2010)

Yann Klimentidis points me to this new paper on predicting human pigmentation phenotype from genotype. The paper is interesting in view of the recent finding that lactose intolerance phenotype is not very well captured by the known genetic variation.

The current paper looks at how well normal pigmentation (skin, hair, and eye color) is predicted from known genotypes. The sample consists of individuals from the University of Arizona.

From the paper:

The three most frequent SNPs found in the range from the highest R² model to the first inflection of the graph were used to construct an MLR model for each trait. These models accounted for significant variation in each of the four measured traits: scalp-hair total melanin (76.3%), natural log of the ratio of eumelanin-to-pheomelanin (43.2%), skin reflectance (45.7%), and eye color (74.8%) (Table 3).

Obviously two caveats should be raised:

(i) that the associations are dependent on the sample. It is not clear how the percentage of variation explained would be altered in a population of different ethnic origins -not represented in the UoA.

(ii) that the associations may be mediated by other genetic factors, not yet discovered.

With respect to (ii), pigmentation appears to be a "success story" of genome-wide association studies, as a relatively small number of SNPs accounts for such a high level of variation (about 3/4 for the best traits). However, the missing 1/4 should also make us cautious when we attempt to infer the pigmentation of a sample, in either a forensic or an archaeological context.

Journal of Forensic Science doi:10.1111/j.1556-4029.2009.01317.x

Predicting Phenotype from Genotype: Normal Pigmentation

Robert K. Valenzuela et al.

Abstract

Genetic information in forensic studies is largely limited to CODIS data and the ability to match samples and assign them to an individual. However, there are circumstances, in which a given DNA sample does not match anyone in the CODIS database, and no other information about the donor is available. In this study, we determined 75 SNPs in 24 genes (previously implicated in human or animal pigmentation studies) for the analysis of single- and multi-locus associations with hair, skin, and eye color in 789 individuals of various ethnic backgrounds. Using multiple linear regression modeling, five SNPs in five genes were found to account for large proportions of pigmentation variation in hair, skin, and eyes in our across-population analyses. Thus, these models may be of predictive value to determine an individual’s pigmentation type from a forensic sample, independent of ethnic origin.

Link

Common variant for straight hair in Europeans

American Journal of Human Genetics doi:10.1016/j.ajhg.2009.10.009

Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans

Sarah E. Medland et al.

Abstract

Hair morphology is highly differentiated between populations and among people of European ancestry. Whereas hair morphology in East Asian populations has been studied extensively, relatively little is known about the genetics of this trait in Europeans. We performed a genome-wide association scan for hair morphology (straight, wavy, curly) in three Australian samples of European descent. All three samples showed evidence of association implicating the Trichohyalin gene (TCHH), which is expressed in the developing inner root sheath of the hair follicle, and explaining ∼6% of variance (p = 1.5 × 10⁻³¹). These variants are at their highest frequency in Northern Europeans, paralleling the distribution of the straight-hair EDAR variant in Asian populations.

Link

More on prehistoric South Siberians (Keyser et al. 2009)

This seems like a compendium of these authors' previous work (see here and links therein) which had appeared in forensic journals so far; there seems to be more material in this paper than in the previous shorter papers, but as far as I can tell, no new genetic results.

There is also supplementary data in the article.

From the paper:

The additional analysis performed on Xiongnu specimens revealed that whereas none of the specimens from the Egyin Gol valley bore this haplogroup, the Scytho-Siberian skeleton from the Sebÿstei site exhibited R1a1 haplogroup.

A previous study on Egyin Gol from Mongolia by Keyser et al.

More from the paper:

A search in the YHRD database as well as in our own databank revealed that none of the Y-STR haplotypes obtained from the south Siberian samples perfectly matched (at 17 loci) those included in the databases. Nevertheless, when not all loci were scored, matches were found for all samples except two (S07 and S32) for which even the search based on the 9-loci minimal haplotype was fruitless (Table 4).

The article includes fairly comprehensive searches of the discovered Y-chromosome and mtDNA types in modern populations.

The mtDNA results:

Twenty samples were found to belong to west Eurasian haplogroups (U2, U4,
U5a1, T1, T3, T4, H5a, H6, HV, K, and I), whereas the 6 remaining samples were attributed to east Eurasian haplogroups (Z, G2a, C, F1b and N9a).

Interestingly:

Moreover, it is likely that some mtDNA lineages were carried to southern Siberia from the Volga–Ural region. Incidentally, in the fifth century BC, Herodotus mentioned transit trade occurring in Central Asia along a route that stretched from the Urals in the west to the Altai and the Minusinsk Basin in the east (Hemphill and Mallory 2004). In Altai, the presence of the R1a1 haplogroup in the middle of the fifth century BC is confirmed by the sample SEB 96K2 of Ricaut et al. (2004) which was found to belong to this Y-haplogroup. The boundary of the eastern European influence seems to be fixed at the peri-Baikal area since no R1a1 haplogroup was found in the Xiongnu specimens of the Northern border of Mongolia.

Link to Ricaut et al. (2004). This is in good agreement with the anthropological picture by Alexeev:

"The boundary of the Europeoid movement is clearly fixed at Lake Baikal. To the east of Baikal no palaeoanthropological find bears any traces of Europeoid admixture."

See also my compendium on ancient Y-chromosome studies.

Human Genetics doi:10.1007/s00439-009-0683-0

Ancient DNA provides new insights into the history of south Siberian Kurgan people.

Keyser C. et al.

Abstract

To help unravel some of the early Eurasian steppe migration movements, we determined the Y-chromosomal and mitochondrial haplotypes and haplogroups of 26 ancient human specimens from the Krasnoyarsk area dated from between the middle of the second millennium BC. to the fourth century AD. In order to go further in the search of the geographic origin and physical traits of these south Siberian specimens, we also typed phenotype-informative single nucleotide polymorphisms. Our autosomal, Y-chromosomal and mitochondrial DNA analyses reveal that whereas few specimens seem to be related matrilineally or patrilineally, nearly all subjects belong to haplogroup R1a1-M17 which is thought to mark the eastward migration of the early Indo-Europeans. Our results also confirm that at the Bronze and Iron Ages, south Siberia was a region of overwhelmingly predominant European settlement, suggesting an eastward migration of Kurgan people across the Russo-Kazakh steppe. Finally, our data indicate that at the Bronze and Iron Age timeframe, south Siberians were blue (or green)-eyed, fair-skinned and light-haired people and that they might have played a role in the early development of the Tarim Basin civilization. To the best of our knowledge, no equivalent molecular analysis has been undertaken so far.

Link

Light-pigmented Caucasoids from prehistoric Siberia

This sample was previously tested for Y-chromosome and mtDNA polymorphisms.

The pigmentation-related loci tested can be seen in the labels of my post, which should lead you to some earlier studies on them.

Most individuals were found to be most similar to European than to East Asian or African individuals based on these loci, although some (2 from Andronovo) of them were more similar to East Asians or intermediate (1 from Tagar) between East Asians and Europeans.

Interestingly, 1 of the Andronovo Mongoloids (S07) was previously found to belong to Y chromosome haplogroup C(xC3), while the Caucasoid-Mongoloid individual from Tagar (S32) belonged to haplogroup R1a1.

It should be noted that the use of the term "European individual ancestry" does not mean that these individuals were from Europe, as no test to distinguish between European and Asian Caucasoids was performed, and we know from literary descriptions and occasional archaeological remains about the ancient presence of light-pigmented Caucasoids in Siberia.

From the paper:

The genotype for rs12913832 was obtained for 23 out of the 25 samples, and most had the G/G genotype (n=15), which indicates that at least 60% of ancient specimens were probably blue- or green-eyed individuals. The remaining samples had the A/G (n=5) or A/A (n=3) genotypes, which are predictive of brown eye color phenotype.

International Journal of Legal Medicine doi:10.1007/s00414-009-0348-5

Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis

Caroline Bouakaze et al.

Abstract

In the present study, a multiplexed genotyping assay for ten single nucleotide polymorphisms (SNPs) located within six pigmentation candidate genes was developed on modern biological samples and applied to DNA retrieved from 25 archeological human remains from southern central Siberia dating from the Bronze and Iron Ages. SNP genotyping was successful for the majority of ancient samples and revealed that most probably had typical European pigment features, i.e., blue or green eye color, light hair color and skin type, and were likely of European individual ancestry. To our knowledge, this study reports for the first time the multiplexed typing of autosomal SNPs on aged and degraded DNA. By providing valuable information on pigment traits of an individual and allowing individual biogeographical ancestry estimation, autosomal SNP typing can improve ancient DNA studies and aid human identification in some forensic casework situations when used to complement conventional molecular markers.

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Interaction between loci affecting human pigmentation in Poland

Annals of Human Genetics doi:10.1111/j.1469-1809.2009.00504.x

Interactions Between HERC2, OCA2 and MC1R May Influence Human Pigmentation Phenotype

Wojciech Branicki et al.

Abstract

Human pigmentation is a polygenic trait which may be shaped by different kinds of gene–gene interactions. Recent studies have revealed that interactive effects between HERC2 and OCA2 may be responsible for blue eye colour determination in humans. Here we performed a population association study, examining important polymorphisms within the HERC2 and OCA2 genes. Furthermore, pooling these results with genotyping data for MC1R, ASIP and SLC45A2 obtained for the same population sample we also analysed potential genetic interactions affecting variation in eye, hair and skin colour. Our results confirmed the association of HERC2 rs12913832 with eye colour and showed that this SNP is also significantly associated with skin and hair colouration. It is also concluded that OCA2 rs1800407 is independently associated with eye colour. Finally, using various approaches we were able to show that there is an interaction between MC1R and HERC2 in determination of skin and hair colour in the studied population sample.

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SLC45A2 and human hair color

Yann Klimentidis points me to this new article which shows a link between variations in the SLC45A2 gene and hair color.

Journal of Human Genetics doi: 10.1007/s10038-008-0338-3

Association of the SLC45A2 gene with physiological human hair colour variation

Wojciech Branicki et al.

Abstract

Pigmentation is a complex physical trait with multiple genes involved. Several genes have already been associated with natural differences in human pigmentation. The SLC45A2 gene encoding a transporter protein involved in melanin synthesis is considered to be one of the most important genes affecting human pigmentation. Here we present results of an association study conducted on a population of European origin, where the relationship between two non-synonymous polymorphisms in the SLC45A2 gene — rs26722 (E272K) and rs16891982 (L374F) — and different pigmentation traits was examined. The study revealed a significant association between both variable sites and normal variation in hair colour. Only L374F remained significantly associated with hair colour when both SNPs were included in a logistic regression model. No association with other pigmentation traits was detected in this population sample. Our results indicate that the rare allele L374 significantly increases the possibility of having black hair colour (OR = 7.05) and thus may be considered as a future marker for black hair colour prediction.

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Attractiveness of blonde women in Poland

This seems to be consistent with my theory of hair as a frame. As facial features deteriorate with age (30), the absence-of-frame effect favors blondes at the expense of brunettes. At the even higher age (40) attractiveness overall declines and the absence-of-frame trick is no longer effective.

Percept Mot Skills. 2008 Jun;106(3):737-44.

Attractiveness of blonde women in evolutionary perspective: studies with two Polish samples.

Sorokowski P.

Institute of Psychology, University of Wrocław, ul. J. Dawida 1, 50-527 Wrocław, Poland. sorokowskipiotr@yahoo.co.uk

An experimental study was undertaken to assess the phenomenon of male preference for blondes. In the first study, 360 Polish men ages 18 to 46 years were asked to assess the attractiveness of the presented stimuli using a 9-point scale. Stimuli were 9 different pictures of the same women whose ages (about 20, 30, and 40 years old) and hair colors (blonde, brown, and brunette) were manipulated. Pictures of blonde-haired women were generally rated as younger than the others. The attractiveness ratings of female faces changed with age and hair color. Still, only the 30-yr.-old woman with blonde hair was rated as significantly more attractive than those with brown or brunette hair. In a second study (the analysis of 500 Internet advertisements) mature women dyed their hair blonde more frequently. These results are analyzed with regard to the evolutionarily formed male preference for younger females.

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Embalming in Roman Greece

From the paper:

Even earlier, during the Geometric Periods, there is some evidence to suggest that embalming was not unknown; it has long been recognised that the means by which the bodies of Homeric figures (Achilles, Sarpedon and Hektor) were preserved until their final disposal were, in fact, reminiscent of the art of the Egyptian embalmers (Garland, 2001). Another example is Alexander the Great (356 BC – 323 BC), whose was reported to be preserved in beeswax (Kurtz and Boardman, 1971; Aufderheide, 2003). The same applies for the Roman Period, where, although embalming was looked upon as a foreign custom and was, on the whole, not extensively practised, mummies embalmed according to the ancient Egyptian customs were sporadically discovered both in Italy and the provinces, e.g. the Empress Poppaea Sabina (30-65 AD) (Toynbee, 1971) and the mummy of Grottarossa (Ascenzi et al., 1996; Toynbee, 1971).

...

The current colour of the hair is brown with reddish highlights, a common observation on many mummies, and probably originated through post-mortem alteration (Aufderheide, 2003; Wilson et al., 2001). Sun-exposure, bacterial reaction, and embalming methods are some of the factors that may affect the original hair colour. As a result, hair that was originally black or brown exhibits reddish, orange or even blond colour due to post mortem alterations. All human hair, however, does not turn red over archaeological time-scales (Wilson, 2001). Based on the histological analysis of the unstained hair samples, the limited fungal influence, and the macroscopic view, it can be assumed that the original hair colour was brown. Similar cases of hair preservation have been reported in studies of both mummified and non-mummified human remains (Aufderheide, 2003; Brothwell and Dobney, 1986; Lubec et al., 1987; White, 1993; Wilson et al., 2002, 2007b).

Journal of Archaeological Science doi:10.1016/j.jas.2008.07.003

Indications of embalming in Roman Greece by physical, chemical and histological analysis

C. Papageorgopoulou et al.

Abstract

The partially mummified remains of a high-status female (ca. 1700 BP, Thessaloniki, Greece) were found inside a Roman-type marble sarcophagus containing a lead coffin. The individual was positioned on a wooden pallet, wrapped in bandages, and covered with a gold-embroidered purple silk cloth. Besides the clothes, remnants of
soft tissue as well as the individual’s original hair style and eyebrows were exceptionally well preserved. In addition to the macroscopic examination, icroscopic
and biochemical analyses were undertaken. Scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) analysis, and gas chromatography/mass spectrometry
(GC/MS) were applied to examine the tissue preservation and probable mechanisms of mummification. The presence of chemical components, such as sesquiterpenes,
triterpenoids, and diterpenoids, originating from coniferous and pistacia resins, myrrh, and other spices, verify ancient information on preparation methods of the dead in Greek and Roman times. These chemical components are thought to have played a prominent role in the mummification mechanism in this particular case. The potential effect of the lead coffin in the mummification process was also examined. Energydispersive X-ray analysis failed to detect lead penetration into the tissues, suggesting that the coffin played a limited role in the preservation of soft tissue.

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TPCN2 and ASIP and hair/skin color

Nature Genetics, Published online: 18 May 2008 | doi:10.1038/ng.160

Two newly identified genetic determinants of pigmentation in Europeans

Patrick Sulem et al.

We present results from a genome-wide association study for variants associated with human pigmentation characteristics among 5,130 Icelanders, with follow-up analyses in 2,116 Icelanders and 1,214 Dutch individuals. Two coding variants in TPCN2 are associated with hair color, and a variant at the ASIP locus shows strong association with skin sensitivity to sun, freckling and red hair, phenotypic characteristics similar to those affected by well-known mutations in MC1R.

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